Diff of the two buildlogs: -- --- b1/build.log 2023-06-03 06:46:44.971607913 +0000 +++ b2/build.log 2023-06-03 07:59:45.663750362 +0000 @@ -1,49 +1,8 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Jul 4 23:52:46 -12 2024 -I: pbuilder-time-stamp: 1720180366 +I: Current time: Sat Jun 3 20:46:53 +14 2023 +I: pbuilder-time-stamp: 1685774813 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] -tar: ./usr/share/perl5/Debian: time stamp 2025-08-04 08:27:04 is 34158851.850998501 s in the future -tar: ./usr/share/man/pt/man8: time stamp 2025-08-04 08:27:04 is 34158851.706269309 s in the future -tar: ./usr/share/man/pt/man5: time stamp 2025-08-04 08:27:04 is 34158851.697976902 s in the future -tar: ./usr/share/man/nl/man8: time stamp 2025-08-04 08:27:04 is 34158851.677728323 s in the future -tar: ./usr/share/man/nl/man5: time stamp 2025-08-04 08:27:04 is 34158851.669433645 s in the future -tar: ./usr/share/man/man5: time stamp 2025-08-04 08:27:04 is 34158851.598745411 s in the future -tar: ./usr/share/man/fr/man5: time stamp 2025-08-04 08:27:04 is 34158851.551033469 s in the future -tar: ./usr/share/man/de/man5: time stamp 2025-08-04 08:27:04 is 34158851.479380769 s in the future -tar: ./usr/share/locale/zh_CN/LC_MESSAGES: time stamp 2025-08-04 08:27:04 is 34158850.961322903 s in the future -tar: ./usr/share/locale/vi/LC_MESSAGES: time stamp 2025-08-04 08:27:04 is 34158850.941043384 s in the future -tar: ./usr/share/locale/uk/LC_MESSAGES: time stamp 2025-08-04 08:27:04 is 34158850.903747063 s in the future -tar: ./usr/share/locale/sv/LC_MESSAGES: time stamp 2025-08-04 08:27:04 is 34158850.872186397 s in the future -tar: ./usr/share/locale/sk/LC_MESSAGES: time stamp 2025-08-04 08:27:04 is 34158850.862784103 s in the future -tar: ./usr/share/locale/ru/LC_MESSAGES: time stamp 2025-08-04 08:27:04 is 34158850.821407554 s in the future -tar: ./usr/share/locale/pt_BR/LC_MESSAGES: time stamp 2025-08-04 08:27:04 is 34158850.804822269 s in the future -tar: ./usr/share/locale/pt/LC_MESSAGES: time stamp 2025-08-04 08:27:04 is 34158850.779992751 s in the future -tar: ./usr/share/locale/pl/LC_MESSAGES: time stamp 2025-08-04 08:27:04 is 34158850.761878986 s in the future -tar: ./usr/share/locale/nl/LC_MESSAGES: time stamp 2025-08-04 08:27:04 is 34158850.741969348 s in the future -tar: ./usr/share/locale/nb/LC_MESSAGES: time stamp 2025-08-04 08:27:04 is 34158850.729511069 s in the future -tar: ./usr/share/locale/ko/LC_MESSAGES: time stamp 2025-08-04 08:27:04 is 34158850.708356481 s in the future -tar: ./usr/share/locale/ja/LC_MESSAGES: time stamp 2025-08-04 08:27:04 is 34158850.685992842 s in the future -tar: ./usr/share/locale/it/LC_MESSAGES: time stamp 2025-08-04 08:27:04 is 34158850.668743567 s in the future -tar: ./usr/share/locale/hu/LC_MESSAGES: time stamp 2025-08-04 08:27:04 is 34158850.652354572 s in the future -tar: ./usr/share/locale/gl/LC_MESSAGES: time stamp 2025-08-04 08:27:04 is 34158850.645933725 s in the future -tar: ./usr/share/locale/fr/LC_MESSAGES: time stamp 2025-08-04 08:27:04 is 34158850.610837372 s in the future -tar: ./usr/share/locale/eu/LC_MESSAGES: time stamp 2025-08-04 08:27:04 is 34158850.606295439 s in the future -tar: ./usr/share/locale/es/LC_MESSAGES: time stamp 2025-08-04 08:27:04 is 34158850.570180082 s in the future -tar: ./usr/share/locale/de/LC_MESSAGES: time stamp 2025-08-04 08:27:04 is 34158850.549149981 s in the future -tar: ./usr/share/locale/da/LC_MESSAGES: time stamp 2025-08-04 08:27:04 is 34158850.529140417 s in the future -tar: ./usr/share/locale/cs/LC_MESSAGES: time stamp 2025-08-04 08:27:04 is 34158850.509867004 s in the future -tar: ./usr/share/locale/ca/LC_MESSAGES: time stamp 2025-08-04 08:27:04 is 34158850.491939138 s in the future -tar: ./usr/share/doc/adduser/examples/adduser.local.conf.examples/skel.other: time stamp 2025-08-04 08:27:04 is 34158850.309017776 s in the future -tar: ./usr/share/doc/adduser/examples/adduser.local.conf.examples/skel: time stamp 2025-08-04 08:27:04 is 34158850.308872212 s in the future -tar: ./usr/share/doc/adduser/examples/adduser.local.conf.examples: time stamp 2025-08-04 08:27:04 is 34158850.308801558 s in the future -tar: ./usr/share/doc/adduser/examples: time stamp 2025-08-04 08:27:04 is 34158850.307929033 s in the future -tar: ./usr/share/doc/adduser: time stamp 2025-08-04 08:27:04 is 34158850.307234459 s in the future -tar: ./var/lib/dpkg/info/adduser.list: time stamp 2025-08-04 08:27:04 is 34158842.328659303 s in the future -tar: ./usr/share/man/de/man8: time stamp 2025-08-04 08:27:04 is 34158841.215772331 s in the future -tar: ./usr/share/man/fr/man8: time stamp 2025-08-04 08:27:04 is 34158841.215669108 s in the future -tar: ./usr/share/man/man8: time stamp 2025-08-04 08:27:04 is 34158841.215609771 s in the future -tar: ./usr/sbin: time stamp 2025-08-04 08:27:04 is 34158841.209813857 s in the future I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem @@ -57,7 +16,7 @@ I: copying [./openstructure_2.3.1.orig.tar.gz] I: copying [./openstructure_2.3.1-9.debian.tar.xz] I: Extracting source -gpgv: Signature made Tue May 23 16:59:49 2023 -12 +gpgv: Signature made Wed May 24 18:59:49 2023 +14 gpgv: using RSA key 772292F6F7AC85FAE041D41EE5F43F9C2734F287 gpgv: issuer "merkys@debian.org" gpgv: Can't check signature: No public key @@ -76,135 +35,167 @@ dpkg-source: info: applying b2798f24c37cb2ff0f46b929a4d41b4f3ce54a68.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2995182/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1244763/tmp/hooks/D01_modify_environment starting +debug: Running on ionos1-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Jun 3 20:47 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/1244763/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1244763/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16 ' - DISTRIBUTION='bookworm' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.15(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15 ' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='e1f42a2db86d479cbffb37d81d80da1c' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='2995182' - PS1='# ' - PS2='> ' + INVOCATION_ID=3ad4c0b8084c4464855214d8877ecc3e + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=1244763 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.B5mJfpLp/pbuilderrc_VHtK --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.B5mJfpLp/b1 --logfile b1/build.log openstructure_2.3.1-9.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://85.184.249.68:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.B5mJfpLp/pbuilderrc_VzCL --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.B5mJfpLp/b2 --logfile b2/build.log --extrapackages usrmerge openstructure_2.3.1-9.dsc' + SUDO_GID=110 + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://78.137.99.97:3128 I: uname -a - Linux ionos15-amd64 6.1.0-0.deb11.7-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.20-2~bpo11+1 (2023-04-23) x86_64 GNU/Linux + Linux i-capture-the-hostname 5.10.0-23-amd64 #1 SMP Debian 5.10.179-1 (2023-05-12) x86_64 GNU/Linux I: ls -l /bin total 5632 - -rwxr-xr-x 1 root root 1265648 Apr 23 2023 bash - -rwxr-xr-x 3 root root 39224 Sep 18 2022 bunzip2 - -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzcat - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep - -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzip2 - -rwxr-xr-x 1 root root 14568 Sep 18 2022 bzip2recover - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore - -rwxr-xr-x 1 root root 44016 Sep 20 2022 cat - -rwxr-xr-x 1 root root 68656 Sep 20 2022 chgrp - -rwxr-xr-x 1 root root 64496 Sep 20 2022 chmod - -rwxr-xr-x 1 root root 72752 Sep 20 2022 chown - -rwxr-xr-x 1 root root 151152 Sep 20 2022 cp - -rwxr-xr-x 1 root root 125640 Jan 5 2023 dash - -rwxr-xr-x 1 root root 121904 Sep 20 2022 date - -rwxr-xr-x 1 root root 89240 Sep 20 2022 dd - -rwxr-xr-x 1 root root 102200 Sep 20 2022 df - -rwxr-xr-x 1 root root 151344 Sep 20 2022 dir - -rwxr-xr-x 1 root root 88656 Mar 22 2023 dmesg - lrwxrwxrwx 1 root root 8 Dec 19 2022 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Dec 19 2022 domainname -> hostname - -rwxr-xr-x 1 root root 43856 Sep 20 2022 echo - -rwxr-xr-x 1 root root 41 Jan 24 2023 egrep - -rwxr-xr-x 1 root root 35664 Sep 20 2022 false - -rwxr-xr-x 1 root root 41 Jan 24 2023 fgrep - -rwxr-xr-x 1 root root 85600 Mar 22 2023 findmnt - -rwsr-xr-x 1 root root 35128 Mar 22 2023 fusermount - -rwxr-xr-x 1 root root 203152 Jan 24 2023 grep - -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip - -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe - -rwxr-xr-x 1 root root 98136 Apr 9 2022 gzip - -rwxr-xr-x 1 root root 22680 Dec 19 2022 hostname - -rwxr-xr-x 1 root root 72824 Sep 20 2022 ln - -rwxr-xr-x 1 root root 53024 Mar 23 2023 login - -rwxr-xr-x 1 root root 151344 Sep 20 2022 ls - -rwxr-xr-x 1 root root 207168 Mar 22 2023 lsblk - -rwxr-xr-x 1 root root 97552 Sep 20 2022 mkdir - -rwxr-xr-x 1 root root 72912 Sep 20 2022 mknod - -rwxr-xr-x 1 root root 43952 Sep 20 2022 mktemp - -rwxr-xr-x 1 root root 59712 Mar 22 2023 more - -rwsr-xr-x 1 root root 59704 Mar 22 2023 mount - -rwxr-xr-x 1 root root 18744 Mar 22 2023 mountpoint - -rwxr-xr-x 1 root root 142968 Sep 20 2022 mv - lrwxrwxrwx 1 root root 8 Dec 19 2022 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 2 2023 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 43952 Sep 20 2022 pwd - lrwxrwxrwx 1 root root 4 Apr 23 2023 rbash -> bash - -rwxr-xr-x 1 root root 52112 Sep 20 2022 readlink - -rwxr-xr-x 1 root root 72752 Sep 20 2022 rm - -rwxr-xr-x 1 root root 56240 Sep 20 2022 rmdir - -rwxr-xr-x 1 root root 27560 Nov 2 2022 run-parts - -rwxr-xr-x 1 root root 126424 Jan 5 2023 sed - lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash - -rwxr-xr-x 1 root root 43888 Sep 20 2022 sleep - -rwxr-xr-x 1 root root 85008 Sep 20 2022 stty - -rwsr-xr-x 1 root root 72000 Mar 22 2023 su - -rwxr-xr-x 1 root root 39824 Sep 20 2022 sync - -rwxr-xr-x 1 root root 531984 Apr 6 2023 tar - -rwxr-xr-x 1 root root 14520 Nov 2 2022 tempfile - -rwxr-xr-x 1 root root 109616 Sep 20 2022 touch - -rwxr-xr-x 1 root root 35664 Sep 20 2022 true - -rwxr-xr-x 1 root root 14568 Mar 22 2023 ulockmgr_server - -rwsr-xr-x 1 root root 35128 Mar 22 2023 umount - -rwxr-xr-x 1 root root 43888 Sep 20 2022 uname - -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress - -rwxr-xr-x 1 root root 151344 Sep 20 2022 vdir - -rwxr-xr-x 1 root root 72024 Mar 22 2023 wdctl - lrwxrwxrwx 1 root root 8 Dec 19 2022 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat - -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp - -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff - -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep - -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep - -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce - -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep - -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless - -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore - -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew -I: user script /srv/workspace/pbuilder/2995182/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1265648 Apr 24 11:23 bash + -rwxr-xr-x 3 root root 39224 Sep 19 2022 bunzip2 + -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzcat + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4893 Nov 28 2021 bzexe + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep + -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzip2 + -rwxr-xr-x 1 root root 14568 Sep 19 2022 bzip2recover + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore + -rwxr-xr-x 1 root root 44016 Sep 21 2022 cat + -rwxr-xr-x 1 root root 68656 Sep 21 2022 chgrp + -rwxr-xr-x 1 root root 64496 Sep 21 2022 chmod + -rwxr-xr-x 1 root root 72752 Sep 21 2022 chown + -rwxr-xr-x 1 root root 151152 Sep 21 2022 cp + -rwxr-xr-x 1 root root 125640 Jan 6 03:20 dash + -rwxr-xr-x 1 root root 121904 Sep 21 2022 date + -rwxr-xr-x 1 root root 89240 Sep 21 2022 dd + -rwxr-xr-x 1 root root 102200 Sep 21 2022 df + -rwxr-xr-x 1 root root 151344 Sep 21 2022 dir + -rwxr-xr-x 1 root root 88656 Mar 24 00:02 dmesg + lrwxrwxrwx 1 root root 8 Dec 20 03:33 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Dec 20 03:33 domainname -> hostname + -rwxr-xr-x 1 root root 43856 Sep 21 2022 echo + -rwxr-xr-x 1 root root 41 Jan 25 04:43 egrep + -rwxr-xr-x 1 root root 35664 Sep 21 2022 false + -rwxr-xr-x 1 root root 41 Jan 25 04:43 fgrep + -rwxr-xr-x 1 root root 85600 Mar 24 00:02 findmnt + -rwsr-xr-x 1 root root 35128 Mar 23 22:35 fusermount + -rwxr-xr-x 1 root root 203152 Jan 25 04:43 grep + -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip + -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe + -rwxr-xr-x 1 root root 98136 Apr 10 2022 gzip + -rwxr-xr-x 1 root root 22680 Dec 20 03:33 hostname + -rwxr-xr-x 1 root root 72824 Sep 21 2022 ln + -rwxr-xr-x 1 root root 53024 Mar 24 02:40 login + -rwxr-xr-x 1 root root 151344 Sep 21 2022 ls + -rwxr-xr-x 1 root root 207168 Mar 24 00:02 lsblk + -rwxr-xr-x 1 root root 97552 Sep 21 2022 mkdir + -rwxr-xr-x 1 root root 72912 Sep 21 2022 mknod + -rwxr-xr-x 1 root root 43952 Sep 21 2022 mktemp + -rwxr-xr-x 1 root root 59712 Mar 24 00:02 more + -rwsr-xr-x 1 root root 59704 Mar 24 00:02 mount + -rwxr-xr-x 1 root root 18744 Mar 24 00:02 mountpoint + -rwxr-xr-x 1 root root 142968 Sep 21 2022 mv + lrwxrwxrwx 1 root root 8 Dec 20 03:33 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 3 20:25 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 43952 Sep 21 2022 pwd + lrwxrwxrwx 1 root root 4 Apr 24 11:23 rbash -> bash + -rwxr-xr-x 1 root root 52112 Sep 21 2022 readlink + -rwxr-xr-x 1 root root 72752 Sep 21 2022 rm + -rwxr-xr-x 1 root root 56240 Sep 21 2022 rmdir + -rwxr-xr-x 1 root root 27560 Nov 3 2022 run-parts + -rwxr-xr-x 1 root root 126424 Jan 6 09:55 sed + lrwxrwxrwx 1 root root 9 Jun 3 20:47 sh -> /bin/bash + -rwxr-xr-x 1 root root 43888 Sep 21 2022 sleep + -rwxr-xr-x 1 root root 85008 Sep 21 2022 stty + -rwsr-xr-x 1 root root 72000 Mar 24 00:02 su + -rwxr-xr-x 1 root root 39824 Sep 21 2022 sync + -rwxr-xr-x 1 root root 531984 Apr 7 04:25 tar + -rwxr-xr-x 1 root root 14520 Nov 3 2022 tempfile + -rwxr-xr-x 1 root root 109616 Sep 21 2022 touch + -rwxr-xr-x 1 root root 35664 Sep 21 2022 true + -rwxr-xr-x 1 root root 14568 Mar 23 22:35 ulockmgr_server + -rwsr-xr-x 1 root root 35128 Mar 24 00:02 umount + -rwxr-xr-x 1 root root 43888 Sep 21 2022 uname + -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress + -rwxr-xr-x 1 root root 151344 Sep 21 2022 vdir + -rwxr-xr-x 1 root root 72024 Mar 24 00:02 wdctl + lrwxrwxrwx 1 root root 8 Dec 20 03:33 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat + -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp + -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff + -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep + -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep + -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce + -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep + -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless + -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore + -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew +I: user script /srv/workspace/pbuilder/1244763/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -718,7 +709,7 @@ Get: 430 http://deb.debian.org/debian bookworm/main amd64 python3-pyqt5 amd64 5.15.9+dfsg-1 [2489 kB] Get: 431 http://deb.debian.org/debian bookworm/main amd64 sip-dev amd64 4.19.25+dfsg-5+b1 [253 kB] Get: 432 http://deb.debian.org/debian bookworm/main amd64 voronota amd64 1.22.3149-2 [2057 kB] -Fetched 268 MB in 7s (37.5 MB/s) +Fetched 268 MB in 12s (21.6 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19591 files and directories currently installed.) @@ -2478,8 +2469,19 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +usrmerge is already the newest version (35). +0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/openstructure-2.3.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../openstructure_2.3.1-9_source.changes +I: user script /srv/workspace/pbuilder/1244763/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +removed '/etc/unsupported-skip-usrmerge-conversion' +The system has been successfully converted. +I: user script /srv/workspace/pbuilder/1244763/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/openstructure-2.3.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../openstructure_2.3.1-9_source.changes dpkg-buildpackage: info: source package openstructure dpkg-buildpackage: info: source version 2.3.1-9 dpkg-buildpackage: info: source distribution unstable @@ -2577,7 +2579,7 @@ -- Build files have been written to: /build/openstructure-2.3.1/obj-x86_64-linux-gnu make[1]: Leaving directory '/build/openstructure-2.3.1' dh_auto_build - cd obj-x86_64-linux-gnu && make -j16 "INSTALL=install --strip-program=true" VERBOSE=1 + cd obj-x86_64-linux-gnu && make -j15 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/openstructure-2.3.1 -B/build/openstructure-2.3.1/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/openstructure-2.3.1/obj-x86_64-linux-gnu/CMakeFiles /build/openstructure-2.3.1/obj-x86_64-linux-gnu//CMakeFiles/progress.marks @@ -2593,1068 +2595,1114 @@ make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/bindings/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod/CMakeFiles/ost_bindings_pymod.dir/DependInfo.cmake --color= make -f modules/conop/pymod/CMakeFiles/ost_conop_pymod.dir/build.make modules/conop/pymod/CMakeFiles/ost_conop_pymod.dir/depend -make -f modules/db/pymod/CMakeFiles/ost_db_pymod.dir/build.make modules/db/pymod/CMakeFiles/ost_db_pymod.dir/depend make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/conop/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/pymod/CMakeFiles/ost_conop_pymod.dir/DependInfo.cmake --color= -make -f modules/geom/pymod/CMakeFiles/ost_geom_pymod.dir/build.make modules/geom/pymod/CMakeFiles/ost_geom_pymod.dir/depend +make -f modules/db/pymod/CMakeFiles/ost_db_pymod.dir/build.make modules/db/pymod/CMakeFiles/ost_db_pymod.dir/depend make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/db/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/pymod/CMakeFiles/ost_db_pymod.dir/DependInfo.cmake --color= -make -f modules/gfx/pymod/CMakeFiles/ost_gfx_pymod.dir/build.make modules/gfx/pymod/CMakeFiles/ost_gfx_pymod.dir/depend +make -f modules/geom/pymod/CMakeFiles/ost_geom_pymod.dir/build.make modules/geom/pymod/CMakeFiles/ost_geom_pymod.dir/depend make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/geom/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/pymod/CMakeFiles/ost_geom_pymod.dir/DependInfo.cmake --color= +make -f modules/gfx/pymod/CMakeFiles/ost_gfx_pymod.dir/build.make modules/gfx/pymod/CMakeFiles/ost_gfx_pymod.dir/depend make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/gfx/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/pymod/CMakeFiles/ost_gfx_pymod.dir/DependInfo.cmake --color= +make -f modules/base/src/CMakeFiles/create_stage.dir/build.make modules/base/src/CMakeFiles/create_stage.dir/build +make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E make_directory /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib make -f modules/base/pymod/CMakeFiles/subst___init__.py.dir/build.make modules/base/pymod/CMakeFiles/subst___init__.py.dir/build make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/gui/share/CMakeFiles/scene_icons.dir/build.make modules/gui/share/CMakeFiles/scene_icons.dir/depend -make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/cmake -DINPUT_FILE=/build/openstructure-2.3.1/modules/base/pymod/__init__.py.in -DOUT_FILE=__init__.py -DALL_ADDITIONAL_MODULES=,\'gui\',\'gfx\',\'img\',\'info\' -P /build/openstructure-2.3.1/cmake_support/substitute.cmake +make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +make -f modules/gui/share/CMakeFiles/scene_icons.dir/build.make modules/gui/share/CMakeFiles/scene_icons.dir/depend make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/gui/share /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/share /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/share/CMakeFiles/scene_icons.dir/DependInfo.cmake --color= -make -f modules/base/src/CMakeFiles/create_stage.dir/build.make modules/base/src/CMakeFiles/create_stage.dir/build +make -f modules/bindings/pymod/CMakeFiles/ost_bindings_pymod.dir/build.make modules/bindings/pymod/CMakeFiles/ost_bindings_pymod.dir/build make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E make_directory /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/bindings/pymod/./__init__.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./__init__.py +make -f modules/db/pymod/CMakeFiles/ost_db_pymod.dir/build.make modules/db/pymod/CMakeFiles/ost_db_pymod.dir/build make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/bindings/pymod/CMakeFiles/ost_bindings_pymod.dir/build.make modules/bindings/pymod/CMakeFiles/ost_bindings_pymod.dir/build make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/bindings/pymod/./__init__.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./__init__.py +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/db/pymod/./__init__.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/db/./__init__.py make -f modules/conop/pymod/CMakeFiles/ost_conop_pymod.dir/build.make modules/conop/pymod/CMakeFiles/ost_conop_pymod.dir/build +make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/pymod/./__init__.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/conop/./__init__.py -make -f modules/db/pymod/CMakeFiles/ost_db_pymod.dir/build.make modules/db/pymod/CMakeFiles/ost_db_pymod.dir/build +make -f modules/geom/pymod/CMakeFiles/ost_geom_pymod.dir/build.make modules/geom/pymod/CMakeFiles/ost_geom_pymod.dir/build +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E make_directory /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/bin make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/db/pymod/./__init__.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/db/./__init__.py +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/pymod/./__init__.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/geom/./__init__.py +make -f modules/gfx/pymod/CMakeFiles/ost_gfx_pymod.dir/build.make modules/gfx/pymod/CMakeFiles/ost_gfx_pymod.dir/build +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/bindings/pymod/./lga.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./lga.py +make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/pymod/./__init__.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gfx/./__init__.py make -f modules/gui/share/CMakeFiles/gui_images.dir/build.make modules/gui/share/CMakeFiles/gui_images.dir/depend -make -f modules/gui/pymod/CMakeFiles/ost_gui_scene_pymod.dir/build.make modules/gui/pymod/CMakeFiles/ost_gui_scene_pymod.dir/depend make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/gui/share /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/share /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/share/CMakeFiles/gui_images.dir/DependInfo.cmake --color= +make -f modules/gui/pymod/CMakeFiles/ost_gui_scene_pymod.dir/build.make modules/gui/pymod/CMakeFiles/ost_gui_scene_pymod.dir/depend +make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/gui/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod/CMakeFiles/ost_gui_scene_pymod.dir/DependInfo.cmake --color= +make -f modules/gui/share/CMakeFiles/scene_icons.dir/build.make modules/gui/share/CMakeFiles/scene_icons.dir/build +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E make_directory /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/openstructure/libexec +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/pymod/./cleanup.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/conop/./cleanup.py +make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/share/icons/add_icon.png /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/add_icon.png +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/pymod/./py_gfx_obj.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gfx/./py_gfx_obj.py +make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/gui/pymod/CMakeFiles/ost_gui_dng_pymod.dir/build.make modules/gui/pymod/CMakeFiles/ost_gui_dng_pymod.dir/depend +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/bindings/pymod/./hbplus.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./hbplus.py make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/gui/pymod/CMakeFiles/ost_gui_pymod.dir/build.make modules/gui/pymod/CMakeFiles/ost_gui_pymod.dir/depend +[ 0%] Built target subst___init__.py make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +make -f modules/gui/share/CMakeFiles/gui_images.dir/build.make modules/gui/share/CMakeFiles/gui_images.dir/build make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/gui/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod/CMakeFiles/ost_gui_dng_pymod.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/gui/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod/CMakeFiles/ost_gui_pymod.dir/DependInfo.cmake --color= -make -f modules/geom/pymod/CMakeFiles/ost_geom_pymod.dir/build.make modules/geom/pymod/CMakeFiles/ost_geom_pymod.dir/build -make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/pymod/./__init__.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/geom/./__init__.py -make -f modules/gfx/pymod/CMakeFiles/ost_gfx_pymod.dir/build.make modules/gfx/pymod/CMakeFiles/ost_gfx_pymod.dir/build +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/share/images/logo-small.png /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/share/openstructure/gui/images/logo-small.png +make -f modules/gui/pymod/CMakeFiles/ost_gui_scene_pymod.dir/build.make modules/gui/pymod/CMakeFiles/ost_gui_scene_pymod.dir/build make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/pymod/./__init__.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gfx/./__init__.py -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/bindings/pymod/./lga.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./lga.py -make -f modules/gui/share/CMakeFiles/scene_icons.dir/build.make modules/gui/share/CMakeFiles/scene_icons.dir/build +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/__init__.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/__init__.py +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/share/icons/close_icon.png /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/close_icon.png +make -f modules/gui/pymod/CMakeFiles/ost_gui_pymod.dir/build.make modules/gui/pymod/CMakeFiles/ost_gui_pymod.dir/depend +[ 0%] Built target ost_db_pymod +[ 0%] Built target ost_geom_pymod make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/pymod/./cleanup.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/conop/./cleanup.py +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E make_directory /build/openstructure-2.3.1/obj-x86_64-linux-gnu/tests make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/share/icons/add_icon.png /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/add_icon.png -make -f modules/gui/pymod/CMakeFiles/ost_gui_scene_pymod.dir/build.make modules/gui/pymod/CMakeFiles/ost_gui_scene_pymod.dir/build +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/gui/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod/CMakeFiles/ost_gui_pymod.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/__init__.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/__init__.py -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E make_directory /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/bin +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/bindings/pymod/./msms.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./msms.py +make -f modules/img/base/pymod/CMakeFiles/ost_img_pymod.dir/build.make modules/img/base/pymod/CMakeFiles/ost_img_pymod.dir/depend make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/img/base/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/pymod/CMakeFiles/ost_img_pymod.dir/DependInfo.cmake --color= make -f modules/gui/pymod/CMakeFiles/ost_gui_dng_pymod.dir/build.make modules/gui/pymod/CMakeFiles/ost_gui_dng_pymod.dir/build -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/pymod/./py_gfx_obj.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gfx/./py_gfx_obj.py make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/dng/__init__.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/dng/__init__.py -make -f modules/img/base/pymod/CMakeFiles/ost_img_pymod.dir/build.make modules/img/base/pymod/CMakeFiles/ost_img_pymod.dir/depend +make -f modules/img/alg/pymod/CMakeFiles/ost_img_alg_pymod.dir/build.make modules/img/alg/pymod/CMakeFiles/ost_img_alg_pymod.dir/depend +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/share/icons/critical_icon.png /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/critical_icon.png make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/color_options_widget.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/color_options_widget.py make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/img/base/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/pymod/CMakeFiles/ost_img_pymod.dir/DependInfo.cmake --color= +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/img/alg/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/pymod/CMakeFiles/ost_img_alg_pymod.dir/DependInfo.cmake --color= +[ 0%] Built target ost_gfx_pymod +[ 0%] Built target ost_conop_pymod +make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/bindings/pymod/./tmtools.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./tmtools.py +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/dng/termuse.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/dng/termuse.py make -f modules/gui/pymod/CMakeFiles/ost_gui_pymod.dir/build.make modules/gui/pymod/CMakeFiles/ost_gui_pymod.dir/build make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 0%] Built target subst___init__.py make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/./__init__.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./__init__.py -make -f modules/gui/share/CMakeFiles/gui_images.dir/build.make modules/gui/share/CMakeFiles/gui_images.dir/build -make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/share/images/logo-small.png /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/share/openstructure/gui/images/logo-small.png -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/share/icons/close_icon.png /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/close_icon.png -make -f modules/img/alg/pymod/CMakeFiles/ost_img_alg_pymod.dir/build.make modules/img/alg/pymod/CMakeFiles/ost_img_alg_pymod.dir/depend +make -f modules/img/base/pymod/CMakeFiles/ost_img_pymod.dir/build.make modules/img/base/pymod/CMakeFiles/ost_img_pymod.dir/build +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/color_select_widget.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/color_select_widget.py +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/share/icons/delete_icon.png /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/delete_icon.png make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/img/alg/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/pymod/CMakeFiles/ost_img_alg_pymod.dir/DependInfo.cmake --color= +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/pymod/./__init__.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/img/./__init__.py make -f modules/info/pymod/CMakeFiles/ost_info_pymod.dir/build.make modules/info/pymod/CMakeFiles/ost_info_pymod.dir/depend -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/bindings/pymod/./hbplus.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./hbplus.py -[ 0%] Built target ost_db_pymod -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E make_directory /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/openstructure/libexec +[ 0%] Built target gui_images +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/bindings/pymod/./dssp.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./dssp.py make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/info/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/pymod/CMakeFiles/ost_info_pymod.dir/DependInfo.cmake --color= make -f modules/io/pymod/CMakeFiles/ost_io_pymod.dir/build.make modules/io/pymod/CMakeFiles/ost_io_pymod.dir/depend -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/dng/termuse.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/dng/termuse.py -make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[ 0%] Built target create_stage make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/io/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/pymod/CMakeFiles/ost_io_pymod.dir/DependInfo.cmake --color= -make -f modules/img/base/pymod/CMakeFiles/ost_img_pymod.dir/build.make modules/img/base/pymod/CMakeFiles/ost_img_pymod.dir/build -make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/color_options_widget.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/color_options_widget.py -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/share/icons/critical_icon.png /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/critical_icon.png -make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/pymod/./__init__.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/img/./__init__.py -make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/./init_context_menu.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./init_context_menu.py -[ 0%] Built target ost_geom_pymod -make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/bindings/pymod/./msms.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./msms.py make -f modules/img/alg/pymod/CMakeFiles/ost_img_alg_pymod.dir/build.make modules/img/alg/pymod/CMakeFiles/ost_img_alg_pymod.dir/build -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/color_select_widget.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/color_select_widget.py make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/pymod/./__init__.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/img/alg/./__init__.py -make -f modules/mol/base/pymod/CMakeFiles/ost_mol_pymod.dir/build.make modules/mol/base/pymod/CMakeFiles/ost_mol_pymod.dir/depend cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/dng/superpositiondialog.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/dng/superpositiondialog.py -make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +make -f modules/mol/base/pymod/CMakeFiles/ost_mol_pymod.dir/build.make modules/mol/base/pymod/CMakeFiles/ost_mol_pymod.dir/depend make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/base/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/pymod/CMakeFiles/ost_mol_pymod.dir/DependInfo.cmake --color= -make -f modules/info/pymod/CMakeFiles/ost_info_pymod.dir/build.make modules/info/pymod/CMakeFiles/ost_info_pymod.dir/build -make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 0%] Built target ost_conop_pymod -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E make_directory /build/openstructure-2.3.1/obj-x86_64-linux-gnu/tests -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/./init_menubar.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./init_menubar.py -make -f modules/io/pymod/CMakeFiles/ost_io_pymod.dir/build.make modules/io/pymod/CMakeFiles/ost_io_pymod.dir/build -make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/pymod/./__init__.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/info/./__init__.py -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/share/icons/delete_icon.png /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/delete_icon.png -[ 0%] Built target ost_gfx_pymod -make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/pymod/./__init__.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/io/./__init__.py make -f modules/mol/alg/pymod/CMakeFiles/ost_mol_alg_pymod.dir/build.make modules/mol/alg/pymod/CMakeFiles/ost_mol_alg_pymod.dir/depend +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/./init_context_menu.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./init_context_menu.py +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/combo_options_widget.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/combo_options_widget.py make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/alg/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod/CMakeFiles/ost_mol_alg_pymod.dir/DependInfo.cmake --color= +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/share/icons/distance_icon.png /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/distance_icon.png +make -f modules/mol/mm/src/CMakeFiles/ost_mol_mm_headers.dir/build.make modules/mol/mm/src/CMakeFiles/ost_mol_mm_headers.dir/depend +make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/mm/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src/CMakeFiles/ost_mol_mm_headers.dir/DependInfo.cmake --color= make -f modules/mol/mm/pymod/CMakeFiles/ost_mol_mm_pymod.dir/build.make modules/mol/mm/pymod/CMakeFiles/ost_mol_mm_pymod.dir/depend -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/combo_options_widget.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/combo_options_widget.py -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/dng/init.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/dng/init.py -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/bindings/pymod/./tmtools.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./tmtools.py +make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/mm/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/pymod/CMakeFiles/ost_mol_mm_pymod.dir/DependInfo.cmake --color= +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/bindings/pymod/./clustalw.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./clustalw.py +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/dng/init.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/dng/init.py make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 0%] Built target gui_images -make -f modules/seq/base/pymod/CMakeFiles/ost_seq_pymod.dir/build.make modules/seq/base/pymod/CMakeFiles/ost_seq_pymod.dir/depend make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +make -f modules/info/pymod/CMakeFiles/ost_info_pymod.dir/build.make modules/info/pymod/CMakeFiles/ost_info_pymod.dir/build make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/seq/base/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/pymod/CMakeFiles/ost_seq_pymod.dir/DependInfo.cmake --color= +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/pymod/./__init__.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/info/./__init__.py +make -f modules/io/pymod/CMakeFiles/ost_io_pymod.dir/build.make modules/io/pymod/CMakeFiles/ost_io_pymod.dir/build +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/cpk_widget.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/cpk_widget.py +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/share/icons/find_icon.png /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/find_icon.png +make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/pymod/./__init__.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/io/./__init__.py +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/./init_menubar.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./init_menubar.py make -f modules/mol/base/pymod/CMakeFiles/ost_mol_pymod.dir/build.make modules/mol/base/pymod/CMakeFiles/ost_mol_pymod.dir/build -[ 0%] Built target ost_img_pymod make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/pymod/./__init__.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/./__init__.py -make -f modules/seq/alg/pymod/CMakeFiles/ost_seq_alg_pymod.dir/build.make modules/seq/alg/pymod/CMakeFiles/ost_seq_alg_pymod.dir/depend +make -f modules/mol/alg/pymod/CMakeFiles/ost_mol_alg_pymod.dir/build.make modules/mol/alg/pymod/CMakeFiles/ost_mol_alg_pymod.dir/build +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/bindings/pymod/./utils.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./utils.py make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/share/icons/distance_icon.png /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/distance_icon.png +[ 0%] Built target ost_img_pymod +make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +make -f modules/mol/mm/src/CMakeFiles/ost_mol_mm_headers.dir/build.make modules/mol/mm/src/CMakeFiles/ost_mol_mm_headers.dir/build make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/seq/alg/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/pymod/CMakeFiles/ost_seq_alg_pymod.dir/DependInfo.cmake --color= +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/pymod/./__init__.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./__init__.py +make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./forcefield.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./forcefield.hh +make -f modules/mol/mm/pymod/CMakeFiles/ost_mol_mm_pymod.dir/build.make modules/mol/mm/pymod/CMakeFiles/ost_mol_mm_pymod.dir/build +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/dng/menu.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/dng/menu.py +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/share/icons/information_icon.png /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/information_icon.png +make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/pymod/./__init__.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/mm/./__init__.py +make -f modules/seq/base/pymod/CMakeFiles/ost_seq_pymod.dir/build.make modules/seq/base/pymod/CMakeFiles/ost_seq_pymod.dir/depend +[ 0%] Built target ost_img_alg_pymod +make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/seq/base/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/pymod/CMakeFiles/ost_seq_pymod.dir/DependInfo.cmake --color= +make -f modules/seq/alg/pymod/CMakeFiles/ost_seq_alg_pymod.dir/build.make modules/seq/alg/pymod/CMakeFiles/ost_seq_alg_pymod.dir/depend cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/pymod/./remote.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/io/./remote.py +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/custom_widget.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/custom_widget.py make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/./init_spacenav.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./init_spacenav.py -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/cpk_widget.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/cpk_widget.py +make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/seq/alg/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/pymod/CMakeFiles/ost_seq_alg_pymod.dir/DependInfo.cmake --color= make -f scripts/CMakeFiles/subst_ost_startup.py.dir/build.make scripts/CMakeFiles/subst_ost_startup.py.dir/depend -make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/dng/menu.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/dng/menu.py +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/bindings/pymod/./naccess.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./naccess.py make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/scripts /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/scripts /build/openstructure-2.3.1/obj-x86_64-linux-gnu/scripts/CMakeFiles/subst_ost_startup.py.dir/DependInfo.cmake --color= -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/bindings/pymod/./dssp.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./dssp.py -make -f modules/mol/alg/pymod/CMakeFiles/ost_mol_alg_pymod.dir/build.make modules/mol/alg/pymod/CMakeFiles/ost_mol_alg_pymod.dir/build -make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/pymod/./__init__.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./__init__.py make -f scripts/CMakeFiles/subst_ost_config.dir/build.make scripts/CMakeFiles/subst_ost_config.dir/depend -[ 0%] Built target ost_img_alg_pymod +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/share/icons/map_icon.png /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/map_icon.png make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/scripts /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/scripts /build/openstructure-2.3.1/obj-x86_64-linux-gnu/scripts/CMakeFiles/subst_ost_config.dir/DependInfo.cmake --color= -[ 0%] Built target ost_info_pymod +make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/pymod/./views.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./views.py +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./ff_reader.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./ff_reader.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/pymod/./repository.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/io/./repository.py +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/pymod/./antechamber.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/mm/./antechamber.py make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/seq/base/pymod/CMakeFiles/ost_seq_pymod.dir/build.make modules/seq/base/pymod/CMakeFiles/ost_seq_pymod.dir/build make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/pymod/./__init__.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/seq/./__init__.py +[ 0%] Built target ost_info_pymod make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/pymod/./repository.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/io/./repository.py -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/share/icons/find_icon.png /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/find_icon.png -make -f modules/mol/mm/pymod/CMakeFiles/ost_mol_mm_pymod.dir/build.make modules/mol/mm/pymod/CMakeFiles/ost_mol_mm_pymod.dir/build +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/gradient_editor_widget.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/gradient_editor_widget.py make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/pymod/./__init__.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/mm/./__init__.py -make -f scripts/CMakeFiles/subst_ost.dir/build.make scripts/CMakeFiles/subst_ost.dir/depend -[ 0%] Built target create_stage -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/bindings/pymod/./clustalw.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./clustalw.py -make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/pymod/./__init__.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/seq/./__init__.py +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/bindings/pymod/./hhblits.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./hhblits.py cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/./init_splash.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./init_splash.py -make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/scripts /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/scripts /build/openstructure-2.3.1/obj-x86_64-linux-gnu/scripts/CMakeFiles/subst_ost.dir/DependInfo.cmake --color= make -f modules/seq/alg/pymod/CMakeFiles/ost_seq_alg_pymod.dir/build.make modules/seq/alg/pymod/CMakeFiles/ost_seq_alg_pymod.dir/build -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/pymod/./views.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./views.py +make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/share/icons/menubar_icon.png /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/menubar_icon.png +[ 0%] Built target ost_mol_pymod make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/pymod/./__init__.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/seq/alg/./__init__.py -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/custom_widget.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/custom_widget.py -make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f scripts/CMakeFiles/subst_ost_startup.py.dir/build.make scripts/CMakeFiles/subst_ost_startup.py.dir/build +make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/pymod/./superpose.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./superpose.py make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -DINPUT_FILE=/build/openstructure-2.3.1/scripts/ost_startup.py.in -DOUT_FILE=ost_startup.py -DBUILD_TYPE=Release -DPython_EXECUTABLE=/usr/bin/python3 -DPython_VERSION=3.11.2 -DLIBDIR=lib -DLIBEXEC_PATH=lib/openstructure/libexec -DPYTHON_MODULE_PATH=python3.11/dist-packages/ -P /build/openstructure-2.3.1/cmake_support/substitute.cmake +make -f scripts/CMakeFiles/subst_ost_config.dir/build.make scripts/CMakeFiles/subst_ost_config.dir/build +make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f scripts/CMakeFiles/subst_dng.dir/build.make scripts/CMakeFiles/subst_dng.dir/depend -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/pymod/./antechamber.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/mm/./antechamber.py -[ 0%] Built target ost_mol_pymod make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/scripts /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/scripts /build/openstructure-2.3.1/obj-x86_64-linux-gnu/scripts/CMakeFiles/subst_dng.dir/DependInfo.cmake --color= -make -f scripts/CMakeFiles/subst_ost_config.dir/build.make scripts/CMakeFiles/subst_ost_config.dir/build +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -DINPUT_FILE=/build/openstructure-2.3.1/scripts/ost_config.in -DOUT_FILE=ost_config -DBUILD_TYPE=Release -DPython_EXECUTABLE=/usr/bin/python3 -DPython_VERSION=3.11.2 -DLIBDIR=lib -DLIBEXEC_PATH=lib/openstructure/libexec -DPYTHON_MODULE_PATH=python3.11/dist-packages/ -P /build/openstructure-2.3.1/cmake_support/substitute.cmake [ 0%] Built target ost_gui_dng_pymod +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/./trajectory_viewer.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./trajectory_viewer.py +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./buildingblock.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./buildingblock.hh +make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/gradient_info_handler.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/gradient_info_handler.py +make -f scripts/CMakeFiles/subst_ost.dir/build.make scripts/CMakeFiles/subst_ost.dir/depend +make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/pymod/./mat.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/seq/alg/./mat.py +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/bindings/pymod/./hhblits2.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./hhblits2.py make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -DINPUT_FILE=/build/openstructure-2.3.1/scripts/ost_config.in -DOUT_FILE=ost_config -DBUILD_TYPE=Release -DPython_EXECUTABLE=/usr/bin/python3 -DPython_VERSION=3.11.2 -DLIBDIR=lib -DLIBEXEC_PATH=lib/openstructure/libexec -DPYTHON_MODULE_PATH=python3.11/dist-packages/ -P /build/openstructure-2.3.1/cmake_support/substitute.cmake +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/scripts /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/scripts /build/openstructure-2.3.1/obj-x86_64-linux-gnu/scripts/CMakeFiles/subst_ost.dir/DependInfo.cmake --color= +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/pymod/./qsscoring.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./qsscoring.py +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/share/icons/rigid_body_manipulator_icon.png /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/rigid_body_manipulator_icon.png +make -f scripts/CMakeFiles/subst_dng.dir/build.make scripts/CMakeFiles/subst_dng.dir/depend +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/./helpwidget.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./helpwidget.py +[ 0%] Built target ost_mol_mm_pymod +[ 0%] Built target ost_seq_pymod make -f actions/CMakeFiles/actions.dir/build.make actions/CMakeFiles/actions.dir/depend -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/share/icons/information_icon.png /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/information_icon.png +make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/scripts /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/scripts /build/openstructure-2.3.1/obj-x86_64-linux-gnu/scripts/CMakeFiles/subst_dng.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[ 0%] Built target ost_io_pymod +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./block_modifiers.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./block_modifiers.hh make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/actions /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/actions /build/openstructure-2.3.1/obj-x86_64-linux-gnu/actions/CMakeFiles/actions.dir/DependInfo.cmake --color= -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/bindings/pymod/./utils.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./utils.py -make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/pymod/./mat.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/seq/alg/./mat.py +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/gradient_list_model.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/gradient_list_model.py make -f modules/geom/src/CMakeFiles/ost_geom_headers.dir/build.make modules/geom/src/CMakeFiles/ost_geom_headers.dir/depend -make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/./trajectory_viewer.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./trajectory_viewer.py +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/bindings/pymod/./hhblits3.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./hhblits3.py make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/geom/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src/CMakeFiles/ost_geom_headers.dir/DependInfo.cmake --color= -make -f scripts/CMakeFiles/subst_ost.dir/build.make scripts/CMakeFiles/subst_ost.dir/build -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/gradient_editor_widget.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/gradient_editor_widget.py -make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f scripts/CMakeFiles/subst_dng.dir/build.make scripts/CMakeFiles/subst_dng.dir/build -make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -DINPUT_FILE=/build/openstructure-2.3.1/scripts/ost.in -DOUT_FILE=ost -DBUILD_TYPE=Release -DPython_EXECUTABLE=/usr/bin/python3 -DPython_VERSION=3.11.2 -DLIBDIR=lib -DLIBEXEC_PATH=lib/openstructure/libexec -DPYTHON_MODULE_PATH=python3.11/dist-packages/ -P /build/openstructure-2.3.1/cmake_support/substitute.cmake -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/pymod/./superpose.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./superpose.py -make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -DINPUT_FILE=/build/openstructure-2.3.1/scripts/dng.in -DOUT_FILE=dng -DBUILD_TYPE=Release -DPython_EXECUTABLE=/usr/bin/python3 -DPython_VERSION=3.11.2 -DLIBDIR=lib -DLIBEXEC_PATH=lib/openstructure/libexec -DPYTHON_MODULE_PATH=python3.11/dist-packages/ -P /build/openstructure-2.3.1/cmake_support/substitute.cmake make -f modules/config/CMakeFiles/ost_config_headers.dir/build.make modules/config/CMakeFiles/ost_config_headers.dir/depend -make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 0%] Built target ost_io_pymod +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/pymod/./renumber.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/seq/alg/./renumber.py +[ 0%] Built target subst_ost_startup.py make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/config /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/config /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/config/CMakeFiles/ost_config_headers.dir/DependInfo.cmake --color= -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/bindings/pymod/./naccess.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./naccess.py +make -f modules/base/src/CMakeFiles/ost_base_headers.dir/build.make modules/base/src/CMakeFiles/ost_base_headers.dir/depend +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/pymod/./trajectory_analysis.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./trajectory_analysis.py make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/share/icons/map_icon.png /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/map_icon.png -[ 0%] Built target ost_seq_pymod -make -f actions/CMakeFiles/actions.dir/build.make actions/CMakeFiles/actions.dir/build make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/base/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src/CMakeFiles/ost_base_headers.dir/DependInfo.cmake --color= +make -f scripts/CMakeFiles/subst_ost.dir/build.make scripts/CMakeFiles/subst_ost.dir/build +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/share/icons/selection_icon.png /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/selection_icon.png +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/./table.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./table.py +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./gromacs_block_modifiers.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./gromacs_block_modifiers.hh +make -f actions/CMakeFiles/actions.dir/build.make actions/CMakeFiles/actions.dir/build +make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -DINPUT_FILE=/build/openstructure-2.3.1/scripts/ost.in -DOUT_FILE=ost -DBUILD_TYPE=Release -DPython_EXECUTABLE=/usr/bin/python3 -DPython_VERSION=3.11.2 -DLIBDIR=lib -DLIBEXEC_PATH=lib/openstructure/libexec -DPYTHON_MODULE_PATH=python3.11/dist-packages/ -P /build/openstructure-2.3.1/cmake_support/substitute.cmake +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/bindings/pymod/./blast.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./blast.py +make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/actions/ost-compare-structures /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/openstructure/libexec/ost-compare-structures -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/gradient_info_handler.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/gradient_info_handler.py +[ 0%] Built target subst_ost_config make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/geom/src/CMakeFiles/ost_geom_headers.dir/build.make modules/geom/src/CMakeFiles/ost_geom_headers.dir/build -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/./helpwidget.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./helpwidget.py +make -f modules/base/pymod/CMakeFiles/ost_base_pymod.dir/build.make modules/base/pymod/CMakeFiles/ost_base_pymod.dir/depend +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/gradient_preset_widget.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/gradient_preset_widget.py make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/export_helper/vector.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/export_helper/vector.hh -make -f modules/base/src/CMakeFiles/ost_base_headers.dir/build.make modules/base/src/CMakeFiles/ost_base_headers.dir/depend -make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/pymod/./renumber.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/seq/alg/./renumber.py -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/pymod/./qsscoring.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./qsscoring.py +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/base/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/pymod/CMakeFiles/ost_base_pymod.dir/DependInfo.cmake --color= +make -f scripts/CMakeFiles/subst_dng.dir/build.make scripts/CMakeFiles/subst_dng.dir/build +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/share/icons/show_sidebar_icon.png /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/show_sidebar_icon.png +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/pymod/./aaindex.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/seq/alg/./aaindex.py make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/base/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src/CMakeFiles/ost_base_headers.dir/DependInfo.cmake --color= -make -f modules/base/pymod/CMakeFiles/ost_base_pymod.dir/build.make modules/base/pymod/CMakeFiles/ost_base_pymod.dir/depend +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -DINPUT_FILE=/build/openstructure-2.3.1/scripts/dng.in -DOUT_FILE=dng -DBUILD_TYPE=Release -DPython_EXECUTABLE=/usr/bin/python3 -DPython_VERSION=3.11.2 -DLIBDIR=lib -DLIBEXEC_PATH=lib/openstructure/libexec -DPYTHON_MODULE_PATH=python3.11/dist-packages/ -P /build/openstructure-2.3.1/cmake_support/substitute.cmake +make -f modules/seq/base/src/CMakeFiles/ost_seq_headers.dir/build.make modules/seq/base/src/CMakeFiles/ost_seq_headers.dir/depend make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 0%] Built target ost_mol_mm_pymod +make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/pymod/./structure_analysis.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./structure_analysis.py make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/base/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/pymod/CMakeFiles/ost_base_pymod.dir/DependInfo.cmake --color= -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/share/icons/menubar_icon.png /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/menubar_icon.png -[ 0%] Built target subst_ost_startup.py -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/gradient_list_model.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/gradient_list_model.py +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/seq/base/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src/CMakeFiles/ost_seq_headers.dir/DependInfo.cmake --color= +make -f modules/geom/src/CMakeFiles/ost_geom_headers.dir/build.make modules/geom/src/CMakeFiles/ost_geom_headers.dir/build make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/./gosty_startup.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./gosty_startup.py +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/bindings/pymod/./cadscore.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./cadscore.py make -f modules/config/CMakeFiles/ost_config_headers.dir/build.make modules/config/CMakeFiles/ost_config_headers.dir/build -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/pymod/./aaindex.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/seq/alg/./aaindex.py -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/bindings/pymod/./hhblits.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./hhblits.py -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/./table.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./table.py -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./def.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./def.hh make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/config && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/config/./base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./base.hh -make -f modules/seq/base/src/CMakeFiles/ost_seq_headers.dir/build.make modules/seq/base/src/CMakeFiles/ost_seq_headers.dir/depend +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/export_helper/vector.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/export_helper/vector.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./heuristic_block_modifiers.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./heuristic_block_modifiers.hh make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 0%] Built target subst_dng +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/hsc_widget.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/hsc_widget.py make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/seq/base/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src/CMakeFiles/ost_seq_headers.dir/DependInfo.cmake --color= +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/config && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/config/./base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./base.hh make -f modules/base/src/CMakeFiles/ost_base_headers.dir/build.make modules/base/src/CMakeFiles/ost_base_headers.dir/build -[ 0%] Built target subst_ost_config -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/pymod/./trajectory_analysis.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./trajectory_analysis.py make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/export_helper/generic_property_def.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/export_helper/generic_property_def.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/share/icons/site_icon.png /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/site_icon.png +make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/pymod/aaindex1 /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/share/openstructure/aaindex/aaindex1 +make -f modules/base/pymod/CMakeFiles/ost_base_pymod.dir/build.make modules/base/pymod/CMakeFiles/ost_base_pymod.dir/build +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/pymod/./helix_kinks.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./helix_kinks.py +make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/bindings/pymod/./kclust.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./kclust.py +make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/pymod/./settings.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/./settings.py +make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./interaction.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./interaction.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/immutable_gradient_info_handler.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/immutable_gradient_info_handler.py +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/share/icons/split_icon.png /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/split_icon.png +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/export_helper/pair_to_tuple_conv.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/export_helper/pair_to_tuple_conv.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/config && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/config/./config.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./config.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./def.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./def.hh +[ 0%] Built target subst_ost +make -f modules/seq/base/src/CMakeFiles/ost_seq_headers.dir/build.make modules/seq/base/src/CMakeFiles/ost_seq_headers.dir/build +make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/impl/sequence_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_impl.hh make -f modules/info/src/CMakeFiles/ost_info_headers.dir/build.make modules/info/src/CMakeFiles/ost_info_headers.dir/depend -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/share/icons/rigid_body_manipulator_icon.png /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/rigid_body_manipulator_icon.png -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/gradient_preset_widget.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/gradient_preset_widget.py make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/info/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src/CMakeFiles/ost_info_headers.dir/DependInfo.cmake --color= -make -f modules/mol/base/src/CMakeFiles/ost_mol_headers.dir/build.make modules/mol/base/src/CMakeFiles/ost_mol_headers.dir/depend -[ 0%] Built target subst_ost +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/pymod/./stutil.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/./stutil.py +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/pymod/aaindex2 /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/share/openstructure/aaindex/aaindex2 [ 0%] Built target actions +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/share/icons/warning_icon.png /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/warning_icon.png +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/config && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/config/./dllexport.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./dllexport.hh +make -f modules/mol/base/src/CMakeFiles/ost_mol_headers.dir/build.make modules/mol/base/src/CMakeFiles/ost_mol_headers.dir/depend +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/pymod/./hbond.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./hbond.py +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/bindings/pymod/./ialign.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./ialign.py make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/base/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src/CMakeFiles/ost_mol_headers.dir/DependInfo.cmake --color= +[ 0%] Built target ost_gui_pymod +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/immutable_preset_info_handler.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/immutable_preset_info_handler.py make -f modules/bindings/src/CMakeFiles/ost_bindings_headers.dir/build.make modules/bindings/src/CMakeFiles/ost_bindings_headers.dir/depend -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./exc.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./exc.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/export_helper/vec_to_list_conv.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/export_helper/vec_to_list_conv.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./settings.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./settings.hh +[ 0%] Built target subst_dng make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/bindings/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/src/CMakeFiles/ost_bindings_headers.dir/DependInfo.cmake --color= make -f modules/conop/src/CMakeFiles/ost_conop_headers.dir/build.make modules/conop/src/CMakeFiles/ost_conop_headers.dir/depend -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/bindings/pymod/./hhblits2.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./hhblits2.py -make -f modules/db/src/CMakeFiles/ost_db_headers.dir/build.make modules/db/src/CMakeFiles/ost_db_headers.dir/depend -make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./exc.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./exc.hh make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/conop/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src/CMakeFiles/ost_conop_headers.dir/DependInfo.cmake --color= -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/pymod/aaindex1 /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/share/openstructure/aaindex/aaindex1 -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/config && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/config/./config.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./config.hh -make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/db/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/src/CMakeFiles/ost_db_headers.dir/DependInfo.cmake --color= -make -f modules/base/pymod/CMakeFiles/ost_base_pymod.dir/build.make modules/base/pymod/CMakeFiles/ost_base_pymod.dir/build -make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/export_helper/pair_to_tuple_conv.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/export_helper/pair_to_tuple_conv.hh -make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/pymod/./settings.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/./settings.py -make -f modules/seq/base/src/CMakeFiles/ost_seq_headers.dir/build.make modules/seq/base/src/CMakeFiles/ost_seq_headers.dir/build -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/./gosty_startup.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./gosty_startup.py -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/hsc_widget.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/hsc_widget.py -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/share/icons/selection_icon.png /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/selection_icon.png -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./geom.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./geom.hh -make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/impl/sequence_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_impl.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/share/icons/refresh.png /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/refresh.png +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/pymod/./table.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/./table.py +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/config && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/config/./version.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./version.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/impl/sequence_impl_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_impl_fw.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/pymod/aaindex3 /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/share/openstructure/aaindex/aaindex3 make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/info/src/CMakeFiles/ost_info_headers.dir/build.make modules/info/src/CMakeFiles/ost_info_headers.dir/build make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/pymod/./stutil.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/./stutil.py -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/pymod/./structure_analysis.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./structure_analysis.py +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/bindings/pymod/./mmseqs2.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./mmseqs2.py make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./info.hh -make -f modules/mol/base/src/CMakeFiles/ost_mol_headers.dir/build.make modules/mol/base/src/CMakeFiles/ost_mol_headers.dir/build +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/init_inspector.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/init_inspector.py +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/pymod/./table_selector.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/./table_selector.py make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/bindings/pymod/./hhblits3.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./hhblits3.py -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/pymod/aaindex2 /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/share/openstructure/aaindex/aaindex2 -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./mat.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./mat.hh make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./simulation.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./simulation.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/test_utils/compare_files.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/test_utils/compare_files.hh +make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./geom.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./geom.hh +make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +make -f modules/mol/base/src/CMakeFiles/ost_mol_headers.dir/build.make modules/mol/base/src/CMakeFiles/ost_mol_headers.dir/build +make -f modules/bindings/src/CMakeFiles/ost_bindings_headers.dir/build.make modules/bindings/src/CMakeFiles/ost_bindings_headers.dir/build make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/pointer_iterator.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh -make -f modules/bindings/src/CMakeFiles/ost_bindings_headers.dir/build.make modules/bindings/src/CMakeFiles/ost_bindings_headers.dir/build -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/immutable_gradient_info_handler.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/immutable_gradient_info_handler.py -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/config && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/config/./dllexport.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./dllexport.hh +make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[ 0%] Built target ost_mol_alg_pymod +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/impl/sequence_list_impl_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_impl_fw.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info_error.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./info_error.hh +make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/bindings/src/./wrap_tmalign.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/bindings/./wrap_tmalign.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./modeller.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./modeller.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/pymod/./xmlrunner.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/./xmlrunner.py +make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./generic_property.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./generic_property.hh +[ 0%] Built target ost_config_headers +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./mat.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./mat.hh +[ 0%] Built target scene_icons make -f modules/conop/src/CMakeFiles/ost_conop_headers.dir/build.make modules/conop/src/CMakeFiles/ost_conop_headers.dir/build -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/share/icons/show_sidebar_icon.png /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/show_sidebar_icon.png -make -f modules/db/src/CMakeFiles/ost_db_headers.dir/build.make modules/db/src/CMakeFiles/ost_db_headers.dir/build +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/inspector_widget.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/inspector_widget.py make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./conop.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/./conop.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/impl/sequence_impl_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_impl_fw.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/export_helper/vec_to_list_conv.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/export_helper/vec_to_list_conv.hh -make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/db/src/./sqlite_wrap.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/db/./sqlite_wrap.hh -make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./mat2.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./mat2.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/pymod/./helix_kinks.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./helix_kinks.py -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/bindings/pymod/./blast.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./blast.py -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/config && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/config/./version.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./version.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/pymod/aaindex3 /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/share/openstructure/aaindex/aaindex3 -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/pymod/./table.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/./table.py -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info_error.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./info_error.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/share/icons/site_icon.png /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/site_icon.png -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./mat3.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./mat3.hh -make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/impl/sequence_list_impl_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_impl_fw.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/atom_group.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/atom_group.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/immutable_preset_info_handler.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/immutable_preset_info_handler.py -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/db/src/./sqlite_conv.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/db/./sqlite_conv.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/pymod/./table_selector.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/./table_selector.py -[ 0%] Built target ost_gui_pymod -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./processor.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/./processor.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/test_utils/compare_files.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/test_utils/compare_files.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./mat4.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./mat4.hh +make -f modules/db/src/CMakeFiles/ost_db_headers.dir/build.make modules/db/src/CMakeFiles/ost_db_headers.dir/depend +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./info_impl.hh make -f modules/seq/alg/src/CMakeFiles/ost_seq_alg_headers.dir/build.make modules/seq/alg/src/CMakeFiles/ost_seq_alg_headers.dir/depend make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/db/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/src/CMakeFiles/ost_db_headers.dir/DependInfo.cmake --color= +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./observer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./observer.hh +make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/seq/alg/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src/CMakeFiles/ost_seq_alg_headers.dir/DependInfo.cmake --color= -make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/bindings/pymod/./cadscore.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./cadscore.py -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./info_impl.hh -make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/impl/sequence_list_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_impl.hh -[ 0%] Built target ost_bindings_headers -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/db/src/./module_config.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/db/./module_config.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/pymod/./hbond.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./hbond.py -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/pymod/./xmlrunner.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/./xmlrunner.py -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/share/icons/split_icon.png /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/split_icon.png make -f modules/img/base/src/CMakeFiles/ost_img_headers.dir/build.make modules/img/base/src/CMakeFiles/ost_img_headers.dir/depend -make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/img/base/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src/CMakeFiles/ost_img_headers.dir/DependInfo.cmake --color= -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./vec.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./vec.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/atom_prop.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/atom_prop.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./generic_property.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./generic_property.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/pymod/./testutils.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/./testutils.py +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/impl/sequence_list_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_impl.hh +[ 0%] Built target ost_seq_alg_pymod make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/seq/alg/src/CMakeFiles/ost_seq_alg_headers.dir/build.make modules/seq/alg/src/CMakeFiles/ost_seq_alg_headers.dir/build -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/init_inspector.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/init_inspector.py +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./integrity_error.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./integrity_error.hh make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./alignment_opts.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./alignment_opts.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/bindings/pymod/./kclust.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./kclust.py -[ 0%] Built target ost_config_headers -[ 0%] Built target ost_seq_alg_pymod -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/impl/sequence_list_iterator.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./amino_acids.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/./amino_acids.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/img/base/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src/CMakeFiles/ost_img_headers.dir/DependInfo.cmake --color= +[ 0%] Built target ost_bindings_pymod +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/atom_group.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/atom_group.hh make -f modules/img/alg/src/CMakeFiles/ost_img_alg_headers.dir/build.make modules/img/alg/src/CMakeFiles/ost_img_alg_headers.dir/depend -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/db/src/./linear_indexer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/db/./linear_indexer.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./mat2.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./mat2.hh make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/img/alg/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src/CMakeFiles/ost_img_alg_headers.dir/DependInfo.cmake --color= make -f modules/io/src/CMakeFiles/ost_io_headers.dir/build.make modules/io/src/CMakeFiles/ost_io_headers.dir/depend +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./processor.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/./processor.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info_impl_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./info_impl_fw.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./vec2.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./vec2.hh make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/io/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src/CMakeFiles/ost_io_headers.dir/DependInfo.cmake --color= -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/share/icons/warning_icon.png /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/warning_icon.png +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/impl/sequence_list_iterator.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/map_level_widget.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/map_level_widget.py +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./state_extractor.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./state_extractor.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./invalid_handle.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./invalid_handle.hh make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/inspector_widget.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/inspector_widget.py +make -f modules/seq/alg/src/CMakeFiles/ost_seq_alg_headers.dir/build.make modules/seq/alg/src/CMakeFiles/ost_seq_alg_headers.dir/build +make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/cmake -E copy_if_different __init__.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/__init__.py +[ 0%] Built target ost_bindings_headers +make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./mat3.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./mat3.hh +make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./alignment_opts.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./alignment_opts.hh +make -f modules/db/src/CMakeFiles/ost_db_headers.dir/build.make modules/db/src/CMakeFiles/ost_db_headers.dir/build +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info_handle.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./info_handle.hh +make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/db/src/./sqlite_wrap.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/db/./sqlite_wrap.hh make -f modules/img/base/src/CMakeFiles/ost_img_headers.dir/build.make modules/img/base/src/CMakeFiles/ost_img_headers.dir/build +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./amino_acids.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/./amino_acids.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/./sequence_list.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/./sequence_list.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/atom_prop.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/atom_prop.hh make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/raster_image/raster_image.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/raster_image/raster_image.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./integrity_error.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./integrity_error.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/./sequence_list.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/./sequence_list.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/pymod/./testutils.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/./testutils.py -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/atom_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/atom_impl.hh -make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/bindings/pymod/./ialign.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./ialign.py -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./clip_alignment.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./clip_alignment.hh +make -f modules/mol/alg/src/CMakeFiles/ost_mol_alg_headers.dir/build.make modules/mol/alg/src/CMakeFiles/ost_mol_alg_headers.dir/depend make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/img/alg/src/CMakeFiles/ost_img_alg_headers.dir/build.make modules/img/alg/src/CMakeFiles/ost_img_alg_headers.dir/build -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/map_level_widget.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/map_level_widget.py make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./anisotropic.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./anisotropic.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info_handle.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./info_handle.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./vec3.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./vec3.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./diag.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/./diag.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/share/icons/refresh.png /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/refresh.png +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/alg/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src/CMakeFiles/ost_mol_alg_headers.dir/DependInfo.cmake --color= +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./system_creator.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./system_creator.hh make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./invalid_handle.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./invalid_handle.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./ptr_observer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./ptr_observer.hh make -f modules/io/src/CMakeFiles/ost_io_headers.dir/build.make modules/io/src/CMakeFiles/ost_io_headers.dir/build -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./conservation.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./conservation.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/atom_impl_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/atom_impl_fw.hh -[ 0%] Built target ost_mol_alg_pymod -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/cmake -E copy_if_different __init__.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/__init__.py make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/chemdict_parser.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/chemdict_parser.hh -make -f modules/mol/alg/src/CMakeFiles/ost_mol_alg_headers.dir/build.make modules/mol/alg/src/CMakeFiles/ost_mol_alg_headers.dir/depend -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./vec4.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./vec4.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./anisotropic.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./anisotropic.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./clip_alignment.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./clip_alignment.hh +make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/preset.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/preset.py make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/alg/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src/CMakeFiles/ost_mol_alg_headers.dir/DependInfo.cmake --color= -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/db/src/./binary_container.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/db/./binary_container.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./contact_prediction_score.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./contact_prediction_score.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/bindings/pymod/./mmseqs2.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./mmseqs2.py -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/dispatch.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/dispatch.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/chemdict_parser.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/chemdict_parser.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/db/src/./sqlite_conv.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/db/./sqlite_conv.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./mat4.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./mat4.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info_group.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./info_group.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/dispatch.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/dispatch.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/atom_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/atom_impl.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./conservation.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./conservation.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./diag.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/./diag.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./topology_creator.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./topology_creator.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/./sequence_handle.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/./sequence_handle.hh -make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/preset.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/preset.py -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./auto_correlate.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./auto_correlate.hh -make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/chain_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/chain_impl.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./vecmat_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./vecmat_op.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./ptr_observer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./ptr_observer.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./contact_weight_matrix.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./contact_weight_matrix.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./model_check.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/./model_check.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/star_parser.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/star_parser.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/db/src/./extract_data_helper.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/db/./extract_data_helper.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info_item.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./info_item.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/./alignment_handle.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/./alignment_handle.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./vecmat2_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./vecmat2_op.hh -[ 0%] Built target scene_icons -make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./log.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./log.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/db/src/./module_config.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/db/./module_config.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/remote.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/remote.py -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./clear.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./clear.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/chain_impl_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/chain_impl_fw.hh -make -f modules/gfx/src/CMakeFiles/ost_gfx_headers.dir/build.make modules/gfx/src/CMakeFiles/ost_gfx_headers.dir/depend -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./distance_map.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./distance_map.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./heuristic.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/./heuristic.hh [ 0%] Built target ost_base_pymod +make -f modules/gfx/src/CMakeFiles/ost_gfx_headers.dir/build.make modules/gfx/src/CMakeFiles/ost_gfx_headers.dir/depend make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/gfx/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src/CMakeFiles/ost_gfx_headers.dir/DependInfo.cmake --color= -make -f modules/gui/src/CMakeFiles/ost_gui_headers.dir/build.make modules/gui/src/CMakeFiles/ost_gui_headers.dir/depend -make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_fw.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./info_fw.hh make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/mmcif_reader.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/mmcif_reader.hh -make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/gui/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/CMakeFiles/ost_gui_headers.dir/DependInfo.cmake --color= -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./vecmat3_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./vecmat3_op.hh make -f modules/mol/alg/src/CMakeFiles/ost_mol_alg_headers.dir/build.make modules/mol/alg/src/CMakeFiles/ost_mol_alg_headers.dir/build -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/preset_editor_list_model.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/preset_editor_list_model.py +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info_item.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./info_item.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/star_parser.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/star_parser.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./vec.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./vec.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./auto_correlate.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./auto_correlate.hh make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./svd_superpose.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./svd_superpose.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/./module_config.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/./module_config.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/connector_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/connector_impl.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./log.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./log.hh -[ 0%] Built target ost_bindings_pymod -make -f modules/mol/mm/src/CMakeFiles/ost_mol_mm_headers.dir/build.make modules/mol/mm/src/CMakeFiles/ost_mol_mm_headers.dir/depend -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./entropy.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./entropy.hh -make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/mm/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src/CMakeFiles/ost_mol_mm_headers.dir/DependInfo.cmake --color= -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./compound.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/./compound.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./clip_min_max.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./clip_min_max.hh -make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/gui/src/CMakeFiles/ost_gui_headers.dir/build.make modules/gui/src/CMakeFiles/ost_gui_headers.dir/build -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_base.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./module_config.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./module_config.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./log_sink.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./log_sink.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./model_check.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/./model_check.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/atom_impl_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/atom_impl_fw.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/./alignment_handle.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/./alignment_handle.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/db/src/./linear_indexer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/db/./linear_indexer.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./contact_prediction_score.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./contact_prediction_score.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./index.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./index.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/preset_editor_list_model.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/preset_editor_list_model.py make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/tool.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool.hh make -f modules/gfx/src/CMakeFiles/ost_gfx_headers.dir/build.make modules/gfx/src/CMakeFiles/ost_gfx_headers.dir/build -[ 0%] Built target ost_db_headers -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/mmcif_info.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/mmcif_info.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/mmcif_reader.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/mmcif_reader.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./vec2.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./vec2.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./info_fw.hh make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/map_iso_gen.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/map_iso_gen.hh -make -f modules/config/CMakeFiles/ost_config.dir/build.make modules/config/CMakeFiles/ost_config.dir/depend -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./vecmat4_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./vecmat4_op.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/preset_editor_widget.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/preset_editor_widget.py +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_fw.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./clear.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./clear.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./topology.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./topology.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./module_config.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./module_config.hh -make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./global_align.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./global_align.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/config /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/config /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/config/CMakeFiles/ost_config.dir/DependInfo.cmake --color= +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./profile.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./profile.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/db/src/./binary_container.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/db/./binary_container.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/chain_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/chain_impl.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/./module_config.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/./module_config.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./contact_weight_matrix.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./contact_weight_matrix.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./heuristic.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/./heuristic.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_base.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/mmcif_info.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/mmcif_info.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./vec3.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./vec3.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/preset_editor_widget.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/preset_editor_widget.py +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./module_config.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./module_config.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/map_iso_gen_s.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/map_iso_gen_s.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./clip_min_max.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./clip_min_max.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./dyn_cast.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./dyn_cast.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/chain_impl_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/chain_impl_fw.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/./sequence_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/./sequence_op.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/connector_impl_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/connector_impl_fw.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./steep.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./steep.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/db/src/./extract_data_helper.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/db/./extract_data_helper.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./distance_map.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./distance_map.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./sec_structure_segments.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./sec_structure_segments.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_base_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_base_fw.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./log_sink.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./log_sink.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./compound.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/./compound.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./vec4.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./vec4.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./conjugate.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./conjugate.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./stdint.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./stdint.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/preset_info_handler.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/preset_info_handler.py +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info_path.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./info_path.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/io_profile.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/io_profile.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./sec_structure_segments.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./sec_structure_segments.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/connector_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/connector_impl.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/map_iso_gen_s.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/map_iso_gen_s.hh make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/mol/mm/src/CMakeFiles/ost_mol_mm_headers.dir/build.make modules/mol/mm/src/CMakeFiles/ost_mol_mm_headers.dir/build -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/preset_info_handler.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/preset_info_handler.py +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/./aligned_region.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/./aligned_region.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./entropy.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./entropy.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./compound_lib.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/./compound_lib.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/tool_option_group.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool_option_group.hh -make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./forcefield.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./forcefield.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./ins_del.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./ins_del.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./circular_iterator.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./circular_iterator.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./convolute.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./convolute.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info_path.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./info_path.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/./aligned_region.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/./aligned_region.hh -make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/dihedral.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/dihedral.hh -make -f modules/config/CMakeFiles/ost_config.dir/build.make modules/config/CMakeFiles/ost_config.dir/build -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/tool_options.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool_options.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/preset_list_model.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/preset_list_model.py -make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make[3]: Nothing to be done for 'modules/config/CMakeFiles/ost_config.dir/build'. make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/map_iso_gen_s.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/map_iso_gen_s.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_def.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./ff_reader.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./ff_reader.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./vecmat_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./vecmat_op.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./stdint_msc.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./stdint_msc.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./local_dist_diff_test.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./local_dist_diff_test.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info_set.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./info_set.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/preset_list_model.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/preset_list_model.py +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/map_iso_spec.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/map_iso_spec.hh +[ 0%] Built target ost_mol_mm_headers cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/dcd_io.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/dcd_io.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./local_align.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./local_align.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./profile.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./profile.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/connector_impl_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/connector_impl_fw.hh +make -f modules/gui/src/CMakeFiles/ost_gui_headers.dir/build.make modules/gui/src/CMakeFiles/ost_gui_headers.dir/depend cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./module_config.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/./module_config.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./local_dist_diff_test.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./local_dist_diff_test.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./constants.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./constants.hh -[ 0%] Built target ost_config -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/tool_bar.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool_bar.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./correlate.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./correlate.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/preset_widget.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/preset_widget.py cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/./aligned_column.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/./aligned_column.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./buildingblock.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./buildingblock.hh +[ 0%] Built target ost_db_headers +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./vecmat2_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./vecmat2_op.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./correlate.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./correlate.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./range.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./range.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_factory.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_factory.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info_set.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./info_set.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./merge_pairwise_alignments.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./merge_pairwise_alignments.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/map_iso_gen_s.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/map_iso_gen_s.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./rule_based.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/./rule_based.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/entity_io_crd_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/entity_io_crd_handler.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./dyn_cast.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./dyn_cast.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./global_align.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./global_align.hh +make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/gui/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/CMakeFiles/ost_gui_headers.dir/DependInfo.cmake --color= +make -f modules/config/CMakeFiles/ost_config.dir/build.make modules/config/CMakeFiles/ost_config.dir/depend +make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/config /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/config /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/config/CMakeFiles/ost_config.dir/DependInfo.cmake --color= cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./distance_test_common.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./distance_test_common.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./composite.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./composite.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/selection_tool.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/selection_tool.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./module_config.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./module_config.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/render_mode_widget.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/render_mode_widget.py -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./cross_correlate.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./cross_correlate.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./block_modifiers.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./block_modifiers.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info_visitor.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./info_visitor.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/preset_widget.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/preset_widget.py +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/map_octree.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/map_octree.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_frequency_domain.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_frequency_domain.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./module_config.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./module_config.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./vecmat3_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./vecmat3_op.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/entity_io_crd_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/entity_io_crd_handler.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/dihedral.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/dihedral.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./rule_based.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/./rule_based.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./cross_correlate.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./cross_correlate.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/./aligned_column_iterator.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/./aligned_column_iterator.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./minimal_compound_lib.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/./minimal_compound_lib.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info_visitor.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./info_visitor.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./ins_del.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./ins_del.hh +make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./units.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./units.hh +make -f modules/gui/src/CMakeFiles/ost_gui_headers.dir/build.make modules/gui/src/CMakeFiles/ost_gui_headers.dir/build +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_half_frequency_domain.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_half_frequency_domain.hh +make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/tool.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info_verbose_visitor.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./info_verbose_visitor.hh +make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./distance_rmsd_test.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./distance_rmsd_test.hh +make -f modules/config/CMakeFiles/ost_config.dir/build.make modules/config/CMakeFiles/ost_config.dir/build +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/octree_isocont.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/octree_isocont.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/render_mode_widget.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/render_mode_widget.py +make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +make[3]: Nothing to be done for 'modules/config/CMakeFiles/ost_config.dir/build'. +make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./minimal_compound_lib.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/./minimal_compound_lib.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./vecmat4_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./vecmat4_op.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./density_slice.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./density_slice.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/entity_io_pqr_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/entity_io_pqr_handler.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./pair_subst_weight_matrix.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./pair_subst_weight_matrix.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./composite2.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./composite2.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/measure_tool.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/measure_tool.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/entity_impl_fw.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/map_iso_spec.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/map_iso_spec.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./compound_lib_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/./compound_lib_base.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./stdint.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./stdint.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./gromacs_block_modifiers.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./gromacs_block_modifiers.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./message.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./message.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./local_align.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./local_align.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/./invalid_sequence.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/./invalid_sequence.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./superpose_frames.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./superpose_frames.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_half_frequency_domain.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_half_frequency_domain.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/render_op.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/render_op.py +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/tool_option_group.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool_option_group.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/cartoon_renderer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/cartoon_renderer.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./item_type.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./item_type.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/entity_io_mae_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/entity_io_mae_handler.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./semiglobal_align.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./semiglobal_align.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./density_slice.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./density_slice.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info_verbose_visitor.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./info_verbose_visitor.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./composite3.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./composite3.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/tool_option.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool_option.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/fragment_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/fragment_impl.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./heuristic_block_modifiers.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./heuristic_block_modifiers.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/map_octree.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/map_octree.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./ring_finder.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/./ring_finder.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/./views_from_sequences.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/./views_from_sequences.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./sequence_identity.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./sequence_identity.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./filter_clashes.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./filter_clashes.hh +[ 0%] Built target ost_config +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./superpose_frames.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./superpose_frames.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_spatial_domain.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_spatial_domain.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./compound_lib_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/./compound_lib_base.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./platform.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./platform.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./circular_iterator.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./circular_iterator.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./dft.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./dft.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/tool_manager.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool_manager.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./merge_pairwise_alignments.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./merge_pairwise_alignments.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/./views_from_sequences.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/./views_from_sequences.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/entity_impl_fw.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/tool_options.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool_options.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/render_options_widget.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/render_options_widget.py -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./item_type.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./item_type.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/entity_io_mmcif_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/entity_io_mmcif_handler.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./stdint_msc.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./stdint_msc.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/fragment_impl_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/fragment_impl_fw.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./composite_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./composite_op.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./sequence_similarity.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./sequence_similarity.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./interaction.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./interaction.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/custom_renderer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/custom_renderer.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_visitor.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_visitor.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./geom_info_conversion.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./geom_info_conversion.hh -make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/octree_isocont.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/octree_isocont.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/./profile_handle.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/./profile_handle.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/entity_io_mmcif_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/entity_io_mmcif_handler.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./filter_clashes.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./filter_clashes.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./item_type_cast.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./item_type_cast.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./string_ref.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./string_ref.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./ring_finder.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/./ring_finder.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./fft.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./fft.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./subst_weight_matrix.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./subst_weight_matrix.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/tool_options_widget.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool_options_widget.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./construct_cbeta.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./construct_cbeta.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./module_config.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./module_config.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./constants.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./constants.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/fragment_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/fragment_impl.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/cpk_renderer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/cpk_renderer.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/./profile_handle.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/./profile_handle.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/tool_bar.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool_bar.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/scene_observer_impl.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/scene_observer_impl.py -[ 0%] Built target ost_conop_headers -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./variance_map.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./variance_map.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/entity_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/entity_io_handler.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/cartoon_renderer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/cartoon_renderer.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./range.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./range.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_spatial_domain.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_spatial_domain.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/query_ast.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/query_ast.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./settings.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./settings.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./item_type_cast.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./item_type_cast.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/manipulator.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/manipulator.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./data/default_contact_weight_matrix.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./default_contact_weight_matrix.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./composite2_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./composite2_op.hh make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_algorithm.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_algorithm.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./pod_vector.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./pod_vector.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./fftw_helper.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./fftw_helper.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./clash_score.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./clash_score.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/pdb_reader.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/query_ast_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/query_ast_fw.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./module_config.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./module_config.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/scene_selection_helper.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/scene_selection_helper.py +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./composite.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./composite.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/fragment_impl_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/fragment_impl_fw.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/debug_renderer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/debug_renderer.hh make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/custom_renderer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/custom_renderer.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/tool_options_win.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool_options_win.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_visitor.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_visitor.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./composite3_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./composite3_op.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./construct_cbeta.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./construct_cbeta.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./pair_subst_weight_matrix.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./pair_subst_weight_matrix.hh +[ 0%] Built target ost_info_headers +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/selection_tool.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/selection_tool.hh +[ 0%] Built target ost_conop_headers +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/scene_selection_helper.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/scene_selection_helper.py +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/pdb_reader.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./fill.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./fill.hh [ 0%] Built target ost_seq_headers -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./trajectory_analysis.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./trajectory_analysis.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/query_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/query_impl.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./simulation.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./simulation.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./fixed_string.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./fixed_string.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_visitor_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_visitor_fw.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/query_ast.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/query_ast.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./composite2.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./composite2.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/simple_renderer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/simple_renderer.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/measure_tool.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/measure_tool.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./semiglobal_align.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./semiglobal_align.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/entity_io_pdb_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/entity_io_pdb_handler.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./fill.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./fill.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./data/default_pair_subst_weight_matrix.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./default_pair_subst_weight_matrix.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./units.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./units.hh -[ 0%] Built target ost_info_headers -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/mouse_event.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./aligned_cuboid.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./aligned_cuboid.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./clash_score.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./clash_score.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/simple_widget.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/simple_widget.py -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/pdb_writer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/pdb_writer.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/cpk_renderer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/cpk_renderer.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./modeller.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./modeller.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_algorithm.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_algorithm.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./filter.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./filter.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./composite3.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./composite3.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/index.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/index.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/query_ast_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/query_ast_fw.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./tri_matrix.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./tri_matrix.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/sline_renderer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/sline_renderer.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/tool_option.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool_option.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./sequence_identity.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./sequence_identity.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./fourier_filters.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./fourier_filters.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/pdb_writer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/pdb_writer.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/sline_widget.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/sline_widget.py +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./trajectory_analysis.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./trajectory_analysis.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./boost_filesystem_helper.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./boost_filesystem_helper.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./composite_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./composite_op.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/type_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/type_fw.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/tool_manager.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool_manager.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/query_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/query_impl.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./gaussian_gradient_magnitude.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./gaussian_gradient_magnitude.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/trace_renderer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/trace_renderer.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./structure_analysis.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./structure_analysis.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/toolbar_options_widget.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/toolbar_options_widget.py cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/entity_io_sdf_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/entity_io_sdf_handler.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./paged_array.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./paged_array.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./composite2_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./composite2_op.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/tool_options_widget.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool_options_widget.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./sequence_similarity.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./sequence_similarity.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/value_holder.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/value_holder.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./gaussian.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./gaussian.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/query_impl_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/query_impl_fw.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/map_tool.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/map_tool.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./message.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./message.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./structure_analysis.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./structure_analysis.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./vec_mat_predicates.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./vec_mat_predicates.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/debug_renderer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/debug_renderer.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./hmm_pseudo_counts.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./hmm_pseudo_counts.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./observer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./observer.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/trace_widget.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/trace_widget.py +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/line_trace_renderer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/line_trace_renderer.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./consistency_checks.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./consistency_checks.hh +make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./subst_weight_matrix.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./subst_weight_matrix.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./composite3_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./composite3_op.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/manipulator.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/manipulator.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/sdf_reader.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/sdf_reader.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/sline_widget.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/sline_widget.py +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./algorithm.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./algorithm.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./pdbize.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./pdbize.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/tube_widget.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/tube_widget.py +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./gaussian_laplacian.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./gaussian_laplacian.hh +[ 0%] Built target ost_base_headers +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/backbone_trace.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/backbone_trace.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/residue_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/residue_impl.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_visitor_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_visitor_fw.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./platform.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./platform.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./hmm_score.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./hmm_score.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./consistency_checks.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./consistency_checks.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/simple_renderer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/simple_renderer.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./variance_map.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./variance_map.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./aligned_cuboid.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./aligned_cuboid.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/sdf_writer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/sdf_writer.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/tool_options_win.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool_options_win.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./adjacency_bitmap.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./adjacency_bitmap.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/uniform_color_widget.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/uniform_color_widget.py +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./circle_mask.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./circle_mask.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./highest_peak_search_3d.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./highest_peak_search_3d.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/entity_detail.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/entity_detail.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/residue_impl_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/residue_impl_fw.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/align_properties_painter.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/align_properties_painter.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./fourier_filters.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./fourier_filters.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./quat.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./quat.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./vec_mat_predicates.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./vec_mat_predicates.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/save_entity.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/save_entity.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./data/default_contact_weight_matrix.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./default_contact_weight_matrix.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/visibility_op.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/visibility_op.py +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./consistency_checks.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./consistency_checks.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/mouse_event.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./composite_mask.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./composite_mask.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/entity_renderer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./histogram.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./histogram.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/surface_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/surface_impl.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./state_extractor.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./state_extractor.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/sdf_writer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/sdf_writer.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./string_ref.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./string_ref.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/toolbar_options_widget.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/toolbar_options_widget.py -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./pdbize.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./pdbize.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./data/default_pair_subst_weight_matrix.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./default_pair_subst_weight_matrix.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./quat.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./quat.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/load_entity.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/load_entity.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/line_trace_widget.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/line_trace_widget.py +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./contact_overlap.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./contact_overlap.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/trace_renderer_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/trace_renderer_base.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/map_tool.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/map_tool.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./data_algorithm.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./data_algorithm.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./line_iterator.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./line_iterator.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/surface_impl_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/surface_impl_fw.hh -make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./transform.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./transform.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/index.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/index.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/sline_renderer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/sline_renderer.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./pod_vector.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./pod_vector.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./system_creator.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./system_creator.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/trace_widget.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/trace_widget.py -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./gaussian_gradient_magnitude.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./gaussian_gradient_magnitude.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./hmm_pseudo_counts.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./hmm_pseudo_counts.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/surface_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/surface_io_handler.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/wireframe_widget.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/wireframe_widget.py +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./domain_find.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./domain_find.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/connect_renderer_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/connect_renderer_base.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/align_properties_painter.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/align_properties_painter.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./local_sigma_threshold.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./local_sigma_threshold.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./data_observer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./data_observer.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./hmm_score.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./hmm_score.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/torsion_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/torsion_impl.hh -[ 0%] Built target ost_seq_alg_headers cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./point_cloud.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./point_cloud.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/query_editor.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/query_editor.py +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/load_surface.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/load_surface.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/mapped_property.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/mapped_property.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./similarity_matrix.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./similarity_matrix.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./mask_image.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./mask_image.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/base_row.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/base_row.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./adjacency_bitmap.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./adjacency_bitmap.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./fixed_string.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./fixed_string.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/save_entity.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/save_entity.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/type_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/type_fw.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/trace_renderer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/trace_renderer.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./gaussian.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./gaussian.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./topology_creator.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./topology_creator.hh +make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./data_types.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./data_types.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/surface_io_msms_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/surface_io_msms_handler.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/torsion_impl_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/torsion_impl_fw.hh +make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./module_config.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./module_config.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./gaussian_laplacian.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./gaussian_laplacian.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/entity_renderer_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer_fw.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./accessibility.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./accessibility.hh +[ 0%] Built target ost_seq_alg_headers cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/background_painter.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/background_painter.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/load_entity.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/load_entity.hh +[ 0%] Built target ost_gui_scene_pymod +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./negate.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./negate.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/pdb_str.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/pdb_str.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./atom_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./atom_base.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/tabulated_trig.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/tabulated_trig.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./sec_struct.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./sec_struct.hh make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/value_holder.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/value_holder.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/tube_widget.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/tube_widget.py -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./consistency_checks.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./consistency_checks.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/torsion_impl_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/torsion_impl_fw.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./data.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./data.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/conservation_painter.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/conservation_painter.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./normalizer_factory.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./normalizer_factory.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/fast_spheres.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/fast_spheres.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./nonstandard.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./nonstandard.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./atom_handle.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./atom_handle.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./debug.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./debug.hh [ 0%] Built target ost_geom_headers +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/stereochemical_params_reader.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/stereochemical_params_reader.hh make -f modules/geom/src/CMakeFiles/ost_geom.dir/build.make modules/geom/src/CMakeFiles/ost_geom.dir/depend make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/geom/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src/CMakeFiles/ost_geom.dir/DependInfo.cmake --color= -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./tri_matrix.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./tri_matrix.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./index.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./index.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/line_trace_renderer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/line_trace_renderer.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./atom_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./atom_base.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./boost_filesystem_helper.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./boost_filesystem_helper.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/conservation_painter.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/conservation_painter.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./contact_overlap.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./contact_overlap.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./highest_peak_search_3d.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./highest_peak_search_3d.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./algorithm.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./algorithm.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./atom_handle.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./atom_handle.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/surface_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/surface_io_handler.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/uniform_color_widget.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/uniform_color_widget.py -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./domain_find.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./domain_find.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/painter.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/painter.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/render_options/render_options.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/render_options.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./molck.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./molck.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./atom_view.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./atom_view.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/omf.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/omf.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./norm.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./norm.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./dllexport.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./dllexport.hh make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/geom/src/CMakeFiles/ost_geom.dir/build.make modules/geom/src/CMakeFiles/ost_geom.dir/build -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/backbone_trace.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/backbone_trace.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./topology.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./topology.hh make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./circle_mask.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./circle_mask.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./atom_view.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./atom_view.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/painter.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/painter.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./similarity_matrix.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./similarity_matrix.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./paged_array.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./paged_array.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./steep.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./steep.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/visibility_op.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/visibility_op.py -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/load_surface.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/load_surface.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./histogram.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./histogram.hh -[ 0%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/mat3.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/secstr_row.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/secstr_row.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/render_options/line_render_options.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/line_render_options.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./find_membrane.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./find_membrane.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/load_map.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/load_map.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./bond_handle.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./bond_handle.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./extent_iterator.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./extent_iterator.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./normalizer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./normalizer.hh [ 0%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/mat2.cc.o -[ 0%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/mat4.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./composite_mask.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./composite_mask.hh +[ 0%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/mat3.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/seq_secstr_painter.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/seq_secstr_painter.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/c++ -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/src/CMakeFiles/ost_geom.dir/mat2.cc.o -MF CMakeFiles/ost_geom.dir/mat2.cc.o.d -o CMakeFiles/ost_geom.dir/mat2.cc.o -c /build/openstructure-2.3.1/modules/geom/src/mat2.cc -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/entity_detail.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/entity_detail.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./entity_to_density.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./entity_to_density.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/render_options/custom_render_options.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/custom_render_options.hh +[ 0%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/mat4.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/c++ -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/src/CMakeFiles/ost_geom.dir/mat3.cc.o -MF CMakeFiles/ost_geom.dir/mat3.cc.o.d -o CMakeFiles/ost_geom.dir/mat3.cc.o -c /build/openstructure-2.3.1/modules/geom/src/mat3.cc +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./bond_table.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./bond_table.hh [ 1%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/vec3.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/c++ -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/src/CMakeFiles/ost_geom.dir/mat4.cc.o -MF CMakeFiles/ost_geom.dir/mat4.cc.o.d -o CMakeFiles/ost_geom.dir/mat4.cc.o -c /build/openstructure-2.3.1/modules/geom/src/mat4.cc -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./bond_handle.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./bond_handle.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_df3_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_df3_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/c++ -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/src/CMakeFiles/ost_geom.dir/vec3.cc.o -MF CMakeFiles/ost_geom.dir/vec3.cc.o.d -o CMakeFiles/ost_geom.dir/vec3.cc.o -c /build/openstructure-2.3.1/modules/geom/src/vec3.cc -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./accessibility.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./accessibility.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./line_iterator.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./line_iterator.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/secstr_row.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/secstr_row.hh -make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 1%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/vecmat2_op.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./norm_linear.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./norm_linear.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./extent_mask.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./extent_mask.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/seq_selection_painter.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/seq_selection_painter.hh +[ 1%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/vecmat3_op.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/c++ -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/src/CMakeFiles/ost_geom.dir/vecmat2_op.cc.o -MF CMakeFiles/ost_geom.dir/vecmat2_op.cc.o.d -o CMakeFiles/ost_geom.dir/vecmat2_op.cc.o -c /build/openstructure-2.3.1/modules/geom/src/vecmat2_op.cc make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 1%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/vecmat3_op.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./data_algorithm.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./data_algorithm.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/render_options/cpk_render_options.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/cpk_render_options.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/c++ -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/src/CMakeFiles/ost_geom.dir/vecmat3_op.cc.o -MF CMakeFiles/ost_geom.dir/vecmat3_op.cc.o.d -o CMakeFiles/ost_geom.dir/vecmat3_op.cc.o -c /build/openstructure-2.3.1/modules/geom/src/vecmat3_op.cc -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/surface_io_msms_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/surface_io_msms_handler.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/line_trace_widget.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/line_trace_widget.py -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./bond_table.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./bond_table.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./sec_struct.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./sec_struct.hh -[ 1%] Built target ost_base_headers -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./local_sigma_threshold.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./local_sigma_threshold.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/entity_renderer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/seq_secstr_painter.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/seq_secstr_painter.hh -[ 1%] Built target ost_mol_mm_headers -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./data_observer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./data_observer.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/wireframe_widget.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/wireframe_widget.py -[ 1%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/vecmat4_op.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/c++ -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/src/CMakeFiles/ost_geom.dir/vecmat4_op.cc.o -MF CMakeFiles/ost_geom.dir/vecmat4_op.cc.o.d -o CMakeFiles/ost_geom.dir/vecmat4_op.cc.o -c /build/openstructure-2.3.1/modules/geom/src/vecmat4_op.cc +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/image_format.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/image_format.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./chain_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./chain_base.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/pdb_str.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/pdb_str.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/seq_selection_painter.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/seq_selection_painter.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./nonstandard.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./nonstandard.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/trace_renderer_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/trace_renderer_base.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./mask_image.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./mask_image.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./norm_log.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./norm_log.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./extent.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./extent.hh [ 1%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/composite2.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/c++ -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/src/CMakeFiles/ost_geom.dir/composite2.cc.o -MF CMakeFiles/ost_geom.dir/composite2.cc.o.d -o CMakeFiles/ost_geom.dir/composite2.cc.o -c /build/openstructure-2.3.1/modules/geom/src/composite2.cc -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./molck.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./molck.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/query_editor.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/query_editor.py -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./data_types.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./data_types.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/stereochemical_params_reader.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/stereochemical_params_reader.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/connect_renderer_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/connect_renderer_base.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./negate.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./negate.hh +[ 1%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/vecmat4_op.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/seq_text_painter.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/seq_text_painter.hh +[ 1%] Built target ost_mol_alg_headers +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/render_options/simple_render_options.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/simple_render_options.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/c++ -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/src/CMakeFiles/ost_geom.dir/vecmat4_op.cc.o -MF CMakeFiles/ost_geom.dir/vecmat4_op.cc.o.d -o CMakeFiles/ost_geom.dir/vecmat4_op.cc.o -c /build/openstructure-2.3.1/modules/geom/src/vecmat4_op.cc +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_dx_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_dx_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./chain_handle.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./chain_handle.hh -make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/omf.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/omf.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/mapped_property.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/mapped_property.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./chain_view.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./chain_view.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./data.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./data.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./find_membrane.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./find_membrane.hh -[ 1%] Built target ost_gui_scene_pymod -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./normalizer_factory.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./normalizer_factory.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./norm_od.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./norm_od.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./image_factory.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./image_factory.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_spi_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_spi_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_delegate.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_delegate.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/entity_renderer_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer_fw.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./debug.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./debug.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/load_map.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/load_map.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./chain_type.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./chain_type.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./entity_to_density.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./entity_to_density.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./norm.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./norm.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/render_options/sline_render_options.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/sline_render_options.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./chain_view.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./chain_view.hh [ 1%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/composite3.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/c++ -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/src/CMakeFiles/ost_geom.dir/composite3.cc.o -MF CMakeFiles/ost_geom.dir/composite3.cc.o.d -o CMakeFiles/ost_geom.dir/composite3.cc.o -c /build/openstructure-2.3.1/modules/geom/src/composite3.cc -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_df3_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_df3_handler.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./image_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./image_fw.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./power_spectrum.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./power_spectrum.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_situs_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_situs_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_model.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_model.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/tabulated_trig.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/tabulated_trig.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/image_format.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/image_format.hh -make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./chem_class.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./chem_class.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./dllexport.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./dllexport.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_dx_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_dx_handler.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./normalizer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./normalizer.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/fast_spheres.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/fast_spheres.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/render_options/line_trace_render_options.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/line_trace_render_options.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./chain_type.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./chain_type.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./image_handle_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./image_handle_fw.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./randomize.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./randomize.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_row.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_row.hh -[ 1%] Built target ost_mol_alg_headers -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_spi_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_spi_handler.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./chem_type.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./chem_type.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./extent_iterator.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./extent_iterator.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_search_bar.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_search_bar.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_situs_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_situs_handler.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/render_options/render_options.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/render_options.hh -[ 1%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/composite2_op.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./extent_mask.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./extent_mask.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./coord_group.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./coord_group.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/c++ -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/src/CMakeFiles/ost_geom.dir/composite2_op.cc.o -MF CMakeFiles/ost_geom.dir/composite2_op.cc.o.d -o CMakeFiles/ost_geom.dir/composite2_op.cc.o -c /build/openstructure-2.3.1/modules/geom/src/composite2_op.cc -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./norm_linear.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./norm_linear.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./chem_class.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./chem_class.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_handler.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/render_options/cartoon_render_options.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/cartoon_render_options.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./image_handle.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./image_handle.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./smooth_mask_image.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./smooth_mask_image.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_search_bar.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_search_bar.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/render_options/trace_render_options.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/trace_render_options.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./chem_type.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./chem_type.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_mrc_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_mrc_handler.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./image_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./image_impl.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./stat.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./stat.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/color_ops/color_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/color_op.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_dat_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_dat_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_table_view.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_table_view.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/render_options/line_render_options.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/line_render_options.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./coord_group.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./coord_group.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./image_list.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./image_list.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./stat_accumulator.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./stat_accumulator.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/color_ops/by_element_color_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/by_element_color_op.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_ipl_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_ipl_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./coord_source.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./coord_source.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./extent.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./extent.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_viewer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_viewer.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_mrc_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_mrc_handler.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./norm_log.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./norm_log.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/render_options/custom_render_options.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/custom_render_options.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./stat_min_max.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./stat_min_max.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./image_state_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./image_state_fw.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_jpk_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_jpk_handler.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/color_ops/by_chain_color_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/by_chain_color_op.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./in_mem_coord_source.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./in_mem_coord_source.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/tick_painter.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/tick_painter.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_dat_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_dat_handler.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./norm_od.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./norm_od.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./image_factory.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./image_factory.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./image_state.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./image_state.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./threshold.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./threshold.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/color_ops/uniform_color_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/uniform_color_op.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./coord_frame.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./coord_frame.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/title_row.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/title_row.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/render_options/cpk_render_options.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/cpk_render_options.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./power_spectrum.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./power_spectrum.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_ipl_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_ipl_handler.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./image_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./image_fw.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./editor_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./editor_base.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_nanoscope_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_nanoscope_handler.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./image.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./image.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./transcendentals.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./transcendentals.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/alignment_view_object.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/alignment_view_object.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/render_options/simple_render_options.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/simple_render_options.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./randomize.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./randomize.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_jpk_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_jpk_handler.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./editor_type_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./editor_type_fw.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/color_ops/gradient_color_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/gradient_color_op.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./editor_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./editor_base.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_png_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_png_handler.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./inverted_mask.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./inverted_mask.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./transform.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./transform.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/base_view_object.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/base_view_object.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./image_handle_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./image_handle_fw.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/render_options/sline_render_options.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/sline_render_options.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./smooth_mask_image.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./smooth_mask_image.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_nanoscope_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_nanoscope_handler.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/color_ops/entity_view_color_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/entity_view_color_op.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_dm3_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_dm3_handler.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./map.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./map.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./editor_type_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./editor_type_fw.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./transform_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./transform_fw.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_view_object.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_view_object.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./mol.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./mol.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./image_handle.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./image_handle.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/render_options/line_trace_render_options.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/line_trace_render_options.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./stat.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./stat.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/color_ops/basic_gradient_color_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/basic_gradient_color_op.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_tiff_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/main_thread_runner.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/main_thread_runner.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_png_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_png_handler.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./mask_base_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./mask_base_fw.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./alg_transform.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./alg_transform.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./mol.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./mol.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/color_ops/gradient_level_color_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/gradient_level_color_op.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./entity_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_base.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./image_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./image_impl.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./stat_accumulator.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./stat_accumulator.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/render_options/cartoon_render_options.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/cartoon_render_options.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./mask_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./mask_base.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/tiff_util.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/tiff_util.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./alg_mirror.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./alg_mirror.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/output_redirector.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/output_redirector.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./entity_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_base.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_dm3_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_dm3_handler.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./image_list.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./image_list.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./stat_min_max.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./stat_min_max.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/render_options/trace_render_options.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/trace_render_options.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/color_ops/map_handle_color_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/map_handle_color_op.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/completer_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/completer_base.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./image_state_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./image_state_fw.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./entity_handle.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_handle.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_tiff_handler.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./threshold.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./threshold.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/color_ops/color_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/color_op.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./entity_observer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_observer.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/color_ops/by_element_color_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/by_element_color_op.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./image_state.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./image_state.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/tiff_util.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/tiff_util.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./transcendentals.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./transcendentals.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./entity_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_base.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./mask_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./mask_op.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./alg_shift.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./alg_shift.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/jpk_util.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/jpk_util.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./render_pass.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./render_pass.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/dir_model.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/dir_model.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./entity_observer_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_observer_fw.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./image.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./image.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./mask_visitor.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./mask_visitor.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/seq/sequence_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./entity_handle.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_handle.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./discrete_shrink.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./discrete_shrink.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./bitmap_io.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./bitmap_io.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/gutter.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/gutter.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/jpk_util.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/jpk_util.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./transform.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./transform.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/color_ops/by_chain_color_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/by_chain_color_op.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./mask.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./mask.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/seq/fasta_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/fasta_io_handler.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./transformation_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./transformation_base.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./entity_observer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_observer.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./collada_exporter.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./collada_exporter.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/path_completer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/path_completer.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./entity_property_mapper.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_property_mapper.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./transform_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./transform_fw.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/seq/sequence_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./inverted_mask.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./inverted_mask.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/color_ops/uniform_color_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/uniform_color_op.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/seq/pir_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/pir_io_handler.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./module_config.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./module_config.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./transformations.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./transformations.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/python_context_parser.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_context_parser.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./map.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./map.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./alg_transform.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./alg_transform.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./entity_view.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_view.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/seq/fasta_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/fasta_io_handler.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/color_ops/gradient_color_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/gradient_color_op.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./color.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./color.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./entity_observer_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_observer_fw.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/seq/promod_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/promod_io_handler.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./normalizer_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./normalizer_fw.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./fractional_shift.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./fractional_shift.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/python_completer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_completer.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./mask_base_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./mask_base_fw.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./alg_mirror.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./alg_mirror.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/seq/pir_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/pir_io_handler.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./entity_visitor.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_visitor.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/color_ops/entity_view_color_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/entity_view_color_op.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./entity.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./entity.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./entity_property_mapper.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_property_mapper.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/seq/profile_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/profile_io_handler.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./normalizer_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./normalizer_impl.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/python_shell.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_shell.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./mask_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./mask_base.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./alg_shift.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./alg_shift.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/seq/promod_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/promod_io_handler.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/color_ops/basic_gradient_color_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/basic_gradient_color_op.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./entity_visitor_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_visitor_fw.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./discrete_shrink.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./discrete_shrink.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./module_config.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./module_config.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./entity_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./entity_fw.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/python_shell_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_shell_fw.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/seq/profile_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/profile_io_handler.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./mask_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./mask_op.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/color_ops/gradient_level_color_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/gradient_level_color_op.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./handle_type_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./handle_type_fw.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./transformation_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./transformation_base.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./entity_view.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_view.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/seq/hhm_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/hhm_io_handler.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./null_data.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./null_data.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./polar.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./polar.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/python_shell_widget.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_shell_widget.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./mask_visitor.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./mask_visitor.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/color_ops/map_handle_color_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/map_handle_color_op.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./ics_editor.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./ics_editor.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gl_helper.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gl_helper.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./line_average.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./line_average.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./observable.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./observable.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/seq/pssm_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/pssm_io_handler.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./entity_visitor.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_visitor.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/python_tokenizer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_tokenizer.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./not_connected_error.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./not_connected_error.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./mask.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./mask.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./transformations.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./transformations.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./paste_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./paste_impl.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./rscrosscorr.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./rscrosscorr.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./entity_visitor_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_visitor_fw.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/seq/clustal_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/clustal_io_handler.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./render_pass.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./render_pass.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./module_config.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./module_config.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./property_id.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./property_id.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gfx.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/python_syntax_highlighter.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_syntax_highlighter.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./peak.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./peak.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/seq/load.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/load.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./fractional_shift.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./fractional_shift.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./bitmap_io.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./bitmap_io.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./query.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./query.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./normalizer_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./normalizer_fw.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gfx_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_fw.hh +make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./handle_type_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./handle_type_fw.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/text_logger.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./module_config.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./module_config.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./phase.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./phase.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/seq/save.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/save.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./query_error.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./query_error.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./polar.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./polar.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gfx_node.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_node.hh +[ 1%] Built target ost_img_alg_headers +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./ics_editor.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./ics_editor.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./collada_exporter.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./collada_exporter.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./physical_units.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./physical_units.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./binary_data_sink.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./binary_data_sink.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./normalizer_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./normalizer_impl.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./query_state.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./query_state.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./line_average.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./line_average.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./color.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./color.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gfx_node_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_node_fw.hh +[ 1%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/composite2_op.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/c++ -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/src/CMakeFiles/ost_geom.dir/composite2_op.cc.o -MF CMakeFiles/ost_geom.dir/composite2_op.cc.o.d -o CMakeFiles/ost_geom.dir/composite2_op.cc.o -c /build/openstructure-2.3.1/modules/geom/src/composite2_op.cc +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./not_connected_error.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./not_connected_error.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter_worker.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./residue_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./residue_base.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./pixel_sampling.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./pixel_sampling.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./io_manager.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./io_manager.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./null_data.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./null_data.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./rscrosscorr.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./rscrosscorr.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./entity.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./entity.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./binary_data_source.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./binary_data_source.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./residue_handle.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./residue_handle.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./observable.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./observable.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gfx_node_visitor.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_node_visitor.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./point_list.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./point_list.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/python_shell_text_document_layout.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_shell_text_document_layout.hh -make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./module_config.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./module_config.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./entity_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./entity_fw.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./residue_prop.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./residue_prop.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./property_id.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./property_id.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./binary_data_source.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./binary_data_source.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gfx_object_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_object_base.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./point.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./point.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/shell_history.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/shell_history.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./container_serialization.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./container_serialization.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./paste_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./paste_impl.hh -[ 1%] Built target ost_img_alg_headers -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./residue_view.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./residue_view.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gl_helper.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gl_helper.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./module_config.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./module_config.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gfx_object.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_object.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./query.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./query.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./polygon_mask.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./polygon_mask.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/state_machine.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/state_machine.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./peak.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./peak.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./query_error.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./query_error.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./container_serialization.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./container_serialization.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gfx_object_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_object_fw.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./progress.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./progress.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./swap_util.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./swap_util.hh -[ 1%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/composite3_op.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/c++ -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/src/CMakeFiles/ost_geom.dir/composite3_op.cc.o -MF CMakeFiles/ost_geom.dir/composite3_op.cc.o.d -o CMakeFiles/ost_geom.dir/composite3_op.cc.o -c /build/openstructure-2.3.1/modules/geom/src/composite3_op.cc -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./sec_structure.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./sec_structure.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./query_state.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./query_state.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gfx_prim.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_prim.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/state.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/state.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gfx.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./phase.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./phase.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./size.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./size.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./io_utils.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./io_utils.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./spatial_organizer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./spatial_organizer.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./physical_units.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./physical_units.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./residue_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./residue_base.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/transition.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/transition.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./symmetry_node.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./symmetry_node.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./spherical_mask.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./spherical_mask.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./io_exception.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./io_exception.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gfx_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_fw.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./surface.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./surface.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./pixel_sampling.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./pixel_sampling.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./convert.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./convert.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./residue_handle.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./residue_handle.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gfx_test_object.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_test_object.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/transition_guard.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/transition_guard.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./surface_builder.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./surface_builder.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gfx_node.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_node.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./converting_streams.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./converting_streams.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./point_list.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./point_list.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gfx_node_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_node_fw.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./builder.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./builder.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./util.cc /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./util.cc +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./residue_prop.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./residue_prop.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./convert.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./convert.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./glwin_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./glwin_base.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/panels/button_bar.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/button_bar.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./formatted_line.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./formatted_line.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./point.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./point.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gfx_node_visitor.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_node_visitor.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./surface_handle.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./surface_handle.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/chemdict_parser.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./chemdict_parser.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./util.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./util.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./residue_view.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./residue_view.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./converting_streams.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./converting_streams.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./input.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./input.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./value_util.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./value_util.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/panels/drop_box.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/drop_box.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./polygon_mask.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./polygon_mask.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./surface_prop.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./surface_prop.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/star_parser.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./star_parser.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gfx_object_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_object_base.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./formatted_line.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./formatted_line.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./sec_structure.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./sec_structure.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./prim_list.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./prim_list.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./vecmat.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./vecmat.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/panels/panel_bar.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/panel_bar.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./progress.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./progress.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./torsion_handle.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./torsion_handle.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gfx_object.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_object.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/mmcif_reader.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./mmcif_reader.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gfx_object_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_object_fw.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/chemdict_parser.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./chemdict_parser.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./scene.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./scene.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./mask_info_convert.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./mask_info_convert.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./spatial_organizer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./spatial_organizer.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/panels/panel_manager.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/panel_manager.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./size.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./size.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./transfer_connectivity.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./transfer_connectivity.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/mmcif_info.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./mmcif_info.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./spherical_mask.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./spherical_mask.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gfx_prim.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_prim.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/star_parser.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./star_parser.hh +make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./selection.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./selection.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/panels/bottom_bar.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/bottom_bar.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./query_view_wrapper.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./query_view_wrapper.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./util.cc /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./util.cc -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./symmetry_node.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./symmetry_node.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./surface.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./surface.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/mmcif_reader.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./mmcif_reader.hh +[ 1%] Built target ost_img_headers +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./surface.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./surface.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/panels/button_box.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/button_box.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/io_profile.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./io_profile.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./view_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./view_op.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gfx_test_object.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_test_object.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./util.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./util.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./view_type_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./view_type_fw.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./surface_builder.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./surface_builder.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/mmcif_info.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./mmcif_info.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./texture.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./texture.hh +[ 1%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/composite3_op.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/c++ -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/src/CMakeFiles/ost_geom.dir/composite3_op.cc.o -MF CMakeFiles/ost_geom.dir/composite3_op.cc.o.d -o CMakeFiles/ost_geom.dir/composite3_op.cc.o -c /build/openstructure-2.3.1/modules/geom/src/composite3_op.cc cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/panels/event_button.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/event_button.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/dcd_io.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./dcd_io.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./glwin_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./glwin_base.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./builder.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./builder.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/io_profile.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./io_profile.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./vertex_array.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./vertex_array.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/panels/panel_widget_container.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/panel_widget_container.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./surface_handle.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./surface_handle.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/dcd_io.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./dcd_io.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/panels/panel_bar_widget_holder.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/panel_bar_widget_holder.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./surface_prop.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./surface_prop.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./vertex_array_helper.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./vertex_array_helper.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/entity_io_crd_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./entity_io_crd_handler.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/panels/side_bar.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/side_bar.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./torsion_handle.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./torsion_handle.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./scene_observer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./scene_observer.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/entity_io_pqr_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./entity_io_pqr_handler.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/panels/splitter_panel_bar.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/splitter_panel_bar.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./transfer_connectivity.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./transfer_connectivity.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gl_include.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gl_include.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/entity_io_mae_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./entity_io_mae_handler.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/panels/tabbed_panel_bar.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/tabbed_panel_bar.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./query_view_wrapper.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./query_view_wrapper.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./glext_include.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./glext_include.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/entity_io_mmcif_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./entity_io_mmcif_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./view_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./view_op.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./value_util.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./value_util.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/scene_win/context_menu.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/context_menu.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./render_mode.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./render_mode.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/entity_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./entity_io_handler.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./view_type_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./view_type_fw.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/scene_win/current_selection_node.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/current_selection_node.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./material.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./material.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/pdb_reader.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./pdb_reader.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./view_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./view_op.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/scene_win/custom_part_node.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/custom_part_node.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./xcs_editor.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./xcs_editor.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gradient.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gradient.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/entity_io_pdb_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./entity_io_pdb_handler.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./bounding_box.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./bounding_box.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gradient_manager.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gradient_manager.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/pdb_writer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./pdb_writer.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/scene_win/entity_node.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/entity_node.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./transform.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./transform.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./module_config.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./module_config.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/entity_io_sdf_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./entity_io_sdf_handler.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./module_config.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./module_config.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/scene_win/entity_part_node.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/entity_part_node.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./primitives.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./primitives.hh +make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/sdf_reader.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./sdf_reader.hh +[ 1%] Built target ost_mol_headers +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/scene_win/gfx_scene_node.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/gfx_scene_node.hh In file included from /build/openstructure-2.3.1/modules/geom/src/composite2.hh:27, from /build/openstructure-2.3.1/modules/geom/src/composite2.cc:23: /build/openstructure-2.3.1/modules/geom/src/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] @@ -3674,152 +3722,104 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/panels/panel_bar_widget_holder.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/panel_bar_widget_holder.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./input.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./input.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/entity_io_pqr_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./entity_io_pqr_handler.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./xcs_editor.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./xcs_editor.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./vecmat.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./vecmat.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/panels/side_bar.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/side_bar.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./prim_list.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./prim_list.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/entity_io_mae_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./entity_io_mae_handler.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./bounding_box.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./bounding_box.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./mask_info_convert.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./mask_info_convert.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/panels/splitter_panel_bar.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/splitter_panel_bar.hh -make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./scene.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./scene.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/entity_io_mmcif_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./entity_io_mmcif_handler.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./transform.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./transform.hh -[ 1%] Built target ost_img_headers -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/panels/tabbed_panel_bar.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/tabbed_panel_bar.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./selection.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./selection.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/entity_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./entity_io_handler.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./module_config.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./module_config.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./povray_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./povray_fw.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/sdf_writer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./sdf_writer.hh [ 1%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/quat.cc.o -make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/c++ -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/src/CMakeFiles/ost_geom.dir/quat.cc.o -MF CMakeFiles/ost_geom.dir/quat.cc.o.d -o CMakeFiles/ost_geom.dir/quat.cc.o -c /build/openstructure-2.3.1/modules/geom/src/quat.cc -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/scene_win/context_menu.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/context_menu.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/pdb_reader.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./pdb_reader.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./surface.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./surface.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/scene_win/current_selection_node.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/current_selection_node.hh -[ 1%] Built target ost_mol_headers -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/entity_io_pdb_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./entity_io_pdb_handler.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./texture.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./texture.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/scene_win/custom_part_node.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/custom_part_node.hh -[ 1%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/transform.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./vertex_array.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./vertex_array.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/c++ -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/src/CMakeFiles/ost_geom.dir/transform.cc.o -MF CMakeFiles/ost_geom.dir/transform.cc.o.d -o CMakeFiles/ost_geom.dir/transform.cc.o -c /build/openstructure-2.3.1/modules/geom/src/transform.cc -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/pdb_writer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./pdb_writer.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/scene_win/entity_node.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/entity_node.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./vertex_array_helper.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./vertex_array_helper.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/entity_io_sdf_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./entity_io_sdf_handler.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/scene_win/entity_part_node.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/entity_part_node.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./scene_observer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./scene_observer.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gl_include.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gl_include.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/scene_win/gfx_scene_node.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/gfx_scene_node.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/sdf_reader.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./sdf_reader.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./glext_include.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./glext_include.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/sdf_writer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./sdf_writer.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./povray.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./povray.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/scene_win/label_node.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/label_node.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./render_mode.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./render_mode.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/save_entity.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./save_entity.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./exporter.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./exporter.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/scene_win/root_node.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/root_node.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/scene_win/render_mode_node.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/render_mode_node.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./material.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./material.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/load_entity.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./load_entity.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./exporter_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./exporter_fw.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/scene_win/render_mode_node.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/render_mode_node.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/surface_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./surface_io_handler.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gost_exporter.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gost_exporter.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/scene_win/render_modes_node.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/render_modes_node.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gradient.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gradient.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/load_surface.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./load_surface.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./color_ops/map_handle_color_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./map_handle_color_op.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/scene_win/scene_node.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/scene_node.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/surface_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./surface_io_handler.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/surface_io_msms_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./surface_io_msms_handler.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./map_iso.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./map_iso.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/scene_win/scene_win.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/scene_win.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gradient_manager.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gradient_manager.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/load_surface.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./load_surface.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/pdb_str.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./pdb_str.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./map_slab.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./map_slab.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/scene_win/scene_win_model.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/scene_win_model.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./module_config.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./module_config.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/surface_io_msms_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./surface_io_msms_handler.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./primitives.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./primitives.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/stereochemical_params_reader.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./stereochemical_params_reader.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./map_iso_prop.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./map_iso_prop.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/messages/message_widget.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/messages/message_widget.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./povray_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./povray_fw.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/pdb_str.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./pdb_str.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/omf.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./omf.hh +make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/messages/message_box_widget.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/messages/message_box_widget.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./povray.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./povray.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./seq/sequence_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./sequence_io_handler.hh +[ 1%] Built target ost_gfx_headers cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/messages/log_reader.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/messages/log_reader.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/stereochemical_params_reader.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./stereochemical_params_reader.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./exporter.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./exporter.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/omf.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./omf.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./exporter_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./exporter_fw.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./seq/fasta_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./fasta_io_handler.hh +[ 1%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/transform.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/c++ -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/src/CMakeFiles/ost_geom.dir/transform.cc.o -MF CMakeFiles/ost_geom.dir/transform.cc.o.d -o CMakeFiles/ost_geom.dir/transform.cc.o -c /build/openstructure-2.3.1/modules/geom/src/transform.cc cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/argand.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/argand.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./seq/sequence_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./sequence_io_handler.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gost_exporter.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gost_exporter.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./seq/pir_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./pir_io_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/data_viewer.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./color_ops/map_handle_color_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./map_handle_color_op.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./seq/fasta_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./fasta_io_handler.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./seq/promod_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./promod_io_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/data_viewer_panel.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./map_iso.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./map_iso.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./seq/pir_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./pir_io_handler.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./seq/profile_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./profile_io_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/data_viewer_panel_base.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./map_slab.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./map_slab.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./seq/promod_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./promod_io_handler.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./seq/hhm_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./hhm_io_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/draw_overlay.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/draw_overlay.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./seq/profile_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./profile_io_handler.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./map_iso_prop.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./map_iso_prop.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./seq/pssm_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./pssm_io_handler.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./seq/clustal_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./clustal_io_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/drawing_functions.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/drawing_functions.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./seq/hhm_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./hhm_io_handler.hh -make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./seq/load.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./load.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/fft_panel.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/fft_panel.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./seq/pssm_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./pssm_io_handler.hh -[ 1%] Built target ost_gfx_headers +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./seq/save.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./save.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/info_panel.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/info_panel.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./seq/clustal_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./clustal_io_handler.hh -[ 1%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/aligned_cuboid.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/c++ -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/src/CMakeFiles/ost_geom.dir/aligned_cuboid.cc.o -MF CMakeFiles/ost_geom.dir/aligned_cuboid.cc.o.d -o CMakeFiles/ost_geom.dir/aligned_cuboid.cc.o -c /build/openstructure-2.3.1/modules/geom/src/aligned_cuboid.cc +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/load_map.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./load_map.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/img2qt.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/img2qt.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./seq/load.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./load.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_df3_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_df3_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/mask_overlay.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/mask_overlay.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./seq/save.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./save.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/image_format.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./image_format.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/null_overlay.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/null_overlay.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/load_map.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./load_map.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_dx_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_dx_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/overlay.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/overlay.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_df3_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_df3_handler.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_spi_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_spi_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/overlay_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/overlay_base.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/image_format.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./image_format.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_situs_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_situs_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/overlay_base_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/overlay_base_fw.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_dx_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_dx_handler.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/overlay_manager.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/overlay_manager.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_spi_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_spi_handler.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_mrc_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_mrc_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/overlay_manager_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/overlay_manager_fw.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_situs_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_situs_handler.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_dat_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_dat_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/overlay_manager_gui.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/overlay_manager_gui.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_handler.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_ipl_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_ipl_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/overlay_manager_observer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/overlay_manager_observer.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_mrc_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_mrc_handler.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_jpk_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_jpk_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/pointlist_overlay.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/pointlist_overlay.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_dat_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_dat_handler.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_nanoscope_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_nanoscope_handler.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_png_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_png_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/pointlist_overlay_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/pointlist_overlay_base.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_ipl_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_ipl_handler.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_dm3_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_dm3_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/strategies.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/strategies.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_jpk_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_jpk_handler.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_tiff_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_tiff_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/strategies_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/strategies_fw.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/tiff_util.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./tiff_util.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/viewer_normalizer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/viewer_normalizer.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_nanoscope_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_nanoscope_handler.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/jpk_util.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./jpk_util.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./file_browser.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./file_browser.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_png_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_png_handler.hh +make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./file_type_dialog.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./file_type_dialog.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_dm3_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_dm3_handler.hh +[ 1%] Built target ost_io_headers cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./file_viewer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./file_viewer.hh +[ 1%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/aligned_cuboid.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/c++ -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/src/CMakeFiles/ost_geom.dir/aligned_cuboid.cc.o -MF CMakeFiles/ost_geom.dir/aligned_cuboid.cc.o.d -o CMakeFiles/ost_geom.dir/aligned_cuboid.cc.o -c /build/openstructure-2.3.1/modules/geom/src/aligned_cuboid.cc cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./gl_canvas.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./gl_canvas.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_tiff_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_tiff_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./gl_win.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./gl_win.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/tiff_util.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./tiff_util.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./scene_menu.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./scene_menu.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./gosty_app.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./gosty_app.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/jpk_util.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./jpk_util.hh -make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./admin.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./admin.hh -[ 1%] Built target ost_io_headers cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./module_config.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./module_config.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./main.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./main.hh -[ 2%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/point_cloud.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/c++ -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/src/CMakeFiles/ost_geom.dir/point_cloud.cc.o -MF CMakeFiles/ost_geom.dir/point_cloud.cc.o.d -o CMakeFiles/ost_geom.dir/point_cloud.cc.o -c /build/openstructure-2.3.1/modules/geom/src/point_cloud.cc cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./main_area.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./main_area.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./perspective.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./perspective.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./scene_selection.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./scene_selection.hh @@ -3834,7 +3834,9 @@ cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./widget_state_saver.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./widget_state_saver.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./file_loader.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./file_loader.hh make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 2%] Built target ost_gui_headers +[ 1%] Built target ost_gui_headers +[ 2%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/point_cloud.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/c++ -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/src/CMakeFiles/ost_geom.dir/point_cloud.cc.o -MF CMakeFiles/ost_geom.dir/point_cloud.cc.o.d -o CMakeFiles/ost_geom.dir/point_cloud.cc.o -c /build/openstructure-2.3.1/modules/geom/src/point_cloud.cc In file included from /build/openstructure-2.3.1/modules/geom/src/composite2.hh:27, from /build/openstructure-2.3.1/modules/geom/src/composite2_op.hh:24, from /build/openstructure-2.3.1/modules/geom/src/composite2_op.cc:24: @@ -3878,36 +3880,36 @@ [ 3%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_vec2.cc.o [ 3%] Building CXX object modules/base/src/CMakeFiles/ost_base.dir/log_sink.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/c++ -DOST_MODULE_OST_BASE -Dost_base_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/src/CMakeFiles/ost_base.dir/log.cc.o -MF CMakeFiles/ost_base.dir/log.cc.o.d -o CMakeFiles/ost_base.dir/log.cc.o -c /build/openstructure-2.3.1/modules/base/src/log.cc -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/pymod && /usr/bin/c++ -D_ost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_vec2.cc.o -MF CMakeFiles/_ost_geom.dir/export_vec2.cc.o.d -o CMakeFiles/_ost_geom.dir/export_vec2.cc.o -c /build/openstructure-2.3.1/modules/geom/pymod/export_vec2.cc [ 3%] Building CXX object modules/base/src/CMakeFiles/ost_base.dir/profile.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/pymod && /usr/bin/c++ -D_ost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_vec2.cc.o -MF CMakeFiles/_ost_geom.dir/export_vec2.cc.o.d -o CMakeFiles/_ost_geom.dir/export_vec2.cc.o -c /build/openstructure-2.3.1/modules/geom/pymod/export_vec2.cc cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/c++ -DOST_MODULE_OST_BASE -Dost_base_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/src/CMakeFiles/ost_base.dir/log_sink.cc.o -MF CMakeFiles/ost_base.dir/log_sink.cc.o.d -o CMakeFiles/ost_base.dir/log_sink.cc.o -c /build/openstructure-2.3.1/modules/base/src/log_sink.cc [ 3%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_vec3.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/c++ -DOST_MODULE_OST_BASE -Dost_base_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/src/CMakeFiles/ost_base.dir/profile.cc.o -MF CMakeFiles/ost_base.dir/profile.cc.o.d -o CMakeFiles/ost_base.dir/profile.cc.o -c /build/openstructure-2.3.1/modules/base/src/profile.cc [ 3%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_vecmat2_op.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/pymod && /usr/bin/c++ -D_ost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_vec3.cc.o -MF CMakeFiles/_ost_geom.dir/export_vec3.cc.o.d -o CMakeFiles/_ost_geom.dir/export_vec3.cc.o -c /build/openstructure-2.3.1/modules/geom/pymod/export_vec3.cc +[ 3%] Building CXX object modules/base/src/CMakeFiles/ost_base.dir/units.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/pymod && /usr/bin/c++ -D_ost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_vecmat2_op.cc.o -MF CMakeFiles/_ost_geom.dir/export_vecmat2_op.cc.o.d -o CMakeFiles/_ost_geom.dir/export_vecmat2_op.cc.o -c /build/openstructure-2.3.1/modules/geom/pymod/export_vecmat2_op.cc [ 3%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_vecmat3_op.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/c++ -DOST_MODULE_OST_BASE -Dost_base_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/src/CMakeFiles/ost_base.dir/profile.cc.o -MF CMakeFiles/ost_base.dir/profile.cc.o.d -o CMakeFiles/ost_base.dir/profile.cc.o -c /build/openstructure-2.3.1/modules/base/src/profile.cc +[ 3%] Building CXX object modules/base/src/CMakeFiles/ost_base.dir/string_ref.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/pymod && /usr/bin/c++ -D_ost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_vec3.cc.o -MF CMakeFiles/_ost_geom.dir/export_vec3.cc.o.d -o CMakeFiles/_ost_geom.dir/export_vec3.cc.o -c /build/openstructure-2.3.1/modules/geom/pymod/export_vec3.cc +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/c++ -DOST_MODULE_OST_BASE -Dost_base_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/src/CMakeFiles/ost_base.dir/units.cc.o -MF CMakeFiles/ost_base.dir/units.cc.o.d -o CMakeFiles/ost_base.dir/units.cc.o -c /build/openstructure-2.3.1/modules/base/src/units.cc [ 3%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_vec4.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/pymod && /usr/bin/c++ -D_ost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_vecmat3_op.cc.o -MF CMakeFiles/_ost_geom.dir/export_vecmat3_op.cc.o.d -o CMakeFiles/_ost_geom.dir/export_vecmat3_op.cc.o -c /build/openstructure-2.3.1/modules/geom/pymod/export_vecmat3_op.cc +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/c++ -DOST_MODULE_OST_BASE -Dost_base_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/src/CMakeFiles/ost_base.dir/string_ref.cc.o -MF CMakeFiles/ost_base.dir/string_ref.cc.o.d -o CMakeFiles/ost_base.dir/string_ref.cc.o -c /build/openstructure-2.3.1/modules/base/src/string_ref.cc cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/pymod && /usr/bin/c++ -D_ost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_vec4.cc.o -MF CMakeFiles/_ost_geom.dir/export_vec4.cc.o.d -o CMakeFiles/_ost_geom.dir/export_vec4.cc.o -c /build/openstructure-2.3.1/modules/geom/pymod/export_vec4.cc [ 3%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_vecmat4_op.cc.o -[ 3%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/wrap_geom.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/pymod && /usr/bin/c++ -D_ost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_vecmat4_op.cc.o -MF CMakeFiles/_ost_geom.dir/export_vecmat4_op.cc.o.d -o CMakeFiles/_ost_geom.dir/export_vecmat4_op.cc.o -c /build/openstructure-2.3.1/modules/geom/pymod/export_vecmat4_op.cc -[ 3%] Building CXX object modules/base/src/CMakeFiles/ost_base.dir/units.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/pymod && /usr/bin/c++ -D_ost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/pymod/CMakeFiles/_ost_geom.dir/wrap_geom.cc.o -MF CMakeFiles/_ost_geom.dir/wrap_geom.cc.o.d -o CMakeFiles/_ost_geom.dir/wrap_geom.cc.o -c /build/openstructure-2.3.1/modules/geom/pymod/wrap_geom.cc [ 3%] Building CXX object modules/base/src/CMakeFiles/ost_base.dir/message.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/c++ -DOST_MODULE_OST_BASE -Dost_base_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/src/CMakeFiles/ost_base.dir/units.cc.o -MF CMakeFiles/ost_base.dir/units.cc.o.d -o CMakeFiles/ost_base.dir/units.cc.o -c /build/openstructure-2.3.1/modules/base/src/units.cc -[ 5%] Building CXX object modules/base/src/CMakeFiles/ost_base.dir/platform.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/c++ -DOST_MODULE_OST_BASE -Dost_base_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/src/CMakeFiles/ost_base.dir/message.cc.o -MF CMakeFiles/ost_base.dir/message.cc.o.d -o CMakeFiles/ost_base.dir/message.cc.o -c /build/openstructure-2.3.1/modules/base/src/message.cc +[ 5%] Building CXX object modules/base/src/CMakeFiles/ost_base.dir/platform.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/c++ -DOST_MODULE_OST_BASE -Dost_base_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/src/CMakeFiles/ost_base.dir/platform.cc.o -MF CMakeFiles/ost_base.dir/platform.cc.o.d -o CMakeFiles/ost_base.dir/platform.cc.o -c /build/openstructure-2.3.1/modules/base/src/platform.cc -[ 5%] Building CXX object modules/base/src/CMakeFiles/ost_base.dir/string_ref.cc.o -[ 5%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_mat2.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/c++ -DOST_MODULE_OST_BASE -Dost_base_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/src/CMakeFiles/ost_base.dir/string_ref.cc.o -MF CMakeFiles/ost_base.dir/string_ref.cc.o.d -o CMakeFiles/ost_base.dir/string_ref.cc.o -c /build/openstructure-2.3.1/modules/base/src/string_ref.cc -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/pymod && /usr/bin/c++ -D_ost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_mat2.cc.o -MF CMakeFiles/_ost_geom.dir/export_mat2.cc.o.d -o CMakeFiles/_ost_geom.dir/export_mat2.cc.o -c /build/openstructure-2.3.1/modules/geom/pymod/export_mat2.cc +[ 5%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/wrap_geom.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/pymod && /usr/bin/c++ -D_ost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/pymod/CMakeFiles/_ost_geom.dir/wrap_geom.cc.o -MF CMakeFiles/_ost_geom.dir/wrap_geom.cc.o.d -o CMakeFiles/_ost_geom.dir/wrap_geom.cc.o -c /build/openstructure-2.3.1/modules/geom/pymod/wrap_geom.cc [ 5%] Building CXX object modules/base/src/CMakeFiles/ost_base.dir/test_utils/compare_files.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/c++ -DOST_MODULE_OST_BASE -Dost_base_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/src/CMakeFiles/ost_base.dir/test_utils/compare_files.cc.o -MF CMakeFiles/ost_base.dir/test_utils/compare_files.cc.o.d -o CMakeFiles/ost_base.dir/test_utils/compare_files.cc.o -c /build/openstructure-2.3.1/modules/base/src/test_utils/compare_files.cc [ 5%] Building CXX object modules/base/src/CMakeFiles/ost_base.dir/boost_filesystem_helper.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/c++ -DOST_MODULE_OST_BASE -Dost_base_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/src/CMakeFiles/ost_base.dir/boost_filesystem_helper.cc.o -MF CMakeFiles/ost_base.dir/boost_filesystem_helper.cc.o.d -o CMakeFiles/ost_base.dir/boost_filesystem_helper.cc.o -c /build/openstructure-2.3.1/modules/base/src/boost_filesystem_helper.cc +[ 5%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_mat2.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/pymod && /usr/bin/c++ -D_ost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_mat2.cc.o -MF CMakeFiles/_ost_geom.dir/export_mat2.cc.o.d -o CMakeFiles/_ost_geom.dir/export_mat2.cc.o -c /build/openstructure-2.3.1/modules/geom/pymod/export_mat2.cc [ 5%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_mat3.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/pymod && /usr/bin/c++ -D_ost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_mat3.cc.o -MF CMakeFiles/_ost_geom.dir/export_mat3.cc.o.d -o CMakeFiles/_ost_geom.dir/export_mat3.cc.o -c /build/openstructure-2.3.1/modules/geom/pymod/export_mat3.cc [ 5%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_mat4.cc.o @@ -3920,11 +3922,10 @@ cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/pymod && /usr/bin/c++ -D_ost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_composite2_op.cc.o -MF CMakeFiles/_ost_geom.dir/export_composite2_op.cc.o.d -o CMakeFiles/_ost_geom.dir/export_composite2_op.cc.o -c /build/openstructure-2.3.1/modules/geom/pymod/export_composite2_op.cc [ 6%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_composite3_op.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/pymod && /usr/bin/c++ -D_ost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_composite3_op.cc.o -MF CMakeFiles/_ost_geom.dir/export_composite3_op.cc.o.d -o CMakeFiles/_ost_geom.dir/export_composite3_op.cc.o -c /build/openstructure-2.3.1/modules/geom/pymod/export_composite3_op.cc -[ 6%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_quat.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/pymod && /usr/bin/c++ -D_ost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_quat.cc.o -MF CMakeFiles/_ost_geom.dir/export_quat.cc.o.d -o CMakeFiles/_ost_geom.dir/export_quat.cc.o -c /build/openstructure-2.3.1/modules/geom/pymod/export_quat.cc [ 6%] Linking CXX shared library ../../../stage/lib/libost_base.so cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_base.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libost_base.so.2.3 -o ../../../stage/lib/libost_base.so.2.3.1 CMakeFiles/ost_base.dir/generic_property.cc.o CMakeFiles/ost_base.dir/log.cc.o CMakeFiles/ost_base.dir/log_sink.cc.o CMakeFiles/ost_base.dir/profile.cc.o CMakeFiles/ost_base.dir/units.cc.o CMakeFiles/ost_base.dir/string_ref.cc.o CMakeFiles/ost_base.dir/platform.cc.o CMakeFiles/ost_base.dir/message.cc.o CMakeFiles/ost_base.dir/test_utils/compare_files.cc.o CMakeFiles/ost_base.dir/boost_filesystem_helper.cc.o -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib: ../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E cmake_symlink_library ../../../stage/lib/libost_base.so.2.3.1 ../../../stage/lib/libost_base.so.2.3 ../../../stage/lib/libost_base.so In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -3938,14 +3939,13 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/geom/pymod/export_vecmat4_op.cc:20: + from /build/openstructure-2.3.1/modules/geom/pymod/wrap_geom.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E cmake_symlink_library ../../../stage/lib/libost_base.so.2.3.1 ../../../stage/lib/libost_base.so.2.3 ../../../stage/lib/libost_base.so make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 6%] Built target ost_base make -f modules/info/src/CMakeFiles/ost_info.dir/build.make modules/info/src/CMakeFiles/ost_info.dir/depend @@ -3956,31 +3956,6 @@ make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 6%] Building CXX object modules/info/src/CMakeFiles/ost_info.dir/info_impl.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/c++ -DOST_MODULE_OST_INFO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_info_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/info/src/CMakeFiles/ost_info.dir/info_impl.cc.o -MF CMakeFiles/ost_info.dir/info_impl.cc.o.d -o CMakeFiles/ost_info.dir/info_impl.cc.o -c /build/openstructure-2.3.1/modules/info/src/info_impl.cc -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/modules/geom/pymod/export_vecmat4_op.cc:23: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/specfun.h:45, - from /usr/include/c++/12/cmath:1935, - from /usr/include/c++/12/math.h:36, - from /usr/include/python3.11/pyport.h:218, - from /usr/include/python3.11/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -3994,47 +3969,7 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/geom/pymod/export_vec2.cc:19: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/geom/pymod/export_vecmat3_op.cc:19: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/geom/pymod/wrap_geom.cc:19: + from /build/openstructure-2.3.1/modules/geom/pymod/export_vecmat4_op.cc:20: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ @@ -4044,7 +3979,7 @@ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/modules/geom/pymod/export_vec2.cc:23: + from /build/openstructure-2.3.1/modules/geom/pymod/wrap_geom.cc:22: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -4066,10 +4001,30 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/openstructure-2.3.1/modules/geom/pymod/export_vec3.cc:19: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/modules/geom/pymod/wrap_geom.cc:22: + from /build/openstructure-2.3.1/modules/geom/pymod/export_vecmat4_op.cc:23: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -4104,10 +4059,13 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/geom/pymod/export_vecmat2_op.cc:19: + from /build/openstructure-2.3.1/modules/geom/pymod/export_vecmat3_op.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -4121,41 +4079,10 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/geom/pymod/export_mat2.cc:19: + from /build/openstructure-2.3.1/modules/geom/pymod/export_vec2.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/modules/geom/pymod/export_vecmat3_op.cc:22: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/specfun.h:45, - from /usr/include/c++/12/cmath:1935, - from /usr/include/c++/12/math.h:36, - from /usr/include/python3.11/pyport.h:218, - from /usr/include/python3.11/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -4169,30 +4096,32 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/geom/pymod/export_composite2.cc:19: + from /build/openstructure-2.3.1/modules/geom/pymod/export_vecmat2_op.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 6%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_transform.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/pymod && /usr/bin/c++ -D_ost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_transform.cc.o -MF CMakeFiles/_ost_geom.dir/export_transform.cc.o.d -o CMakeFiles/_ost_geom.dir/export_transform.cc.o -c /build/openstructure-2.3.1/modules/geom/pymod/export_transform.cc +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/modules/info/src/info_impl.hh:41, - from /build/openstructure-2.3.1/modules/info/src/info_impl.cc:37: + from /build/openstructure-2.3.1/modules/geom/pymod/export_vec3.cc:22: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/12/string:45, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/ostream:38, - from /usr/include/c++/12/iostream:39, - from /build/openstructure-2.3.1/modules/info/src/info_impl.cc:27: +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/bits/specfun.h:45, + from /usr/include/c++/12/cmath:1935, + from /usr/include/c++/12/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -4215,7 +4144,7 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/geom/pymod/export_mat3.cc:19: + from /build/openstructure-2.3.1/modules/geom/pymod/export_vec4.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ @@ -4225,7 +4154,7 @@ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/modules/geom/pymod/export_mat2.cc:22: + from /build/openstructure-2.3.1/modules/geom/pymod/export_vecmat3_op.cc:22: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -4247,30 +4176,10 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/geom/pymod/export_vec3.cc:19: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/modules/geom/pymod/export_composite2.cc:22: + from /build/openstructure-2.3.1/modules/geom/pymod/export_vecmat2_op.cc:22: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -4295,7 +4204,7 @@ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/modules/geom/pymod/export_vecmat2_op.cc:22: + from /build/openstructure-2.3.1/modules/geom/pymod/export_vec2.cc:23: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -4320,7 +4229,7 @@ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/modules/geom/pymod/export_mat3.cc:23: + from /build/openstructure-2.3.1/modules/geom/pymod/export_vec4.cc:22: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -4355,13 +4264,10 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/geom/pymod/export_vec4.cc:19: + from /build/openstructure-2.3.1/modules/geom/pymod/export_mat2.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -4375,40 +4281,36 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/geom/pymod/export_composite3_op.cc:21: + from /build/openstructure-2.3.1/modules/geom/pymod/export_mat3.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 6%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_quat.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/pymod && /usr/bin/c++ -D_ost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_quat.cc.o -MF CMakeFiles/_ost_geom.dir/export_quat.cc.o.d -o CMakeFiles/_ost_geom.dir/export_quat.cc.o -c /build/openstructure-2.3.1/modules/geom/pymod/export_quat.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/modules/geom/pymod/export_vec3.cc:22: + from /build/openstructure-2.3.1/modules/info/src/info_impl.hh:41, + from /build/openstructure-2.3.1/modules/info/src/info_impl.cc:37: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/specfun.h:45, - from /usr/include/c++/12/cmath:1935, - from /usr/include/c++/12/math.h:36, - from /usr/include/python3.11/pyport.h:218, - from /usr/include/python3.11/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ +In file included from /usr/include/c++/12/string:45, + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/ostream:38, + from /usr/include/c++/12/iostream:39, + from /build/openstructure-2.3.1/modules/info/src/info_impl.cc:27: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 6%] Building CXX object modules/info/src/CMakeFiles/ost_info.dir/info_handle.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/c++ -DOST_MODULE_OST_INFO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_info_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/info/src/CMakeFiles/ost_info.dir/info_handle.cc.o -MF CMakeFiles/ost_info.dir/info_handle.cc.o.d -o CMakeFiles/ost_info.dir/info_handle.cc.o -c /build/openstructure-2.3.1/modules/info/src/info_handle.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -4422,29 +4324,10 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/geom/pymod/export_quat.cc:19: + from /build/openstructure-2.3.1/modules/geom/pymod/export_composite2.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/modules/geom/pymod/export_vec4.cc:22: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/specfun.h:45, - from /usr/include/c++/12/cmath:1935, - from /usr/include/c++/12/math.h:36, - from /usr/include/python3.11/pyport.h:218, - from /usr/include/python3.11/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ @@ -4457,7 +4340,7 @@ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/modules/geom/pymod/export_composite3_op.cc:24: + from /build/openstructure-2.3.1/modules/geom/pymod/export_mat3.cc:23: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -4482,7 +4365,7 @@ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/modules/geom/pymod/export_quat.cc:22: + from /build/openstructure-2.3.1/modules/geom/pymod/export_mat2.cc:22: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -4517,13 +4400,15 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/geom/pymod/export_composite2_op.cc:21: + from /build/openstructure-2.3.1/modules/geom/pymod/export_composite3.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 6%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_transform.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/pymod && /usr/bin/c++ -D_ost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_transform.cc.o -MF CMakeFiles/_ost_geom.dir/export_transform.cc.o.d -o CMakeFiles/_ost_geom.dir/export_transform.cc.o -c /build/openstructure-2.3.1/modules/geom/pymod/export_transform.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -4544,6 +4429,31 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/openstructure-2.3.1/modules/geom/pymod/export_composite2.cc:22: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/bits/specfun.h:45, + from /usr/include/c++/12/cmath:1935, + from /usr/include/c++/12/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -4557,19 +4467,37 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/geom/pymod/export_composite3.cc:19: + from /build/openstructure-2.3.1/modules/geom/pymod/export_composite2_op.cc:21: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/openstructure-2.3.1/modules/geom/pymod/export_composite3_op.cc:21: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 6%] Building CXX object modules/info/src/CMakeFiles/ost_info.dir/info_group.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/c++ -DOST_MODULE_OST_INFO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_info_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/info/src/CMakeFiles/ost_info.dir/info_group.cc.o -MF CMakeFiles/ost_info.dir/info_group.cc.o.d -o CMakeFiles/ost_info.dir/info_group.cc.o -c /build/openstructure-2.3.1/modules/info/src/info_group.cc +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/modules/geom/pymod/export_composite2_op.cc:24: + from /build/openstructure-2.3.1/modules/geom/pymod/export_composite3.cc:21: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -4591,10 +4519,12 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 6%] Building CXX object modules/info/src/CMakeFiles/ost_info.dir/info_handle.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/c++ -DOST_MODULE_OST_INFO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_info_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/info/src/CMakeFiles/ost_info.dir/info_handle.cc.o -MF CMakeFiles/ost_info.dir/info_handle.cc.o.d -o CMakeFiles/ost_info.dir/info_handle.cc.o -c /build/openstructure-2.3.1/modules/info/src/info_handle.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/modules/geom/pymod/export_composite3.cc:21: + from /build/openstructure-2.3.1/modules/geom/pymod/export_mat4.cc:25: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -4619,7 +4549,32 @@ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/modules/geom/pymod/export_mat4.cc:25: + from /build/openstructure-2.3.1/modules/geom/pymod/export_composite2_op.cc:24: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/bits/specfun.h:45, + from /usr/include/c++/12/cmath:1935, + from /usr/include/c++/12/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/openstructure-2.3.1/modules/geom/pymod/export_composite3_op.cc:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -4641,6 +4596,10 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 6%] Building CXX object modules/info/src/CMakeFiles/ost_info.dir/info_group.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/c++ -DOST_MODULE_OST_INFO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_info_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/info/src/CMakeFiles/ost_info.dir/info_group.cc.o -MF CMakeFiles/ost_info.dir/info_group.cc.o.d -o CMakeFiles/ost_info.dir/info_group.cc.o -c /build/openstructure-2.3.1/modules/info/src/info_group.cc +[ 6%] Building CXX object modules/info/src/CMakeFiles/ost_info.dir/info_item.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/c++ -DOST_MODULE_OST_INFO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_info_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/info/src/CMakeFiles/ost_info.dir/info_item.cc.o -MF CMakeFiles/ost_info.dir/info_item.cc.o.d -o CMakeFiles/ost_info.dir/info_item.cc.o -c /build/openstructure-2.3.1/modules/info/src/info_item.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -4666,8 +4625,6 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 6%] Building CXX object modules/info/src/CMakeFiles/ost_info.dir/info_item.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/c++ -DOST_MODULE_OST_INFO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_info_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/info/src/CMakeFiles/ost_info.dir/info_item.cc.o -MF CMakeFiles/ost_info.dir/info_item.cc.o.d -o CMakeFiles/ost_info.dir/info_item.cc.o -c /build/openstructure-2.3.1/modules/info/src/info_item.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -4681,7 +4638,7 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/geom/pymod/export_transform.cc:19: + from /build/openstructure-2.3.1/modules/geom/pymod/export_quat.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ @@ -4692,6 +4649,57 @@ cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/c++ -DOST_MODULE_OST_INFO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_info_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/info/src/CMakeFiles/ost_info.dir/info_path.cc.o -MF CMakeFiles/ost_info.dir/info_path.cc.o.d -o CMakeFiles/ost_info.dir/info_path.cc.o -c /build/openstructure-2.3.1/modules/info/src/info_path.cc [ 6%] Building CXX object modules/info/src/CMakeFiles/ost_info.dir/info_set.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/c++ -DOST_MODULE_OST_INFO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_info_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/info/src/CMakeFiles/ost_info.dir/info_set.cc.o -MF CMakeFiles/ost_info.dir/info_set.cc.o.d -o CMakeFiles/ost_info.dir/info_set.cc.o -c /build/openstructure-2.3.1/modules/info/src/info_set.cc +[ 7%] Building CXX object modules/info/src/CMakeFiles/ost_info.dir/info_visitor.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/c++ -DOST_MODULE_OST_INFO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_info_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/info/src/CMakeFiles/ost_info.dir/info_visitor.cc.o -MF CMakeFiles/ost_info.dir/info_visitor.cc.o.d -o CMakeFiles/ost_info.dir/info_visitor.cc.o -c /build/openstructure-2.3.1/modules/info/src/info_visitor.cc +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/openstructure-2.3.1/modules/geom/pymod/export_quat.cc:22: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/bits/specfun.h:45, + from /usr/include/c++/12/cmath:1935, + from /usr/include/c++/12/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 7%] Building CXX object modules/info/src/CMakeFiles/ost_info.dir/geom_info_conversion.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/c++ -DOST_MODULE_OST_INFO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_info_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/info/src/CMakeFiles/ost_info.dir/geom_info_conversion.cc.o -MF CMakeFiles/ost_info.dir/geom_info_conversion.cc.o.d -o CMakeFiles/ost_info.dir/geom_info_conversion.cc.o -c /build/openstructure-2.3.1/modules/info/src/geom_info_conversion.cc +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/openstructure-2.3.1/modules/geom/pymod/export_transform.cc:19: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 7%] Building CXX object modules/info/src/CMakeFiles/ost_info.dir/info_verbose_visitor.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/c++ -DOST_MODULE_OST_INFO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_info_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/info/src/CMakeFiles/ost_info.dir/info_verbose_visitor.cc.o -MF CMakeFiles/ost_info.dir/info_verbose_visitor.cc.o.d -o CMakeFiles/ost_info.dir/info_verbose_visitor.cc.o -c /build/openstructure-2.3.1/modules/info/src/info_verbose_visitor.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -4716,12 +4724,6 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 7%] Building CXX object modules/info/src/CMakeFiles/ost_info.dir/info_visitor.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/c++ -DOST_MODULE_OST_INFO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_info_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/info/src/CMakeFiles/ost_info.dir/info_visitor.cc.o -MF CMakeFiles/ost_info.dir/info_visitor.cc.o.d -o CMakeFiles/ost_info.dir/info_visitor.cc.o -c /build/openstructure-2.3.1/modules/info/src/info_visitor.cc -[ 7%] Building CXX object modules/info/src/CMakeFiles/ost_info.dir/geom_info_conversion.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/c++ -DOST_MODULE_OST_INFO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_info_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/info/src/CMakeFiles/ost_info.dir/geom_info_conversion.cc.o -MF CMakeFiles/ost_info.dir/geom_info_conversion.cc.o.d -o CMakeFiles/ost_info.dir/geom_info_conversion.cc.o -c /build/openstructure-2.3.1/modules/info/src/geom_info_conversion.cc -[ 7%] Building CXX object modules/info/src/CMakeFiles/ost_info.dir/info_verbose_visitor.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/c++ -DOST_MODULE_OST_INFO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_info_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/info/src/CMakeFiles/ost_info.dir/info_verbose_visitor.cc.o -MF CMakeFiles/ost_info.dir/info_verbose_visitor.cc.o.d -o CMakeFiles/ost_info.dir/info_verbose_visitor.cc.o -c /build/openstructure-2.3.1/modules/info/src/info_verbose_visitor.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -4833,43 +4835,41 @@ make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/img/base/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src/CMakeFiles/ost_img.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +make -f modules/mol/base/src/CMakeFiles/ost_mol.dir/build.make modules/mol/base/src/CMakeFiles/ost_mol.dir/build +make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/img/base/src/CMakeFiles/ost_img.dir/build.make modules/img/base/src/CMakeFiles/ost_img.dir/build make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/mol/base/src/CMakeFiles/ost_mol.dir/build.make modules/mol/base/src/CMakeFiles/ost_mol.dir/build make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[ 7%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/atom_base.cc.o [ 7%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/circle_mask.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/circle_mask.cc.o -MF CMakeFiles/ost_img.dir/circle_mask.cc.o.d -o CMakeFiles/ost_img.dir/circle_mask.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/circle_mask.cc +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/atom_base.cc.o -MF CMakeFiles/ost_mol.dir/atom_base.cc.o.d -o CMakeFiles/ost_mol.dir/atom_base.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/atom_base.cc +[ 7%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/atom_handle.cc.o [ 7%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/composite_mask.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/circle_mask.cc.o -MF CMakeFiles/ost_img.dir/circle_mask.cc.o.d -o CMakeFiles/ost_img.dir/circle_mask.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/circle_mask.cc +[ 7%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/atom_view.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/atom_handle.cc.o -MF CMakeFiles/ost_mol.dir/atom_handle.cc.o.d -o CMakeFiles/ost_mol.dir/atom_handle.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/atom_handle.cc [ 7%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/data_algorithm.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/composite_mask.cc.o -MF CMakeFiles/ost_img.dir/composite_mask.cc.o.d -o CMakeFiles/ost_img.dir/composite_mask.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/composite_mask.cc -[ 7%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/atom_base.cc.o -[ 7%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/data.cc.o -[ 7%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/data_observer.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/atom_view.cc.o -MF CMakeFiles/ost_mol.dir/atom_view.cc.o.d -o CMakeFiles/ost_mol.dir/atom_view.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/atom_view.cc cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/data_algorithm.cc.o -MF CMakeFiles/ost_img.dir/data_algorithm.cc.o.d -o CMakeFiles/ost_img.dir/data_algorithm.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/data_algorithm.cc -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/atom_base.cc.o -MF CMakeFiles/ost_mol.dir/atom_base.cc.o.d -o CMakeFiles/ost_mol.dir/atom_base.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/atom_base.cc [ 7%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/bond_handle.cc.o +[ 7%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/data.cc.o +[ 7%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/data_observer.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/data_observer.cc.o -MF CMakeFiles/ost_img.dir/data_observer.cc.o.d -o CMakeFiles/ost_img.dir/data_observer.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/data_observer.cc -[ 7%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/extent_iterator.cc.o -[ 7%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/atom_handle.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/bond_handle.cc.o -MF CMakeFiles/ost_mol.dir/bond_handle.cc.o.d -o CMakeFiles/ost_mol.dir/bond_handle.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/bond_handle.cc cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/data.cc.o -MF CMakeFiles/ost_img.dir/data.cc.o.d -o CMakeFiles/ost_img.dir/data.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/data.cc -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/atom_handle.cc.o -MF CMakeFiles/ost_mol.dir/atom_handle.cc.o.d -o CMakeFiles/ost_mol.dir/atom_handle.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/atom_handle.cc +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/bond_handle.cc.o -MF CMakeFiles/ost_mol.dir/bond_handle.cc.o.d -o CMakeFiles/ost_mol.dir/bond_handle.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/bond_handle.cc +[ 7%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/extent_iterator.cc.o +[ 8%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/chain_base.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/chain_base.cc.o -MF CMakeFiles/ost_mol.dir/chain_base.cc.o.d -o CMakeFiles/ost_mol.dir/chain_base.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/chain_base.cc cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/extent_iterator.cc.o -MF CMakeFiles/ost_img.dir/extent_iterator.cc.o.d -o CMakeFiles/ost_img.dir/extent_iterator.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/extent_iterator.cc -[ 7%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/chain_handle.cc.o -[ 7%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/atom_view.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/chain_handle.cc.o -MF CMakeFiles/ost_mol.dir/chain_handle.cc.o.d -o CMakeFiles/ost_mol.dir/chain_handle.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/chain_handle.cc -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/atom_view.cc.o -MF CMakeFiles/ost_mol.dir/atom_view.cc.o.d -o CMakeFiles/ost_mol.dir/atom_view.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/atom_view.cc -[ 7%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/extent_mask.cc.o +[ 8%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/chain_handle.cc.o +[ 8%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/extent_mask.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/extent_mask.cc.o -MF CMakeFiles/ost_img.dir/extent_mask.cc.o.d -o CMakeFiles/ost_img.dir/extent_mask.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/extent_mask.cc -[ 7%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/chain_view.cc.o -[ 8%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/chain_base.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/chain_handle.cc.o -MF CMakeFiles/ost_mol.dir/chain_handle.cc.o.d -o CMakeFiles/ost_mol.dir/chain_handle.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/chain_handle.cc +[ 8%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/chain_view.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/chain_view.cc.o -MF CMakeFiles/ost_mol.dir/chain_view.cc.o.d -o CMakeFiles/ost_mol.dir/chain_view.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/chain_view.cc [ 10%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/extent.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/chain_base.cc.o -MF CMakeFiles/ost_mol.dir/chain_base.cc.o.d -o CMakeFiles/ost_mol.dir/chain_base.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/chain_base.cc cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/extent.cc.o -MF CMakeFiles/ost_img.dir/extent.cc.o.d -o CMakeFiles/ost_img.dir/extent.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/extent.cc -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/chain_view.cc.o -MF CMakeFiles/ost_mol.dir/chain_view.cc.o.d -o CMakeFiles/ost_mol.dir/chain_view.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/chain_view.cc -[ 10%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/image_factory.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/image_factory.cc.o -MF CMakeFiles/ost_img.dir/image_factory.cc.o.d -o CMakeFiles/ost_img.dir/image_factory.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/image_factory.cc In file included from /usr/include/boost/bind.hpp:30, from /build/openstructure-2.3.1/modules/mol/base/src/chain_view.cc:21: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' @@ -4880,15 +4880,16 @@ from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/img/base/src/vecmat.hh:33, from /build/openstructure-2.3.1/modules/img/base/src/point.hh:35, - from /build/openstructure-2.3.1/modules/img/base/src/data.hh:36, - from /build/openstructure-2.3.1/modules/img/base/src/data.cc:29: + from /build/openstructure-2.3.1/modules/img/base/src/extent.hh:34, + from /build/openstructure-2.3.1/modules/img/base/src/extent_mask.hh:28, + from /build/openstructure-2.3.1/modules/img/base/src/extent_mask.cc:25: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, - from /build/openstructure-2.3.1/modules/img/base/src/data.cc:27: + from /build/openstructure-2.3.1/modules/img/base/src/extent.hh:30: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -4901,17 +4902,16 @@ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/openstructure-2.3.1/modules/img/base/src/mask_base.hh:27, - from /build/openstructure-2.3.1/modules/img/base/src/composite_mask.hh:28, - from /build/openstructure-2.3.1/modules/img/base/src/composite_mask.cc:25: + from /build/openstructure-2.3.1/modules/img/base/src/vecmat.hh:33, + from /build/openstructure-2.3.1/modules/img/base/src/point.hh:35, + from /build/openstructure-2.3.1/modules/img/base/src/extent_iterator.hh:30, + from /build/openstructure-2.3.1/modules/img/base/src/extent_iterator.cc:27: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/specfun.h:45, - from /usr/include/c++/12/cmath:1935, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:30: + from /usr/include/c++/12/vector:60, + from /build/openstructure-2.3.1/modules/img/base/src/point.hh:30: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -4952,42 +4952,17 @@ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/modules/img/base/src/vecmat.hh:33, - from /build/openstructure-2.3.1/modules/img/base/src/point.hh:35, - from /build/openstructure-2.3.1/modules/img/base/src/extent_iterator.hh:30, - from /build/openstructure-2.3.1/modules/img/base/src/extent_iterator.cc:27: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/vector:60, - from /build/openstructure-2.3.1/modules/img/base/src/point.hh:30: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/modules/mol/base/src/residue_view.hh:22, - from /build/openstructure-2.3.1/modules/mol/base/src/atom_view.cc:25: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, + from /build/openstructure-2.3.1/modules/img/base/src/mask_base.hh:27, + from /build/openstructure-2.3.1/modules/img/base/src/composite_mask.hh:28, + from /build/openstructure-2.3.1/modules/img/base/src/composite_mask.cc:25: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, - from /build/openstructure-2.3.1/modules/mol/base/src/atom_view.hh:25, - from /build/openstructure-2.3.1/modules/mol/base/src/atom_view.cc:24: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:30: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -5026,16 +5001,15 @@ from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/img/base/src/vecmat.hh:33, from /build/openstructure-2.3.1/modules/img/base/src/point.hh:35, - from /build/openstructure-2.3.1/modules/img/base/src/extent.hh:34, - from /build/openstructure-2.3.1/modules/img/base/src/extent_mask.hh:28, - from /build/openstructure-2.3.1/modules/img/base/src/extent_mask.cc:25: + from /build/openstructure-2.3.1/modules/img/base/src/data.hh:36, + from /build/openstructure-2.3.1/modules/img/base/src/data.cc:29: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, - from /build/openstructure-2.3.1/modules/img/base/src/extent.hh:30: + from /build/openstructure-2.3.1/modules/img/base/src/data.cc:27: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -5048,34 +5022,36 @@ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/residue_impl.hh:24, - from /build/openstructure-2.3.1/modules/mol/base/src/atom_base.cc:20: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/modules/img/base/src/vecmat.hh:33, - from /build/openstructure-2.3.1/modules/img/base/src/point.hh:35, - from /build/openstructure-2.3.1/modules/img/base/src/extent.hh:34, - from /build/openstructure-2.3.1/modules/img/base/src/extent.cc:31: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, + from /build/openstructure-2.3.1/modules/img/base/src/circle_mask.hh:25, + from /build/openstructure-2.3.1/modules/img/base/src/circle_mask.cc:25: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/bits/specfun.h:45, + from /usr/include/c++/12/cmath:1935, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:30: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/connector_impl.hh:24, - from /build/openstructure-2.3.1/modules/mol/base/src/bond_handle.cc:20: + from /build/openstructure-2.3.1/modules/mol/base/src/chain_handle.hh:26, + from /build/openstructure-2.3.1/modules/mol/base/src/chain_handle.cc:19: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/list:60, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/connector_impl_fw.hh:22, - from /build/openstructure-2.3.1/modules/mol/base/src/bond_handle.hh:22, - from /build/openstructure-2.3.1/modules/mol/base/src/bond_handle.cc:19: + from /usr/include/c++/12/vector:60, + from /build/openstructure-2.3.1/modules/mol/base/src/chain_handle.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -5085,6 +5061,14 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/residue_impl.hh:24, + from /build/openstructure-2.3.1/modules/mol/base/src/atom_base.cc:20: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec3.hh:22, @@ -5099,35 +5083,21 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /usr/include/c++/12/string:45, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/ostream:38, - from /usr/include/c++/12/iostream:39, - from /build/openstructure-2.3.1/modules/img/base/src/extent.cc:28: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/openstructure-2.3.1/modules/img/base/src/circle_mask.hh:25, - from /build/openstructure-2.3.1/modules/img/base/src/circle_mask.cc:25: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/chain_impl.hh:25, + from /build/openstructure-2.3.1/modules/mol/base/src/chain_base.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:30: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, + from /build/openstructure-2.3.1/modules/mol/base/src/chain_base.hh:22, + from /build/openstructure-2.3.1/modules/mol/base/src/chain_base.cc:19: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -5137,19 +5107,25 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 10%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/image_handle.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/image_handle.cc.o -MF CMakeFiles/ost_img.dir/image_handle.cc.o.d -o CMakeFiles/ost_img.dir/image_handle.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/image_handle.cc +[ 10%] Linking CXX shared module ../../../stage/lib/python3.11/dist-packages/ost/geom/_ost_geom.so +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_geom.dir/link.txt --verbose=1 In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/modules/mol/base/src/chain_handle.hh:26, - from /build/openstructure-2.3.1/modules/mol/base/src/chain_handle.cc:19: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/openstructure-2.3.1/modules/mol/base/src/residue_view.hh:22, + from /build/openstructure-2.3.1/modules/mol/base/src/atom_view.cc:25: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/vector:60, - from /build/openstructure-2.3.1/modules/mol/base/src/chain_handle.hh:22: + from /usr/include/c++/12/bits/specfun.h:45, + from /usr/include/c++/12/cmath:1935, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, + from /build/openstructure-2.3.1/modules/mol/base/src/atom_view.hh:25, + from /build/openstructure-2.3.1/modules/mol/base/src/atom_view.cc:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -5159,21 +5135,20 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -o ../../../stage/lib/python3.11/dist-packages/ost/geom/_ost_geom.so CMakeFiles/_ost_geom.dir/export_vec2.cc.o CMakeFiles/_ost_geom.dir/export_vecmat2_op.cc.o CMakeFiles/_ost_geom.dir/export_vec3.cc.o CMakeFiles/_ost_geom.dir/export_vecmat3_op.cc.o CMakeFiles/_ost_geom.dir/export_vec4.cc.o CMakeFiles/_ost_geom.dir/export_vecmat4_op.cc.o CMakeFiles/_ost_geom.dir/wrap_geom.cc.o CMakeFiles/_ost_geom.dir/export_mat2.cc.o CMakeFiles/_ost_geom.dir/export_mat3.cc.o CMakeFiles/_ost_geom.dir/export_mat4.cc.o CMakeFiles/_ost_geom.dir/export_composite2.cc.o CMakeFiles/_ost_geom.dir/export_composite3.cc.o CMakeFiles/_ost_geom.dir/export_composite2_op.cc.o CMakeFiles/_ost_geom.dir/export_composite3_op.cc.o CMakeFiles/_ost_geom.dir/export_quat.cc.o CMakeFiles/_ost_geom.dir/export_transform.cc.o -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib: ../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/chain_impl.hh:25, - from /build/openstructure-2.3.1/modules/mol/base/src/chain_base.cc:20: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/connector_impl.hh:24, + from /build/openstructure-2.3.1/modules/mol/base/src/bond_handle.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/specfun.h:45, - from /usr/include/c++/12/cmath:1935, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, - from /build/openstructure-2.3.1/modules/mol/base/src/chain_base.hh:22, - from /build/openstructure-2.3.1/modules/mol/base/src/chain_base.cc:19: + from /usr/include/c++/12/list:60, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/connector_impl_fw.hh:22, + from /build/openstructure-2.3.1/modules/mol/base/src/bond_handle.hh:22, + from /build/openstructure-2.3.1/modules/mol/base/src/bond_handle.cc:19: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -5183,20 +5158,6 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 10%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/image_impl.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/image_impl.cc.o -MF CMakeFiles/ost_img.dir/image_impl.cc.o.d -o CMakeFiles/ost_img.dir/image_impl.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/image_impl.cc -[ 10%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/image_list.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/image_list.cc.o -MF CMakeFiles/ost_img.dir/image_list.cc.o.d -o CMakeFiles/ost_img.dir/image_list.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/image_list.cc -[ 10%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/inverted_mask.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/inverted_mask.cc.o -MF CMakeFiles/ost_img.dir/inverted_mask.cc.o.d -o CMakeFiles/ost_img.dir/inverted_mask.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/inverted_mask.cc -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:41, - from /build/openstructure-2.3.1/modules/mol/base/src/chain_handle.cc:24: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 27 | class pointer_it : public std::iterator{ - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -5219,25 +5180,31 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 10%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/map.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/map.cc.o -MF CMakeFiles/ost_img.dir/map.cc.o.d -o CMakeFiles/ost_img.dir/map.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/map.cc -[ 10%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/chain_type.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/chain_type.cc.o -MF CMakeFiles/ost_mol.dir/chain_type.cc.o.d -o CMakeFiles/ost_mol.dir/chain_type.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/chain_type.cc +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:41, + from /build/openstructure-2.3.1/modules/mol/base/src/chain_handle.cc:24: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 27 | class pointer_it : public std::iterator{ + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/img/base/src/vecmat.hh:33, from /build/openstructure-2.3.1/modules/img/base/src/point.hh:35, from /build/openstructure-2.3.1/modules/img/base/src/extent.hh:34, - from /build/openstructure-2.3.1/modules/img/base/src/image_factory.hh:32, - from /build/openstructure-2.3.1/modules/img/base/src/image_factory.cc:29: + from /build/openstructure-2.3.1/modules/img/base/src/extent.cc:31: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, - from /usr/include/c++/12/stdexcept:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, - from /build/openstructure-2.3.1/modules/img/base/src/image_factory.cc:27: + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/ostream:38, + from /usr/include/c++/12/iostream:39, + from /build/openstructure-2.3.1/modules/img/base/src/extent.cc:28: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -5247,43 +5214,39 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 10%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/image_factory.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/image_factory.cc.o -MF CMakeFiles/ost_img.dir/image_factory.cc.o.d -o CMakeFiles/ost_img.dir/image_factory.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/image_factory.cc +[ 10%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/image_handle.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/image_handle.cc.o -MF CMakeFiles/ost_img.dir/image_handle.cc.o.d -o CMakeFiles/ost_img.dir/image_handle.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/image_handle.cc +[ 10%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/image_impl.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/image_impl.cc.o -MF CMakeFiles/ost_img.dir/image_impl.cc.o.d -o CMakeFiles/ost_img.dir/image_impl.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/image_impl.cc +[ 10%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/image_list.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/image_list.cc.o -MF CMakeFiles/ost_img.dir/image_list.cc.o.d -o CMakeFiles/ost_img.dir/image_list.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/image_list.cc +[ 10%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/inverted_mask.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/inverted_mask.cc.o -MF CMakeFiles/ost_img.dir/inverted_mask.cc.o.d -o CMakeFiles/ost_img.dir/inverted_mask.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/inverted_mask.cc +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/geom/pymod/__init__.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/geom/./__init__.pyc\",\"__init__.py\",doraise=True)" +make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[ 10%] Built target _ost_geom +make -f modules/base/pymod/CMakeFiles/_ost_base.dir/build.make modules/base/pymod/CMakeFiles/_ost_base.dir/depend +make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/base/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/pymod/CMakeFiles/_ost_base.dir/DependInfo.cmake --color= +make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +make -f modules/base/pymod/CMakeFiles/_ost_base.dir/build.make modules/base/pymod/CMakeFiles/_ost_base.dir/build +make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[ 10%] Building CXX object modules/base/pymod/CMakeFiles/_ost_base.dir/wrap_base.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/c++ -D_ost_base_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/pymod/CMakeFiles/_ost_base.dir/wrap_base.cc.o -MF CMakeFiles/_ost_base.dir/wrap_base.cc.o.d -o CMakeFiles/_ost_base.dir/wrap_base.cc.o -c /build/openstructure-2.3.1/modules/base/pymod/wrap_base.cc +[ 10%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/map.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/map.cc.o -MF CMakeFiles/ost_img.dir/map.cc.o.d -o CMakeFiles/ost_img.dir/map.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/map.cc +[ 10%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/chain_type.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/chain_type.cc.o -MF CMakeFiles/ost_mol.dir/chain_type.cc.o.d -o CMakeFiles/ost_mol.dir/chain_type.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/chain_type.cc [ 10%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/coord_frame.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/coord_frame.cc.o -MF CMakeFiles/ost_mol.dir/coord_frame.cc.o.d -o CMakeFiles/ost_mol.dir/coord_frame.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/coord_frame.cc -[ 10%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/mask_base.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/mask_base.cc.o -MF CMakeFiles/ost_img.dir/mask_base.cc.o.d -o CMakeFiles/ost_img.dir/mask_base.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/mask_base.cc [ 10%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/coord_group.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/coord_group.cc.o -MF CMakeFiles/ost_mol.dir/coord_group.cc.o.d -o CMakeFiles/ost_mol.dir/coord_group.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/coord_group.cc -[ 10%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/mask_op.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/mask_op.cc.o -MF CMakeFiles/ost_img.dir/mask_op.cc.o.d -o CMakeFiles/ost_img.dir/mask_op.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/mask_op.cc [ 10%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/editor_base.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/editor_base.cc.o -MF CMakeFiles/ost_mol.dir/editor_base.cc.o.d -o CMakeFiles/ost_mol.dir/editor_base.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/editor_base.cc -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, - from /build/openstructure-2.3.1/modules/img/base/src/image_list.hh:29, - from /build/openstructure-2.3.1/modules/img/base/src/image_list.cc:26: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/12/string:45, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/istream:38, - from /usr/include/c++/12/sstream:38, - from /build/openstructure-2.3.1/modules/img/base/src/image_list.cc:24: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ +[ 10%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/mask_base.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/mask_base.cc.o -MF CMakeFiles/ost_img.dir/mask_base.cc.o.d -o CMakeFiles/ost_img.dir/mask_base.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/mask_base.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -5307,21 +5270,28 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 10%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_base.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_base.cc.o -MF CMakeFiles/ost_mol.dir/entity_base.cc.o.d -o CMakeFiles/ost_mol.dir/entity_base.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/entity_base.cc +[ 10%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_handle.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_handle.cc.o -MF CMakeFiles/ost_mol.dir/entity_handle.cc.o.d -o CMakeFiles/ost_mol.dir/entity_handle.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/entity_handle.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/modules/img/base/src/vecmat.hh:33, - from /build/openstructure-2.3.1/modules/img/base/src/point.hh:35, - from /build/openstructure-2.3.1/modules/img/base/src/data.hh:36, - from /build/openstructure-2.3.1/modules/img/base/src/image_handle.hh:38, - from /build/openstructure-2.3.1/modules/img/base/src/image_handle.cc:31: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, + from /build/openstructure-2.3.1/modules/img/base/src/image_list.hh:29, + from /build/openstructure-2.3.1/modules/img/base/src/image_list.cc:26: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, - from /usr/include/c++/12/stdexcept:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, - from /build/openstructure-2.3.1/modules/img/base/src/image_handle.cc:27: + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/istream:38, + from /usr/include/c++/12/sstream:38, + from /build/openstructure-2.3.1/modules/img/base/src/image_list.cc:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -5360,10 +5330,6 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 10%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_base.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_base.cc.o -MF CMakeFiles/ost_mol.dir/entity_base.cc.o.d -o CMakeFiles/ost_mol.dir/entity_base.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/entity_base.cc -[ 10%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/mask.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/mask.cc.o -MF CMakeFiles/ost_img.dir/mask.cc.o.d -o CMakeFiles/ost_img.dir/mask.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/mask.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -5393,16 +5359,18 @@ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/openstructure-2.3.1/modules/img/base/src/mask_base.hh:27, - from /build/openstructure-2.3.1/modules/img/base/src/mask_base.cc:24: + from /build/openstructure-2.3.1/modules/img/base/src/vecmat.hh:33, + from /build/openstructure-2.3.1/modules/img/base/src/point.hh:35, + from /build/openstructure-2.3.1/modules/img/base/src/extent.hh:34, + from /build/openstructure-2.3.1/modules/img/base/src/image_factory.hh:32, + from /build/openstructure-2.3.1/modules/img/base/src/image_factory.cc:29: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/specfun.h:45, - from /usr/include/c++/12/cmath:1935, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:30: +In file included from /usr/include/c++/12/string:45, + from /usr/include/c++/12/stdexcept:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, + from /build/openstructure-2.3.1/modules/img/base/src/image_factory.cc:27: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -5412,24 +5380,21 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 11%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/observable.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/observable.cc.o -MF CMakeFiles/ost_img.dir/observable.cc.o.d -o CMakeFiles/ost_img.dir/observable.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/observable.cc -[ 11%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/paste_impl.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/paste_impl.cc.o -MF CMakeFiles/ost_img.dir/paste_impl.cc.o.d -o CMakeFiles/ost_img.dir/paste_impl.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/paste_impl.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/modules/mol/base/src/editor_base.hh:27, - from /build/openstructure-2.3.1/modules/mol/base/src/editor_base.cc:19: + from /build/openstructure-2.3.1/modules/img/base/src/vecmat.hh:33, + from /build/openstructure-2.3.1/modules/img/base/src/point.hh:35, + from /build/openstructure-2.3.1/modules/img/base/src/data.hh:36, + from /build/openstructure-2.3.1/modules/img/base/src/image_handle.hh:38, + from /build/openstructure-2.3.1/modules/img/base/src/image_handle.cc:31: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/specfun.h:45, - from /usr/include/c++/12/cmath:1935, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, - from /build/openstructure-2.3.1/modules/mol/base/src/editor_base.hh:25: +In file included from /usr/include/c++/12/string:45, + from /usr/include/c++/12/stdexcept:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, + from /build/openstructure-2.3.1/modules/img/base/src/image_handle.cc:27: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -5444,8 +5409,8 @@ from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/coord_frame.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/coord_source.hh:27, - from /build/openstructure-2.3.1/modules/mol/base/src/in_mem_coord_source.hh:26, - from /build/openstructure-2.3.1/modules/mol/base/src/coord_group.cc:23: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/in_mem_coord_source.hh:26, + from /build/openstructure-2.3.1/modules/mol/base/src/coord_frame.cc:27: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -5453,7 +5418,7 @@ from /usr/include/c++/12/stdexcept:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/invalid_handle.hh:22, - from /build/openstructure-2.3.1/modules/mol/base/src/coord_group.cc:19: + from /build/openstructure-2.3.1/modules/mol/base/src/coord_frame.cc:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -5463,28 +5428,19 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 11%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/peak.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/peak.cc.o -MF CMakeFiles/ost_img.dir/peak.cc.o.d -o CMakeFiles/ost_img.dir/peak.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/peak.cc -[ 11%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_handle.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_handle.cc.o -MF CMakeFiles/ost_mol.dir/entity_handle.cc.o.d -o CMakeFiles/ost_mol.dir/entity_handle.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/entity_handle.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/modules/img/base/src/mask_base.hh:27, - from /build/openstructure-2.3.1/modules/img/base/src/composite_mask.hh:28, - from /build/openstructure-2.3.1/modules/img/base/src/mask_op.cc:22: + from /build/openstructure-2.3.1/modules/img/base/src/mask_base.cc:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/memory:63, - from /usr/include/boost/smart_ptr/scoped_ptr.hpp:22, - from /usr/include/boost/scoped_ptr.hpp:13, - from /usr/include/boost/smart_ptr.hpp:17, - from /build/openstructure-2.3.1/modules/img/base/src/mask_base_fw.hh:23, - from /build/openstructure-2.3.1/modules/img/base/src/mask_op.hh:24, - from /build/openstructure-2.3.1/modules/img/base/src/mask_op.cc:21: + from /usr/include/c++/12/bits/specfun.h:45, + from /usr/include/c++/12/cmath:1935, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:30: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -5494,23 +5450,13 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 11%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/phase.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/phase.cc.o -MF CMakeFiles/ost_img.dir/phase.cc.o.d -o CMakeFiles/ost_img.dir/phase.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/phase.cc -In file included from /build/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl.hh:41, - from /build/openstructure-2.3.1/modules/mol/base/src/editor_base.cc:22: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 27 | class pointer_it : public std::iterator{ - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/coord_frame.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/coord_source.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/in_mem_coord_source.hh:26, - from /build/openstructure-2.3.1/modules/mol/base/src/coord_frame.cc:27: + from /build/openstructure-2.3.1/modules/mol/base/src/in_mem_coord_source.hh:26, + from /build/openstructure-2.3.1/modules/mol/base/src/coord_group.cc:23: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -5518,7 +5464,7 @@ from /usr/include/c++/12/stdexcept:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/invalid_handle.hh:22, - from /build/openstructure-2.3.1/modules/mol/base/src/coord_frame.cc:24: + from /build/openstructure-2.3.1/modules/mol/base/src/coord_group.cc:19: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -5528,22 +5474,64 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 11%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/physical_units.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/physical_units.cc.o -MF CMakeFiles/ost_img.dir/physical_units.cc.o.d -o CMakeFiles/ost_img.dir/physical_units.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/physical_units.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/openstructure-2.3.1/modules/img/base/src/polygon_mask.hh:28, - from /build/openstructure-2.3.1/modules/img/base/src/mask.hh:29, - from /build/openstructure-2.3.1/modules/img/base/src/mask.cc:26: + from /build/openstructure-2.3.1/modules/mol/base/src/editor_base.hh:27, + from /build/openstructure-2.3.1/modules/mol/base/src/editor_base.cc:19: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/bits/specfun.h:45, + from /usr/include/c++/12/cmath:1935, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, + from /build/openstructure-2.3.1/modules/mol/base/src/editor_base.hh:25: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 10%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/mask_op.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/mask_op.cc.o -MF CMakeFiles/ost_img.dir/mask_op.cc.o.d -o CMakeFiles/ost_img.dir/mask_op.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/mask_op.cc +[ 10%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/mask.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/mask.cc.o -MF CMakeFiles/ost_img.dir/mask.cc.o.d -o CMakeFiles/ost_img.dir/mask.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/mask.cc +[ 11%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/observable.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/observable.cc.o -MF CMakeFiles/ost_img.dir/observable.cc.o.d -o CMakeFiles/ost_img.dir/observable.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/observable.cc +In file included from /build/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl.hh:41, + from /build/openstructure-2.3.1/modules/mol/base/src/editor_base.cc:22: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 27 | class pointer_it : public std::iterator{ + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 11%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/paste_impl.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/paste_impl.cc.o -MF CMakeFiles/ost_img.dir/paste_impl.cc.o.d -o CMakeFiles/ost_img.dir/paste_impl.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/paste_impl.cc +[ 11%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/peak.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/peak.cc.o -MF CMakeFiles/ost_img.dir/peak.cc.o.d -o CMakeFiles/ost_img.dir/peak.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/peak.cc +[ 11%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/phase.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/phase.cc.o -MF CMakeFiles/ost_img.dir/phase.cc.o.d -o CMakeFiles/ost_img.dir/phase.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/phase.cc +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl.hh:28, + from /build/openstructure-2.3.1/modules/mol/base/src/entity_handle.cc:22: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, - from /usr/include/c++/12/stdexcept:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, - from /build/openstructure-2.3.1/modules/img/base/src/mask.hh:28: + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/ostream:38, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, + from /build/openstructure-2.3.1/modules/mol/base/src/entity_handle.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -5553,6 +5541,8 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 11%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_observer.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_observer.cc.o -MF CMakeFiles/ost_mol.dir/entity_observer.cc.o.d -o CMakeFiles/ost_mol.dir/entity_observer.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/entity_observer.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -5584,32 +5574,76 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 11%] Linking CXX shared module ../../../stage/lib/python3.11/dist-packages/ost/geom/_ost_geom.so -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_geom.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -o ../../../stage/lib/python3.11/dist-packages/ost/geom/_ost_geom.so CMakeFiles/_ost_geom.dir/export_vec2.cc.o CMakeFiles/_ost_geom.dir/export_vecmat2_op.cc.o CMakeFiles/_ost_geom.dir/export_vec3.cc.o CMakeFiles/_ost_geom.dir/export_vecmat3_op.cc.o CMakeFiles/_ost_geom.dir/export_vec4.cc.o CMakeFiles/_ost_geom.dir/export_vecmat4_op.cc.o CMakeFiles/_ost_geom.dir/wrap_geom.cc.o CMakeFiles/_ost_geom.dir/export_mat2.cc.o CMakeFiles/_ost_geom.dir/export_mat3.cc.o CMakeFiles/_ost_geom.dir/export_mat4.cc.o CMakeFiles/_ost_geom.dir/export_composite2.cc.o CMakeFiles/_ost_geom.dir/export_composite3.cc.o CMakeFiles/_ost_geom.dir/export_composite2_op.cc.o CMakeFiles/_ost_geom.dir/export_composite3_op.cc.o CMakeFiles/_ost_geom.dir/export_quat.cc.o CMakeFiles/_ost_geom.dir/export_transform.cc.o -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib: ../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so -[ 11%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/pixel_sampling.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/pixel_sampling.cc.o -MF CMakeFiles/ost_img.dir/pixel_sampling.cc.o.d -o CMakeFiles/ost_img.dir/pixel_sampling.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/pixel_sampling.cc -[ 11%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/point_list.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/point_list.cc.o -MF CMakeFiles/ost_img.dir/point_list.cc.o.d -o CMakeFiles/ost_img.dir/point_list.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/point_list.cc -[ 11%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_observer.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_observer.cc.o -MF CMakeFiles/ost_mol.dir/entity_observer.cc.o.d -o CMakeFiles/ost_mol.dir/entity_observer.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/entity_observer.cc +In file included from /build/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl.hh:41: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 27 | class pointer_it : public std::iterator{ + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 11%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/physical_units.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/physical_units.cc.o -MF CMakeFiles/ost_img.dir/physical_units.cc.o.d -o CMakeFiles/ost_img.dir/physical_units.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/physical_units.cc +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/openstructure-2.3.1/modules/base/pymod/wrap_base.cc:19: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/modules/img/base/src/vecmat.hh:33, - from /build/openstructure-2.3.1/modules/img/base/src/point.hh:35, - from /build/openstructure-2.3.1/modules/img/base/src/peak.hh:31, - from /build/openstructure-2.3.1/modules/img/base/src/peak.cc:30: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, + from /build/openstructure-2.3.1/modules/img/base/src/polygon_mask.hh:28, + from /build/openstructure-2.3.1/modules/img/base/src/mask.hh:29, + from /build/openstructure-2.3.1/modules/img/base/src/mask.cc:26: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/istream:38, - from /usr/include/c++/12/fstream:38, - from /build/openstructure-2.3.1/modules/img/base/src/peak.cc:25: + from /usr/include/c++/12/stdexcept:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, + from /build/openstructure-2.3.1/modules/img/base/src/mask.hh:28: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, + from /build/openstructure-2.3.1/modules/img/base/src/mask_base.hh:27, + from /build/openstructure-2.3.1/modules/img/base/src/composite_mask.hh:28, + from /build/openstructure-2.3.1/modules/img/base/src/mask_op.cc:22: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/memory:63, + from /usr/include/boost/smart_ptr/scoped_ptr.hpp:22, + from /usr/include/boost/scoped_ptr.hpp:13, + from /usr/include/boost/smart_ptr.hpp:17, + from /build/openstructure-2.3.1/modules/img/base/src/mask_base_fw.hh:23, + from /build/openstructure-2.3.1/modules/img/base/src/mask_op.hh:24, + from /build/openstructure-2.3.1/modules/img/base/src/mask_op.cc:21: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -5619,8 +5653,6 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 11%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/point.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/point.cc.o -MF CMakeFiles/ost_img.dir/point.cc.o.d -o CMakeFiles/ost_img.dir/point.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/point.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -5644,42 +5676,24 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 11%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/polygon_mask.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/polygon_mask.cc.o -MF CMakeFiles/ost_img.dir/polygon_mask.cc.o.d -o CMakeFiles/ost_img.dir/polygon_mask.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/polygon_mask.cc -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/geom/pymod/__init__.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/geom/./__init__.pyc\",\"__init__.py\",doraise=True)" -make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 11%] Built target _ost_geom -make -f modules/base/pymod/CMakeFiles/_ost_base.dir/build.make modules/base/pymod/CMakeFiles/_ost_base.dir/depend -make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/base/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/pymod/CMakeFiles/_ost_base.dir/DependInfo.cmake --color= -make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/base/pymod/CMakeFiles/_ost_base.dir/build.make modules/base/pymod/CMakeFiles/_ost_base.dir/build -make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 11%] Building CXX object modules/base/pymod/CMakeFiles/_ost_base.dir/wrap_base.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/c++ -D_ost_base_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/pymod/CMakeFiles/_ost_base.dir/wrap_base.cc.o -MF CMakeFiles/_ost_base.dir/wrap_base.cc.o.d -o CMakeFiles/_ost_base.dir/wrap_base.cc.o -c /build/openstructure-2.3.1/modules/base/pymod/wrap_base.cc -[ 11%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_property_mapper.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_property_mapper.cc.o -MF CMakeFiles/ost_mol.dir/entity_property_mapper.cc.o.d -o CMakeFiles/ost_mol.dir/entity_property_mapper.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/entity_property_mapper.cc -[ 11%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/progress.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/progress.cc.o -MF CMakeFiles/ost_img.dir/progress.cc.o.d -o CMakeFiles/ost_img.dir/progress.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/progress.cc -[ 12%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_view.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_view.cc.o -MF CMakeFiles/ost_mol.dir/entity_view.cc.o.d -o CMakeFiles/ost_mol.dir/entity_view.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/entity_view.cc -[ 12%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_visitor.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_visitor.cc.o -MF CMakeFiles/ost_mol.dir/entity_visitor.cc.o.d -o CMakeFiles/ost_mol.dir/entity_visitor.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/entity_visitor.cc -[ 12%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/ics_editor.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/ics_editor.cc.o -MF CMakeFiles/ost_mol.dir/ics_editor.cc.o.d -o CMakeFiles/ost_mol.dir/ics_editor.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/ics_editor.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/modules/img/base/src/vecmat.hh:33, - from /build/openstructure-2.3.1/modules/img/base/src/point.hh:35, - from /build/openstructure-2.3.1/modules/img/base/src/point_list.hh:28, - from /build/openstructure-2.3.1/modules/img/base/src/point_list.cc:25: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, + from /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_algorithm.hh:28, + from /build/openstructure-2.3.1/modules/img/base/src/paste_impl.hh:24, + from /build/openstructure-2.3.1/modules/img/base/src/paste_impl.cc:25: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/vector:60, - from /build/openstructure-2.3.1/modules/img/base/src/point.hh:30: + from /usr/include/c++/12/bits/specfun.h:45, + from /usr/include/c++/12/cmath:1935, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/module_config.hh:23, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:32: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -5689,11 +5703,23 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 11%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_property_mapper.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_property_mapper.cc.o -MF CMakeFiles/ost_mol.dir/entity_property_mapper.cc.o.d -o CMakeFiles/ost_mol.dir/entity_property_mapper.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/entity_property_mapper.cc +[ 12%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_view.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_view.cc.o -MF CMakeFiles/ost_mol.dir/entity_view.cc.o.d -o CMakeFiles/ost_mol.dir/entity_view.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/entity_view.cc +[ 12%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_visitor.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_visitor.cc.o -MF CMakeFiles/ost_mol.dir/entity_visitor.cc.o.d -o CMakeFiles/ost_mol.dir/entity_visitor.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/entity_visitor.cc +[ 12%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/pixel_sampling.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/pixel_sampling.cc.o -MF CMakeFiles/ost_img.dir/pixel_sampling.cc.o.d -o CMakeFiles/ost_img.dir/pixel_sampling.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/pixel_sampling.cc +[ 12%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/ics_editor.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/ics_editor.cc.o -MF CMakeFiles/ost_mol.dir/ics_editor.cc.o.d -o CMakeFiles/ost_mol.dir/ics_editor.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/ics_editor.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl.hh:28, - from /build/openstructure-2.3.1/modules/mol/base/src/entity_handle.cc:22: + from /build/openstructure-2.3.1/modules/img/base/src/vecmat.hh:33, + from /build/openstructure-2.3.1/modules/img/base/src/point.hh:35, + from /build/openstructure-2.3.1/modules/img/base/src/peak.hh:31, + from /build/openstructure-2.3.1/modules/img/base/src/peak.cc:30: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -5701,9 +5727,9 @@ from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/ostream:38, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, - from /build/openstructure-2.3.1/modules/mol/base/src/entity_handle.cc:20: + from /usr/include/c++/12/istream:38, + from /usr/include/c++/12/fstream:38, + from /build/openstructure-2.3.1/modules/img/base/src/peak.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -5713,15 +5739,32 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 12%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/not_connected_error.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/not_connected_error.cc.o -MF CMakeFiles/ost_mol.dir/not_connected_error.cc.o.d -o CMakeFiles/ost_mol.dir/not_connected_error.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/not_connected_error.cc +[ 12%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/point_list.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/point_list.cc.o -MF CMakeFiles/ost_img.dir/point_list.cc.o.d -o CMakeFiles/ost_img.dir/point_list.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/point_list.cc +[ 12%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/point.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/point.cc.o -MF CMakeFiles/ost_img.dir/point.cc.o.d -o CMakeFiles/ost_img.dir/point.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/point.cc +[ 12%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/polygon_mask.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/polygon_mask.cc.o -MF CMakeFiles/ost_img.dir/polygon_mask.cc.o.d -o CMakeFiles/ost_img.dir/polygon_mask.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/polygon_mask.cc +[ 12%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/progress.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/progress.cc.o -MF CMakeFiles/ost_img.dir/progress.cc.o.d -o CMakeFiles/ost_img.dir/progress.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/progress.cc +[ 12%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/property_id.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/property_id.cc.o -MF CMakeFiles/ost_mol.dir/property_id.cc.o.d -o CMakeFiles/ost_mol.dir/property_id.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/property_id.cc +In file included from /usr/include/boost/bind.hpp:30, + from /build/openstructure-2.3.1/modules/mol/base/src/entity_view.cc:25: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +[ 12%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/query.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/query.cc.o -MF CMakeFiles/ost_mol.dir/query.cc.o.d -o CMakeFiles/ost_mol.dir/query.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/query.cc +[ 12%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/size.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/size.cc.o -MF CMakeFiles/ost_img.dir/size.cc.o.d -o CMakeFiles/ost_img.dir/size.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/size.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, - from /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_algorithm.hh:28, - from /build/openstructure-2.3.1/modules/img/base/src/paste_impl.hh:24, - from /build/openstructure-2.3.1/modules/img/base/src/paste_impl.cc:25: + from /build/openstructure-2.3.1/modules/mol/base/src/ics_editor.hh:26, + from /build/openstructure-2.3.1/modules/mol/base/src/ics_editor.cc:19: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -5729,8 +5772,8 @@ from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/module_config.hh:23, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:32: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, + from /build/openstructure-2.3.1/modules/mol/base/src/ics_editor.hh:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -5740,8 +5783,6 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 12%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/size.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/size.cc.o -MF CMakeFiles/ost_img.dir/size.cc.o.d -o CMakeFiles/ost_img.dir/size.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/size.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -5766,35 +5807,55 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 14%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/spherical_mask.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/spherical_mask.cc.o -MF CMakeFiles/ost_img.dir/spherical_mask.cc.o.d -o CMakeFiles/ost_img.dir/spherical_mask.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/spherical_mask.cc -In file included from /build/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl.hh:41: +In file included from /build/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl.hh:41, + from /build/openstructure-2.3.1/modules/mol/base/src/ics_editor.cc:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 27 | class pointer_it : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 14%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/spherical_mask.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/spherical_mask.cc.o -MF CMakeFiles/ost_img.dir/spherical_mask.cc.o.d -o CMakeFiles/ost_img.dir/spherical_mask.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/spherical_mask.cc [ 14%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/mask_info_convert.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/mask_info_convert.cc.o -MF CMakeFiles/ost_img.dir/mask_info_convert.cc.o.d -o CMakeFiles/ost_img.dir/mask_info_convert.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/mask_info_convert.cc -[ 14%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/not_connected_error.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/not_connected_error.cc.o -MF CMakeFiles/ost_mol.dir/not_connected_error.cc.o.d -o CMakeFiles/ost_mol.dir/not_connected_error.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/not_connected_error.cc -[ 14%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/image_state/image_state_factory.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/image_state/image_state_factory.cc.o -MF CMakeFiles/ost_img.dir/image_state/image_state_factory.cc.o.d -o CMakeFiles/ost_img.dir/image_state/image_state_factory.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_factory.cc -[ 14%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/property_id.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/property_id.cc.o -MF CMakeFiles/ost_mol.dir/property_id.cc.o.d -o CMakeFiles/ost_mol.dir/property_id.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/property_id.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/openstructure-2.3.1/modules/img/base/src/polygon_mask.hh:28, - from /build/openstructure-2.3.1/modules/img/base/src/polygon_mask.cc:26: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, + from /build/openstructure-2.3.1/modules/mol/base/src/entity_property_mapper.hh:29, + from /build/openstructure-2.3.1/modules/mol/base/src/entity_property_mapper.cc:19: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/algorithm:60, - from /build/openstructure-2.3.1/modules/img/base/src/polygon_mask.cc:25: + from /usr/include/c++/12/vector:60, + from /build/openstructure-2.3.1/modules/mol/base/src/entity_property_mapper.hh:28: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/openstructure-2.3.1/modules/img/base/src/vecmat.hh:33, + from /build/openstructure-2.3.1/modules/img/base/src/point.hh:35, + from /build/openstructure-2.3.1/modules/img/base/src/point_list.hh:28, + from /build/openstructure-2.3.1/modules/img/base/src/point_list.cc:25: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/vector:60, + from /build/openstructure-2.3.1/modules/img/base/src/point.hh:30: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -5804,6 +5865,8 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 14%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/query_error.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/query_error.cc.o -MF CMakeFiles/ost_mol.dir/query_error.cc.o.d -o CMakeFiles/ost_mol.dir/query_error.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/query_error.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -5826,28 +5889,18 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /usr/include/boost/bind.hpp:30, - from /build/openstructure-2.3.1/modules/mol/base/src/entity_view.cc:25: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -[ 14%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/query.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/query.cc.o -MF CMakeFiles/ost_mol.dir/query.cc.o.d -o CMakeFiles/ost_mol.dir/query.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/query.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, - from /build/openstructure-2.3.1/modules/mol/base/src/entity_property_mapper.hh:29, - from /build/openstructure-2.3.1/modules/mol/base/src/entity_property_mapper.cc:19: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, + from /build/openstructure-2.3.1/modules/img/base/src/polygon_mask.hh:28, + from /build/openstructure-2.3.1/modules/img/base/src/polygon_mask.cc:26: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/vector:60, - from /build/openstructure-2.3.1/modules/mol/base/src/entity_property_mapper.hh:28: + from /usr/include/c++/12/algorithm:60, + from /build/openstructure-2.3.1/modules/img/base/src/polygon_mask.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -5857,22 +5910,19 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 14%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/image_state/index.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/image_state/index.cc.o -MF CMakeFiles/ost_img.dir/image_state/index.cc.o.d -o CMakeFiles/ost_img.dir/image_state/index.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/image_state/index.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/modules/mol/base/src/ics_editor.hh:26, - from /build/openstructure-2.3.1/modules/mol/base/src/ics_editor.cc:19: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/openstructure-2.3.1/modules/mol/base/src/entity_view.hh:32, + from /build/openstructure-2.3.1/modules/mol/base/src/entity_view.cc:30: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/specfun.h:45, - from /usr/include/c++/12/cmath:1935, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, - from /build/openstructure-2.3.1/modules/mol/base/src/ics_editor.hh:25: + from /usr/include/c++/12/algorithm:60, + from /build/openstructure-2.3.1/modules/mol/base/src/entity_view.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -5882,16 +5932,20 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 14%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/image_state/image_state_base.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/image_state/image_state_base.cc.o -MF CMakeFiles/ost_img.dir/image_state/image_state_base.cc.o.d -o CMakeFiles/ost_img.dir/image_state/image_state_base.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_base.cc In file included from /build/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl.hh:41, - from /build/openstructure-2.3.1/modules/mol/base/src/ics_editor.cc:24: + from /build/openstructure-2.3.1/modules/mol/base/src/entity_view.cc:40: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 27 | class pointer_it : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 14%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/query_state.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/query_state.cc.o -MF CMakeFiles/ost_mol.dir/query_state.cc.o.d -o CMakeFiles/ost_mol.dir/query_state.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/query_state.cc +[ 14%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/image_state/image_state_factory.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/image_state/image_state_factory.cc.o -MF CMakeFiles/ost_img.dir/image_state/image_state_factory.cc.o.d -o CMakeFiles/ost_img.dir/image_state/image_state_factory.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_factory.cc +[ 14%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/residue_base.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/residue_base.cc.o -MF CMakeFiles/ost_mol.dir/residue_base.cc.o.d -o CMakeFiles/ost_mol.dir/residue_base.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/residue_base.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -5914,32 +5968,14 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 14%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/raster_image/raster_image.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/raster_image/raster_image.cc.o -MF CMakeFiles/ost_img.dir/raster_image/raster_image.cc.o.d -o CMakeFiles/ost_img.dir/raster_image/raster_image.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/raster_image/raster_image.cc -[ 14%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/query_error.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/query_error.cc.o -MF CMakeFiles/ost_mol.dir/query_error.cc.o.d -o CMakeFiles/ost_mol.dir/query_error.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/query_error.cc -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/info_group.hh:33, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/info.hh:32, - from /build/openstructure-2.3.1/modules/img/base/src/mask_info_convert.cc:28: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/deque:60, - from /usr/include/c++/12/stack:60, - from /build/openstructure-2.3.1/modules/img/base/src/mask_info_convert.cc:25: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ +[ 14%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/residue_handle.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/residue_handle.cc.o -MF CMakeFiles/ost_mol.dir/residue_handle.cc.o.d -o CMakeFiles/ost_mol.dir/residue_handle.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/residue_handle.cc +[ 14%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/image_state/index.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/image_state/index.cc.o -MF CMakeFiles/ost_img.dir/image_state/index.cc.o.d -o CMakeFiles/ost_img.dir/image_state/index.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/image_state/index.cc +[ 14%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/image_state/image_state_base.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/image_state/image_state_base.cc.o -MF CMakeFiles/ost_img.dir/image_state/image_state_base.cc.o.d -o CMakeFiles/ost_img.dir/image_state/image_state_base.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_base.cc +[ 14%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/residue_view.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/residue_view.cc.o -MF CMakeFiles/ost_mol.dir/residue_view.cc.o.d -o CMakeFiles/ost_mol.dir/residue_view.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/residue_view.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -5962,49 +5998,18 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 14%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/query_state.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/query_state.cc.o -MF CMakeFiles/ost_mol.dir/query_state.cc.o.d -o CMakeFiles/ost_mol.dir/query_state.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/query_state.cc -[ 14%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/residue_base.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/residue_base.cc.o -MF CMakeFiles/ost_mol.dir/residue_base.cc.o.d -o CMakeFiles/ost_mol.dir/residue_base.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/residue_base.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/modules/mol/base/src/entity_view.hh:32, - from /build/openstructure-2.3.1/modules/mol/base/src/entity_view.cc:30: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/algorithm:60, - from /build/openstructure-2.3.1/modules/mol/base/src/entity_view.cc:23: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/extent.hh:34, - from /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_factory.hh:31, - from /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_factory.cc:27: + from /build/openstructure-2.3.1/modules/mol/base/src/query.hh:39, + from /build/openstructure-2.3.1/modules/mol/base/src/query.cc:28: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/specfun.h:45, - from /usr/include/c++/12/cmath:1935, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/data_types.hh:30, - from /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_factory.hh:30: + from /usr/include/c++/12/vector:60, + from /build/openstructure-2.3.1/modules/mol/base/src/query.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -6014,59 +6019,23 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl.hh:41, - from /build/openstructure-2.3.1/modules/mol/base/src/entity_view.cc:40: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 27 | class pointer_it : public std::iterator{ - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/base/pymod/wrap_base.cc:19: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -[ 14%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/residue_handle.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/residue_handle.cc.o -MF CMakeFiles/ost_mol.dir/residue_handle.cc.o.d -o CMakeFiles/ost_mol.dir/residue_handle.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/residue_handle.cc -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 14%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/residue_view.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/residue_view.cc.o -MF CMakeFiles/ost_mol.dir/residue_view.cc.o.d -o CMakeFiles/ost_mol.dir/residue_view.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/residue_view.cc +[ 14%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/raster_image/raster_image.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/raster_image/raster_image.cc.o -MF CMakeFiles/ost_img.dir/raster_image/raster_image.cc.o.d -o CMakeFiles/ost_img.dir/raster_image/raster_image.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/raster_image/raster_image.cc [ 15%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/surface_builder.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/surface_builder.cc.o -MF CMakeFiles/ost_mol.dir/surface_builder.cc.o.d -o CMakeFiles/ost_mol.dir/surface_builder.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/surface_builder.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, - from /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_base.hh:34, - from /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_base.cc:25: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/info_group.hh:33, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/info.hh:32, + from /build/openstructure-2.3.1/modules/img/base/src/mask_info_convert.cc:28: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/memory:63, - from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, - from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, - from /usr/include/boost/shared_ptr.hpp:17, - from /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_base_fw.hh:28, - from /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_base.hh:30: + from /usr/include/c++/12/deque:60, + from /usr/include/c++/12/stack:60, + from /build/openstructure-2.3.1/modules/img/base/src/mask_info_convert.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -6078,20 +6047,24 @@ | ^~~~~~~~ [ 15%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/surface_handle.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/surface_handle.cc.o -MF CMakeFiles/ost_mol.dir/surface_handle.cc.o.d -o CMakeFiles/ost_mol.dir/surface_handle.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/surface_handle.cc -[ 15%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/transfer_connectivity.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/transfer_connectivity.cc.o -MF CMakeFiles/ost_mol.dir/transfer_connectivity.cc.o.d -o CMakeFiles/ost_mol.dir/transfer_connectivity.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/transfer_connectivity.cc +In file included from /usr/include/boost/bind.hpp:30, + from /build/openstructure-2.3.1/modules/mol/base/src/residue_view.cc:22: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/openstructure-2.3.1/modules/mol/base/src/query.hh:39, - from /build/openstructure-2.3.1/modules/mol/base/src/query.cc:28: + from /build/openstructure-2.3.1/modules/mol/base/src/query_state.cc:22: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/vector:60, - from /build/openstructure-2.3.1/modules/mol/base/src/query.cc:23: +In file included from /usr/include/c++/12/string:45, + from /usr/include/c++/12/stdexcept:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec2.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec.hh:24, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -6104,8 +6077,8 @@ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/openstructure-2.3.1/modules/mol/base/src/query_state.cc:22: + from /build/openstructure-2.3.1/modules/mol/base/src/residue_base.hh:22, + from /build/openstructure-2.3.1/modules/mol/base/src/residue_base.cc:19: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -6123,19 +6096,25 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 15%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/transfer_connectivity.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/transfer_connectivity.cc.o -MF CMakeFiles/ost_mol.dir/transfer_connectivity.cc.o.d -o CMakeFiles/ost_mol.dir/transfer_connectivity.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/transfer_connectivity.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/openstructure-2.3.1/modules/img/base/src/raster_image/raster_image.hh:31, - from /build/openstructure-2.3.1/modules/img/base/src/raster_image/raster_image.cc:38: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/extent.hh:34, + from /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_factory.hh:31, + from /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_factory.cc:27: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, - from /build/openstructure-2.3.1/modules/img/base/src/raster_image/raster_image.cc:31: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/data_types.hh:30, + from /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_factory.hh:30: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -6153,24 +6132,22 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /usr/include/boost/bind.hpp:30, - from /build/openstructure-2.3.1/modules/mol/base/src/residue_view.cc:22: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ +[ 15%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/torsion_handle.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/torsion_handle.cc.o -MF CMakeFiles/ost_mol.dir/torsion_handle.cc.o.d -o CMakeFiles/ost_mol.dir/torsion_handle.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/torsion_handle.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/modules/mol/base/src/residue_base.hh:22, - from /build/openstructure-2.3.1/modules/mol/base/src/residue_base.cc:19: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, + from /build/openstructure-2.3.1/modules/mol/base/src/residue_handle.cc:19: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec2.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec.hh:24, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:24: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec3.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -6180,26 +6157,25 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 15%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/torsion_handle.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/torsion_handle.cc.o -MF CMakeFiles/ost_mol.dir/torsion_handle.cc.o.d -o CMakeFiles/ost_mol.dir/torsion_handle.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/torsion_handle.cc -[ 15%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/query_view_wrapper.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/query_view_wrapper.cc.o -MF CMakeFiles/ost_mol.dir/query_view_wrapper.cc.o.d -o CMakeFiles/ost_mol.dir/query_view_wrapper.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/query_view_wrapper.cc -[ 15%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/view_op.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/view_op.cc.o -MF CMakeFiles/ost_mol.dir/view_op.cc.o.d -o CMakeFiles/ost_mol.dir/view_op.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/view_op.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, - from /build/openstructure-2.3.1/modules/mol/base/src/residue_handle.cc:19: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, + from /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_base.hh:34, + from /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_base.cc:25: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/12/string:45, - from /usr/include/c++/12/stdexcept:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec3.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:22: +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/memory:63, + from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, + from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, + from /usr/include/boost/shared_ptr.hpp:17, + from /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_base_fw.hh:28, + from /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_base.hh:30: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -6220,20 +6196,36 @@ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/openstructure-2.3.1/modules/mol/base/src/query.hh:39, - from /build/openstructure-2.3.1/modules/mol/base/src/entity_handle.hh:26, - from /build/openstructure-2.3.1/modules/mol/base/src/transfer_connectivity.hh:24, - from /build/openstructure-2.3.1/modules/mol/base/src/transfer_connectivity.cc:20: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/chain_view.hh:23, + from /build/openstructure-2.3.1/modules/mol/base/src/residue_view.cc:25: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/algorithm:60, + from /build/openstructure-2.3.1/modules/mol/base/src/residue_view.cc:19: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, + from /build/openstructure-2.3.1/modules/img/base/src/raster_image/raster_image.hh:31, + from /build/openstructure-2.3.1/modules/img/base/src/raster_image/raster_image.cc:38: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/openstructure-2.3.1/modules/mol/base/src/module_config.hh:22, - from /build/openstructure-2.3.1/modules/mol/base/src/transfer_connectivity.hh:23: + from /build/openstructure-2.3.1/modules/img/base/src/raster_image/raster_image.cc:31: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -6268,19 +6260,20 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 15%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/coord_source.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/coord_source.cc.o -MF CMakeFiles/ost_mol.dir/coord_source.cc.o.d -o CMakeFiles/ost_mol.dir/coord_source.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/coord_source.cc +[ 15%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/query_view_wrapper.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/query_view_wrapper.cc.o -MF CMakeFiles/ost_mol.dir/query_view_wrapper.cc.o.d -o CMakeFiles/ost_mol.dir/query_view_wrapper.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/query_view_wrapper.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/chain_view.hh:23, - from /build/openstructure-2.3.1/modules/mol/base/src/residue_view.cc:25: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/surface_prop.hh:25, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/surface_handle.hh:24, + from /build/openstructure-2.3.1/modules/mol/base/src/surface_handle.cc:19: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/algorithm:60, - from /build/openstructure-2.3.1/modules/mol/base/src/residue_view.cc:19: + from /usr/include/c++/12/vector:60, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/surface_handle.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -6290,20 +6283,23 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 15%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/in_mem_coord_source.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/in_mem_coord_source.cc.o -MF CMakeFiles/ost_mol.dir/in_mem_coord_source.cc.o.d -o CMakeFiles/ost_mol.dir/in_mem_coord_source.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/in_mem_coord_source.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/surface_prop.hh:25, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/surface_handle.hh:24, - from /build/openstructure-2.3.1/modules/mol/base/src/surface_handle.cc:19: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/openstructure-2.3.1/modules/mol/base/src/query.hh:39, + from /build/openstructure-2.3.1/modules/mol/base/src/entity_handle.hh:26, + from /build/openstructure-2.3.1/modules/mol/base/src/transfer_connectivity.hh:24, + from /build/openstructure-2.3.1/modules/mol/base/src/transfer_connectivity.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/vector:60, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/surface_handle.hh:22: + from /usr/include/c++/12/bits/specfun.h:45, + from /usr/include/c++/12/cmath:1935, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, + from /build/openstructure-2.3.1/modules/mol/base/src/module_config.hh:22, + from /build/openstructure-2.3.1/modules/mol/base/src/transfer_connectivity.hh:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -6313,8 +6309,8 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 15%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/bounding_box.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/bounding_box.cc.o -MF CMakeFiles/ost_mol.dir/bounding_box.cc.o.d -o CMakeFiles/ost_mol.dir/bounding_box.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/bounding_box.cc +[ 15%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/view_op.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/view_op.cc.o -MF CMakeFiles/ost_mol.dir/view_op.cc.o.d -o CMakeFiles/ost_mol.dir/view_op.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/view_op.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -6341,6 +6337,16 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 15%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/coord_source.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/coord_source.cc.o -MF CMakeFiles/ost_mol.dir/coord_source.cc.o.d -o CMakeFiles/ost_mol.dir/coord_source.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/coord_source.cc +[ 15%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/in_mem_coord_source.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/in_mem_coord_source.cc.o -MF CMakeFiles/ost_mol.dir/in_mem_coord_source.cc.o.d -o CMakeFiles/ost_mol.dir/in_mem_coord_source.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/in_mem_coord_source.cc +[ 15%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/bounding_box.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/bounding_box.cc.o -MF CMakeFiles/ost_mol.dir/bounding_box.cc.o.d -o CMakeFiles/ost_mol.dir/bounding_box.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/bounding_box.cc +[ 15%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/xcs_editor.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/xcs_editor.cc.o -MF CMakeFiles/ost_mol.dir/xcs_editor.cc.o.d -o CMakeFiles/ost_mol.dir/xcs_editor.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/xcs_editor.cc +[ 16%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/atom_impl.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/atom_impl.cc.o -MF CMakeFiles/ost_mol.dir/impl/atom_impl.cc.o.d -o CMakeFiles/ost_mol.dir/impl/atom_impl.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/impl/atom_impl.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -6369,8 +6375,8 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 15%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/xcs_editor.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/xcs_editor.cc.o -MF CMakeFiles/ost_mol.dir/xcs_editor.cc.o.d -o CMakeFiles/ost_mol.dir/xcs_editor.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/xcs_editor.cc +[ 16%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/chain_impl.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/chain_impl.cc.o -MF CMakeFiles/ost_mol.dir/impl/chain_impl.cc.o.d -o CMakeFiles/ost_mol.dir/impl/chain_impl.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/impl/chain_impl.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -6398,8 +6404,8 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 16%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/atom_impl.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/atom_impl.cc.o -MF CMakeFiles/ost_mol.dir/impl/atom_impl.cc.o.d -o CMakeFiles/ost_mol.dir/impl/atom_impl.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/impl/atom_impl.cc +[ 16%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/connector_impl.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/connector_impl.cc.o -MF CMakeFiles/ost_mol.dir/impl/connector_impl.cc.o.d -o CMakeFiles/ost_mol.dir/impl/connector_impl.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/impl/connector_impl.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:41, from /build/openstructure-2.3.1/modules/mol/base/src/view_op.cc:27: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] @@ -6408,6 +6414,36 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 16%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/dihedral.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/dihedral.cc.o -MF CMakeFiles/ost_mol.dir/impl/dihedral.cc.o.d -o CMakeFiles/ost_mol.dir/impl/dihedral.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/impl/dihedral.cc +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/coord_frame.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/coord_source.hh:27, + from /build/openstructure-2.3.1/modules/mol/base/src/in_mem_coord_source.hh:26, + from /build/openstructure-2.3.1/modules/mol/base/src/in_mem_coord_source.cc:1: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/memory:63, + from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, + from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, + from /usr/include/boost/shared_ptr.hpp:17, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/coord_source.hh:25: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 16%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/entity_impl.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/entity_impl.cc.o -MF CMakeFiles/ost_mol.dir/impl/entity_impl.cc.o.d -o CMakeFiles/ost_mol.dir/impl/entity_impl.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -6432,23 +6468,22 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 16%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/fragment_impl.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/fragment_impl.cc.o -MF CMakeFiles/ost_mol.dir/impl/fragment_impl.cc.o.d -o CMakeFiles/ost_mol.dir/impl/fragment_impl.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/impl/fragment_impl.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/coord_frame.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/coord_source.hh:27, - from /build/openstructure-2.3.1/modules/mol/base/src/in_mem_coord_source.hh:26, - from /build/openstructure-2.3.1/modules/mol/base/src/in_mem_coord_source.cc:1: + from /build/openstructure-2.3.1/modules/mol/base/src/xcs_editor.hh:26, + from /build/openstructure-2.3.1/modules/mol/base/src/xcs_editor.cc:19: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/memory:63, - from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, - from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, - from /usr/include/boost/shared_ptr.hpp:17, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/coord_source.hh:25: + from /usr/include/c++/12/bits/specfun.h:45, + from /usr/include/c++/12/cmath:1935, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, + from /build/openstructure-2.3.1/modules/mol/base/src/xcs_editor.hh:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -6458,28 +6493,18 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 16%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/chain_impl.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/chain_impl.cc.o -MF CMakeFiles/ost_mol.dir/impl/chain_impl.cc.o.d -o CMakeFiles/ost_mol.dir/impl/chain_impl.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/impl/chain_impl.cc -[ 16%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/connector_impl.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/connector_impl.cc.o -MF CMakeFiles/ost_mol.dir/impl/connector_impl.cc.o.d -o CMakeFiles/ost_mol.dir/impl/connector_impl.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/impl/connector_impl.cc -[ 16%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/dihedral.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/dihedral.cc.o -MF CMakeFiles/ost_mol.dir/impl/dihedral.cc.o.d -o CMakeFiles/ost_mol.dir/impl/dihedral.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/impl/dihedral.cc -[ 16%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/entity_impl.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/entity_impl.cc.o -MF CMakeFiles/ost_mol.dir/impl/entity_impl.cc.o.d -o CMakeFiles/ost_mol.dir/impl/entity_impl.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/modules/mol/base/src/xcs_editor.hh:26, - from /build/openstructure-2.3.1/modules/mol/base/src/xcs_editor.cc:19: + from /build/openstructure-2.3.1/modules/mol/base/src/impl/atom_impl.hh:25, + from /build/openstructure-2.3.1/modules/mol/base/src/impl/atom_impl.cc:23: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, - from /build/openstructure-2.3.1/modules/mol/base/src/xcs_editor.hh:25: + from /build/openstructure-2.3.1/modules/mol/base/src/impl/atom_impl.cc:19: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -6489,8 +6514,6 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 16%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/fragment_impl.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/fragment_impl.cc.o -MF CMakeFiles/ost_mol.dir/impl/fragment_impl.cc.o.d -o CMakeFiles/ost_mol.dir/impl/fragment_impl.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/impl/fragment_impl.cc In file included from /build/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl.hh:41, from /build/openstructure-2.3.1/modules/mol/base/src/xcs_editor.cc:26: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] @@ -6499,25 +6522,31 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +In file included from /build/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl.hh:41, + from /build/openstructure-2.3.1/modules/mol/base/src/impl/atom_impl.cc:27: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 27 | class pointer_it : public std::iterator{ + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ [ 16%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/query_ast.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/query_ast.cc.o -MF CMakeFiles/ost_mol.dir/impl/query_ast.cc.o.d -o CMakeFiles/ost_mol.dir/impl/query_ast.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/impl/query_ast.cc -[ 16%] Linking CXX shared library ../../../../stage/lib/libost_img.so -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_img.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libost_img.so.2.3 -o ../../../../stage/lib/libost_img.so.2.3.1 CMakeFiles/ost_img.dir/circle_mask.cc.o CMakeFiles/ost_img.dir/composite_mask.cc.o CMakeFiles/ost_img.dir/data_algorithm.cc.o CMakeFiles/ost_img.dir/data_observer.cc.o CMakeFiles/ost_img.dir/data.cc.o CMakeFiles/ost_img.dir/extent_iterator.cc.o CMakeFiles/ost_img.dir/extent_mask.cc.o CMakeFiles/ost_img.dir/extent.cc.o CMakeFiles/ost_img.dir/image_factory.cc.o CMakeFiles/ost_img.dir/image_handle.cc.o CMakeFiles/ost_img.dir/image_impl.cc.o CMakeFiles/ost_img.dir/image_list.cc.o CMakeFiles/ost_img.dir/inverted_mask.cc.o CMakeFiles/ost_img.dir/map.cc.o CMakeFiles/ost_img.dir/mask_base.cc.o CMakeFiles/ost_img.dir/mask_op.cc.o CMakeFiles/ost_img.dir/mask.cc.o CMakeFiles/ost_img.dir/observable.cc.o CMakeFiles/ost_img.dir/paste_impl.cc.o CMakeFiles/ost_img.dir/peak.cc.o CMakeFiles/ost_img.dir/phase.cc.o CMakeFiles/ost_img.dir/physical_units.cc.o CMakeFiles/ost_img.dir/pixel_sampling.cc.o CMakeFiles/ost_img.dir/point_list.cc.o CMakeFiles/ost_img.dir/point.cc.o CMakeFiles/ost_img.dir/polygon_mask.cc.o CMakeFiles/ost_img.dir/progress.cc.o CMakeFiles/ost_img.dir/size.cc.o CMakeFiles/ost_img.dir/spherical_mask.cc.o CMakeFiles/ost_img.dir/mask_info_convert.cc.o CMakeFiles/ost_img.dir/image_state/image_state_factory.cc.o CMakeFiles/ost_img.dir/image_state/index.cc.o CMakeFiles/ost_img.dir/image_state/image_state_base.cc.o CMakeFiles/ost_img.dir/raster_image/raster_image.cc.o -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib: ../../../../stage/lib/libost_info.so.2.3.1 ../../../../stage/lib/libost_base.so.2.3.1 ../../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 -[ 16%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/query_impl.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/query_impl.cc.o -MF CMakeFiles/ost_mol.dir/impl/query_impl.cc.o.d -o CMakeFiles/ost_mol.dir/impl/query_impl.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/impl/query_impl.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/mol/base/src/impl/atom_impl.hh:25, - from /build/openstructure-2.3.1/modules/mol/base/src/impl/atom_impl.cc:23: + from /build/openstructure-2.3.1/modules/mol/base/src/impl/chain_impl.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/specfun.h:45, - from /usr/include/c++/12/cmath:1935, - from /build/openstructure-2.3.1/modules/mol/base/src/impl/atom_impl.cc:19: +In file included from /usr/include/c++/12/string:45, + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/ostream:38, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, + from /build/openstructure-2.3.1/modules/mol/base/src/impl/chain_impl.cc:19: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -6527,6 +6556,27 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/log_sink.hh:29, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/log.hh:25, + from /build/openstructure-2.3.1/modules/mol/base/src/impl/atom_impl.cc:21: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +In file included from /build/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl.hh:41, + from /build/openstructure-2.3.1/modules/mol/base/src/impl/chain_impl.cc:23: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 27 | class pointer_it : public std::iterator{ + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -6548,37 +6598,33 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl.hh:41, - from /build/openstructure-2.3.1/modules/mol/base/src/impl/atom_impl.cc:27: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 27 | class pointer_it : public std::iterator{ - | ^~~~~~~~ +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/atom_impl.hh:25, + from /build/openstructure-2.3.1/modules/mol/base/src/impl/dihedral.cc:19: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/memory:63, + from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, + from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, + from /usr/include/boost/smart_ptr/weak_ptr.hpp:16, + from /usr/include/boost/smart_ptr/enable_shared_from_this.hpp:16, + from /usr/include/boost/enable_shared_from_this.hpp:16, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/atom_impl.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 16%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/residue_impl.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/residue_impl.cc.o -MF CMakeFiles/ost_mol.dir/impl/residue_impl.cc.o.d -o CMakeFiles/ost_mol.dir/impl/residue_impl.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/impl/residue_impl.cc -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E cmake_symlink_library ../../../../stage/lib/libost_img.so.2.3.1 ../../../../stage/lib/libost_img.so.2.3 ../../../../stage/lib/libost_img.so -make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 16%] Built target ost_img -make -f modules/img/alg/src/CMakeFiles/ost_img_alg.dir/build.make modules/img/alg/src/CMakeFiles/ost_img_alg.dir/depend -make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/img/alg/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src/CMakeFiles/ost_img_alg.dir/DependInfo.cmake --color= -make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/img/alg/src/CMakeFiles/ost_img_alg.dir/build.make modules/img/alg/src/CMakeFiles/ost_img_alg.dir/build -In file included from /build/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl.hh:41, - from /build/openstructure-2.3.1/modules/mol/base/src/impl/connector_impl.cc:24: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 27 | class pointer_it : public std::iterator{ - | ^~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 16%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/surface_impl.cc.o -[ 16%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/anisotropic.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/surface_impl.cc.o -MF CMakeFiles/ost_mol.dir/impl/surface_impl.cc.o.d -o CMakeFiles/ost_mol.dir/impl/surface_impl.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/impl/surface_impl.cc -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/anisotropic.cc.o -MF CMakeFiles/ost_img_alg.dir/anisotropic.cc.o.d -o CMakeFiles/ost_img_alg.dir/anisotropic.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/anisotropic.cc +[ 16%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/query_impl.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/query_impl.cc.o -MF CMakeFiles/ost_mol.dir/impl/query_impl.cc.o.d -o CMakeFiles/ost_mol.dir/impl/query_impl.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/impl/query_impl.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -6587,11 +6633,12 @@ from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/log_sink.hh:29, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/log.hh:25, - from /build/openstructure-2.3.1/modules/mol/base/src/impl/atom_impl.cc:21: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/log.hh:25: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ +[ 16%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/residue_impl.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/residue_impl.cc.o -MF CMakeFiles/ost_mol.dir/impl/residue_impl.cc.o.d -o CMakeFiles/ost_mol.dir/impl/residue_impl.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/impl/residue_impl.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -6619,46 +6666,33 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/modules/mol/base/src/impl/atom_impl.hh:25, - from /build/openstructure-2.3.1/modules/mol/base/src/impl/chain_impl.cc:20: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/12/string:45, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/ostream:38, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, - from /build/openstructure-2.3.1/modules/mol/base/src/impl/chain_impl.cc:19: +In file included from /build/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl.hh:41, + from /build/openstructure-2.3.1/modules/mol/base/src/impl/connector_impl.cc:24: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 27 | class pointer_it : public std::iterator{ + | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:41, + from /build/openstructure-2.3.1/modules/mol/base/src/impl/dihedral.cc:21: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 27 | class pointer_it : public std::iterator{ + | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/atom_impl.hh:25, - from /build/openstructure-2.3.1/modules/mol/base/src/impl/dihedral.cc:19: + from /build/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl.cc:35: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/memory:63, - from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, - from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, - from /usr/include/boost/smart_ptr/weak_ptr.hpp:16, - from /usr/include/boost/smart_ptr/enable_shared_from_this.hpp:16, - from /usr/include/boost/enable_shared_from_this.hpp:16, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/atom_impl.hh:22: + from /usr/include/c++/12/bits/stl_tree.h:63, + from /usr/include/c++/12/map:60, + from /build/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl.cc:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -6690,17 +6724,55 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 16%] Linking CXX shared library ../../../../stage/lib/libost_img.so +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_img.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libost_img.so.2.3 -o ../../../../stage/lib/libost_img.so.2.3.1 CMakeFiles/ost_img.dir/circle_mask.cc.o CMakeFiles/ost_img.dir/composite_mask.cc.o CMakeFiles/ost_img.dir/data_algorithm.cc.o CMakeFiles/ost_img.dir/data_observer.cc.o CMakeFiles/ost_img.dir/data.cc.o CMakeFiles/ost_img.dir/extent_iterator.cc.o CMakeFiles/ost_img.dir/extent_mask.cc.o CMakeFiles/ost_img.dir/extent.cc.o CMakeFiles/ost_img.dir/image_factory.cc.o CMakeFiles/ost_img.dir/image_handle.cc.o CMakeFiles/ost_img.dir/image_impl.cc.o CMakeFiles/ost_img.dir/image_list.cc.o CMakeFiles/ost_img.dir/inverted_mask.cc.o CMakeFiles/ost_img.dir/map.cc.o CMakeFiles/ost_img.dir/mask_base.cc.o CMakeFiles/ost_img.dir/mask_op.cc.o CMakeFiles/ost_img.dir/mask.cc.o CMakeFiles/ost_img.dir/observable.cc.o CMakeFiles/ost_img.dir/paste_impl.cc.o CMakeFiles/ost_img.dir/peak.cc.o CMakeFiles/ost_img.dir/phase.cc.o CMakeFiles/ost_img.dir/physical_units.cc.o CMakeFiles/ost_img.dir/pixel_sampling.cc.o CMakeFiles/ost_img.dir/point_list.cc.o CMakeFiles/ost_img.dir/point.cc.o CMakeFiles/ost_img.dir/polygon_mask.cc.o CMakeFiles/ost_img.dir/progress.cc.o CMakeFiles/ost_img.dir/size.cc.o CMakeFiles/ost_img.dir/spherical_mask.cc.o CMakeFiles/ost_img.dir/mask_info_convert.cc.o CMakeFiles/ost_img.dir/image_state/image_state_factory.cc.o CMakeFiles/ost_img.dir/image_state/index.cc.o CMakeFiles/ost_img.dir/image_state/image_state_base.cc.o CMakeFiles/ost_img.dir/raster_image/raster_image.cc.o -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib: ../../../../stage/lib/libost_info.so.2.3.1 ../../../../stage/lib/libost_base.so.2.3.1 ../../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 +[ 16%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/surface_impl.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/surface_impl.cc.o -MF CMakeFiles/ost_mol.dir/impl/surface_impl.cc.o.d -o CMakeFiles/ost_mol.dir/impl/surface_impl.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/impl/surface_impl.cc +[ 16%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/torsion_impl.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/torsion_impl.cc.o -MF CMakeFiles/ost_mol.dir/impl/torsion_impl.cc.o.d -o CMakeFiles/ost_mol.dir/impl/torsion_impl.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/impl/torsion_impl.cc +In file included from /build/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl.hh:41, + from /build/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl.cc:40: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 27 | class pointer_it : public std::iterator{ + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E cmake_symlink_library ../../../../stage/lib/libost_img.so.2.3.1 ../../../../stage/lib/libost_img.so.2.3 ../../../../stage/lib/libost_img.so +make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[ 16%] Built target ost_img +make -f modules/img/alg/src/CMakeFiles/ost_img_alg.dir/build.make modules/img/alg/src/CMakeFiles/ost_img_alg.dir/depend +make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/img/alg/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src/CMakeFiles/ost_img_alg.dir/DependInfo.cmake --color= +make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +make -f modules/img/alg/src/CMakeFiles/ost_img_alg.dir/build.make modules/img/alg/src/CMakeFiles/ost_img_alg.dir/build +make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[ 16%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/anisotropic.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/anisotropic.cc.o -MF CMakeFiles/ost_img_alg.dir/anisotropic.cc.o.d -o CMakeFiles/ost_img_alg.dir/anisotropic.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/anisotropic.cc +[ 17%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/atom_prop.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/atom_prop.cc.o -MF CMakeFiles/ost_mol.dir/impl/atom_prop.cc.o.d -o CMakeFiles/ost_mol.dir/impl/atom_prop.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/impl/atom_prop.cc +[ 17%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/auto_correlate.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/auto_correlate.cc.o -MF CMakeFiles/ost_img_alg.dir/auto_correlate.cc.o.d -o CMakeFiles/ost_img_alg.dir/auto_correlate.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/auto_correlate.cc +[ 17%] Building CXX object modules/base/pymod/CMakeFiles/_ost_base.dir/export_logger.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/c++ -D_ost_base_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/pymod/CMakeFiles/_ost_base.dir/export_logger.cc.o -MF CMakeFiles/_ost_base.dir/export_logger.cc.o.d -o CMakeFiles/_ost_base.dir/export_logger.cc.o -c /build/openstructure-2.3.1/modules/base/pymod/export_logger.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl.cc:35: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, + from /build/openstructure-2.3.1/modules/mol/base/src/impl/residue_impl.cc:21: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/stl_tree.h:63, - from /usr/include/c++/12/map:60, - from /build/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl.cc:22: +In file included from /usr/include/c++/12/string:45, + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/ostream:38, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, + from /build/openstructure-2.3.1/modules/mol/base/src/impl/residue_impl.cc:19: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -6710,63 +6782,30 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:41, - from /build/openstructure-2.3.1/modules/mol/base/src/impl/dihedral.cc:21: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 27 | class pointer_it : public std::iterator{ - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -[ 16%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/torsion_impl.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/torsion_impl.cc.o -MF CMakeFiles/ost_mol.dir/impl/torsion_impl.cc.o.d -o CMakeFiles/ost_mol.dir/impl/torsion_impl.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/impl/torsion_impl.cc -In file included from /build/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl.hh:41, - from /build/openstructure-2.3.1/modules/mol/base/src/impl/chain_impl.cc:23: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 27 | class pointer_it : public std::iterator{ - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ In file included from /build/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl.hh:41, - from /build/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl.cc:40: + from /build/openstructure-2.3.1/modules/mol/base/src/impl/residue_impl.cc:25: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 27 | class pointer_it : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/log_sink.hh:29, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/log.hh:25: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -[ 17%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/atom_prop.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/atom_prop.cc.o -MF CMakeFiles/ost_mol.dir/impl/atom_prop.cc.o.d -o CMakeFiles/ost_mol.dir/impl/atom_prop.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/impl/atom_prop.cc -[ 17%] Building CXX object modules/base/pymod/CMakeFiles/_ost_base.dir/export_logger.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/c++ -D_ost_base_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/pymod/CMakeFiles/_ost_base.dir/export_logger.cc.o -MF CMakeFiles/_ost_base.dir/export_logger.cc.o.d -o CMakeFiles/_ost_base.dir/export_logger.cc.o -c /build/openstructure-2.3.1/modules/base/pymod/export_logger.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, - from /build/openstructure-2.3.1/modules/mol/base/src/impl/query_impl.hh:36, - from /build/openstructure-2.3.1/modules/mol/base/src/impl/query_impl.cc:22: + from /build/openstructure-2.3.1/modules/mol/base/src/impl/surface_impl.cc:21: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/vector:60, - from /build/openstructure-2.3.1/modules/mol/base/src/impl/query_impl.hh:22: + from /usr/include/c++/12/bits/specfun.h:45, + from /usr/include/c++/12/cmath:1935, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -6776,15 +6815,11 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 17%] Building CXX object modules/base/pymod/CMakeFiles/_ost_base.dir/export_range.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/c++ -D_ost_base_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/pymod/CMakeFiles/_ost_base.dir/export_range.cc.o -MF CMakeFiles/_ost_base.dir/export_range.cc.o.d -o CMakeFiles/_ost_base.dir/export_range.cc.o -c /build/openstructure-2.3.1/modules/base/pymod/export_range.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, - from /build/openstructure-2.3.1/modules/mol/base/src/impl/residue_impl.cc:21: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/torsion_impl.hh:25, + from /build/openstructure-2.3.1/modules/mol/base/src/impl/torsion_impl.cc:21: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -6794,7 +6829,7 @@ from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, - from /build/openstructure-2.3.1/modules/mol/base/src/impl/residue_impl.cc:19: + from /build/openstructure-2.3.1/modules/mol/base/src/impl/torsion_impl.cc:19: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -6804,14 +6839,6 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl.hh:41, - from /build/openstructure-2.3.1/modules/mol/base/src/impl/residue_impl.cc:25: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 27 | class pointer_it : public std::iterator{ - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -6824,31 +6851,8 @@ /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, - from /build/openstructure-2.3.1/modules/mol/base/src/impl/surface_impl.cc:21: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/specfun.h:45, - from /usr/include/c++/12/cmath:1935, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ +[ 17%] Building CXX object modules/base/pymod/CMakeFiles/_ost_base.dir/export_range.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/c++ -D_ost_base_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/pymod/CMakeFiles/_ost_base.dir/export_range.cc.o -MF CMakeFiles/_ost_base.dir/export_range.cc.o.d -o CMakeFiles/_ost_base.dir/export_range.cc.o -c /build/openstructure-2.3.1/modules/base/pymod/export_range.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -6875,25 +6879,29 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 17%] Building CXX object modules/base/pymod/CMakeFiles/_ost_base.dir/export_units.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/c++ -D_ost_base_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/pymod/CMakeFiles/_ost_base.dir/export_units.cc.o -MF CMakeFiles/_ost_base.dir/export_units.cc.o.d -o CMakeFiles/_ost_base.dir/export_units.cc.o -c /build/openstructure-2.3.1/modules/base/pymod/export_units.cc -[ 17%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/auto_correlate.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/auto_correlate.cc.o -MF CMakeFiles/ost_img_alg.dir/auto_correlate.cc.o.d -o CMakeFiles/ost_img_alg.dir/auto_correlate.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/auto_correlate.cc +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:41, + from /build/openstructure-2.3.1/modules/mol/base/src/impl/torsion_impl.cc:27: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 27 | class pointer_it : public std::iterator{ + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/torsion_impl.hh:25, - from /build/openstructure-2.3.1/modules/mol/base/src/impl/torsion_impl.cc:21: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, + from /build/openstructure-2.3.1/modules/mol/base/src/impl/query_impl.hh:36, + from /build/openstructure-2.3.1/modules/mol/base/src/impl/query_impl.cc:22: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/12/string:45, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/ostream:38, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, - from /build/openstructure-2.3.1/modules/mol/base/src/impl/torsion_impl.cc:19: +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/vector:60, + from /build/openstructure-2.3.1/modules/mol/base/src/impl/query_impl.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -6903,14 +6911,6 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:41, - from /build/openstructure-2.3.1/modules/mol/base/src/impl/torsion_impl.cc:27: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 27 | class pointer_it : public std::iterator{ - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ [ 17%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/convolute.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/convolute.cc.o -MF CMakeFiles/ost_img_alg.dir/convolute.cc.o.d -o CMakeFiles/ost_img_alg.dir/convolute.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/convolute.cc [ 17%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/correlate.cc.o @@ -6919,8 +6919,6 @@ cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/cross_correlate.cc.o -MF CMakeFiles/ost_img_alg.dir/cross_correlate.cc.o.d -o CMakeFiles/ost_img_alg.dir/cross_correlate.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/cross_correlate.cc [ 19%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/density_slice.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/density_slice.cc.o -MF CMakeFiles/ost_img_alg.dir/density_slice.cc.o.d -o CMakeFiles/ost_img_alg.dir/density_slice.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/density_slice.cc -[ 19%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/dft.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/dft.cc.o -MF CMakeFiles/ost_img_alg.dir/dft.cc.o.d -o CMakeFiles/ost_img_alg.dir/dft.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/dft.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -6947,28 +6945,10 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 19%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/fft.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/fft.cc.o -MF CMakeFiles/ost_img_alg.dir/fft.cc.o.d -o CMakeFiles/ost_img_alg.dir/fft.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/fft.cc -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/base/pymod/export_range.cc:19: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 19%] Building CXX object modules/base/pymod/CMakeFiles/_ost_base.dir/export_units.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/c++ -D_ost_base_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/pymod/CMakeFiles/_ost_base.dir/export_units.cc.o -MF CMakeFiles/_ost_base.dir/export_units.cc.o.d -o CMakeFiles/_ost_base.dir/export_units.cc.o -c /build/openstructure-2.3.1/modules/base/pymod/export_units.cc +[ 19%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/dft.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/dft.cc.o -MF CMakeFiles/ost_img_alg.dir/dft.cc.o.d -o CMakeFiles/ost_img_alg.dir/dft.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/dft.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -6996,26 +6976,35 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/base/pymod/export_units.cc:25: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, + from /build/openstructure-2.3.1/modules/img/alg/src/cross_correlate.hh:27, + from /build/openstructure-2.3.1/modules/img/alg/src/cross_correlate.cc:25: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/bits/specfun.h:45, + from /usr/include/c++/12/cmath:1935, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/module_config.hh:23, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:31: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 19%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/fft.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/fft.cc.o -MF CMakeFiles/ost_img_alg.dir/fft.cc.o.d -o CMakeFiles/ost_img_alg.dir/fft.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/fft.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -7056,6 +7045,26 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, + from /build/openstructure-2.3.1/modules/base/pymod/export_range.cc:19: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/base/pymod/export_logger.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( @@ -7067,11 +7076,12 @@ from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, - from /build/openstructure-2.3.1/modules/img/alg/src/cross_correlate.hh:27, - from /build/openstructure-2.3.1/modules/img/alg/src/cross_correlate.cc:25: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, + from /build/openstructure-2.3.1/modules/img/alg/src/density_slice.hh:28, + from /build/openstructure-2.3.1/modules/img/alg/src/density_slice.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -7079,8 +7089,7 @@ from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/module_config.hh:23, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:31: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:30: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -7121,38 +7130,10 @@ cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/fourier_filters.cc.o -MF CMakeFiles/ost_img_alg.dir/fourier_filters.cc.o.d -o CMakeFiles/ost_img_alg.dir/fourier_filters.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/fourier_filters.cc [ 19%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/gaussian.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/gaussian.cc.o -MF CMakeFiles/ost_img_alg.dir/gaussian.cc.o.d -o CMakeFiles/ost_img_alg.dir/gaussian.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/gaussian.cc -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, - from /build/openstructure-2.3.1/modules/img/alg/src/density_slice.hh:28, - from /build/openstructure-2.3.1/modules/img/alg/src/density_slice.cc:20: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/specfun.h:45, - from /usr/include/c++/12/cmath:1935, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:30: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ [ 19%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/gaussian_gradient_magnitude.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/gaussian_gradient_magnitude.cc.o -MF CMakeFiles/ost_img_alg.dir/gaussian_gradient_magnitude.cc.o.d -o CMakeFiles/ost_img_alg.dir/gaussian_gradient_magnitude.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/gaussian_gradient_magnitude.cc [ 19%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/gaussian_laplacian.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/gaussian_laplacian.cc.o -MF CMakeFiles/ost_img_alg.dir/gaussian_laplacian.cc.o.d -o CMakeFiles/ost_img_alg.dir/gaussian_laplacian.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/gaussian_laplacian.cc -[ 19%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/highest_peak_search_3d.cc.o In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -7180,19 +7161,34 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 19%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/highest_peak_search_3d.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/highest_peak_search_3d.cc.o -MF CMakeFiles/ost_img_alg.dir/highest_peak_search_3d.cc.o.d -o CMakeFiles/ost_img_alg.dir/highest_peak_search_3d.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/highest_peak_search_3d.cc [ 19%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/histogram.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/histogram.cc.o -MF CMakeFiles/ost_img_alg.dir/histogram.cc.o.d -o CMakeFiles/ost_img_alg.dir/histogram.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/histogram.cc [ 19%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/line_iterator.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/line_iterator.cc.o -MF CMakeFiles/ost_img_alg.dir/line_iterator.cc.o.d -o CMakeFiles/ost_img_alg.dir/line_iterator.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/line_iterator.cc +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/openstructure-2.3.1/modules/base/pymod/export_units.cc:25: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ [ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/local_sigma_threshold.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/local_sigma_threshold.cc.o -MF CMakeFiles/ost_img_alg.dir/local_sigma_threshold.cc.o.d -o CMakeFiles/ost_img_alg.dir/local_sigma_threshold.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/local_sigma_threshold.cc -[ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/mask_image.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/mask_image.cc.o -MF CMakeFiles/ost_img_alg.dir/mask_image.cc.o.d -o CMakeFiles/ost_img_alg.dir/mask_image.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/mask_image.cc -[ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/normalizer.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/normalizer.cc.o -MF CMakeFiles/ost_img_alg.dir/normalizer.cc.o.d -o CMakeFiles/ost_img_alg.dir/normalizer.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/normalizer.cc -[ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/normalizer_factory.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/normalizer_factory.cc.o -MF CMakeFiles/ost_img_alg.dir/normalizer_factory.cc.o.d -o CMakeFiles/ost_img_alg.dir/normalizer_factory.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/normalizer_factory.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -7219,6 +7215,9 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 20%] Linking CXX shared library ../../../../stage/lib/libost_mol.so +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_mol.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libost_mol.so.2.3 -o ../../../../stage/lib/libost_mol.so.2.3.1 CMakeFiles/ost_mol.dir/atom_base.cc.o CMakeFiles/ost_mol.dir/atom_handle.cc.o CMakeFiles/ost_mol.dir/atom_view.cc.o CMakeFiles/ost_mol.dir/bond_handle.cc.o CMakeFiles/ost_mol.dir/chain_base.cc.o CMakeFiles/ost_mol.dir/chain_handle.cc.o CMakeFiles/ost_mol.dir/chain_view.cc.o CMakeFiles/ost_mol.dir/chain_type.cc.o CMakeFiles/ost_mol.dir/coord_frame.cc.o CMakeFiles/ost_mol.dir/coord_group.cc.o CMakeFiles/ost_mol.dir/editor_base.cc.o CMakeFiles/ost_mol.dir/entity_base.cc.o CMakeFiles/ost_mol.dir/entity_handle.cc.o CMakeFiles/ost_mol.dir/entity_observer.cc.o CMakeFiles/ost_mol.dir/entity_property_mapper.cc.o CMakeFiles/ost_mol.dir/entity_view.cc.o CMakeFiles/ost_mol.dir/entity_visitor.cc.o CMakeFiles/ost_mol.dir/ics_editor.cc.o CMakeFiles/ost_mol.dir/not_connected_error.cc.o CMakeFiles/ost_mol.dir/property_id.cc.o CMakeFiles/ost_mol.dir/query.cc.o CMakeFiles/ost_mol.dir/query_error.cc.o CMakeFiles/ost_mol.dir/query_state.cc.o CMakeFiles/ost_mol.dir/residue_base.cc.o CMakeFiles/ost_mol.dir/residue_handle.cc.o CMakeFiles/ost_mol.dir/residue_view.cc.o CMakeFiles/ost_mol.dir/surface_builder.cc.o CMakeFiles/ost_mol.dir/surface_handle.cc.o CMakeFiles/ost_mol.dir/transfer_connectivity.cc.o CMakeFiles/ost_mol.dir/torsion_handle.cc.o CMakeFiles/ost_mol.dir/query_view_wrapper.cc.o CMakeFiles/ost_mol.dir/view_op.cc.o CMakeFiles/ost_mol.dir/coord_source.cc.o CMakeFiles/ost_mol.dir/in_mem_coord_source.cc.o CMakeFiles/ost_mol.dir/bounding_box.cc.o CMakeFiles/ost_mol.dir/xcs_editor.cc.o CMakeFiles/ost_mol.dir/impl/atom_impl.cc.o CMakeFiles/ost_mol.dir/impl/chain_impl.cc.o CMakeFiles/ost_mol.dir/impl/connector_impl.cc.o CMakeFiles/ost_mol.dir/impl/dihedral.cc.o CMakeFiles/ost_mol.dir/impl/entity_impl.cc.o CMakeFiles/ost_mol.dir/impl/fragment_impl.cc.o CMakeFiles/ost_mol.dir/impl/query_ast.cc.o CMakeFiles/ost_mol.dir/impl/query_impl.cc.o CMakeFiles/ost_mol.dir/impl/residue_impl.cc.o CMakeFiles/ost_mol.dir/impl/surface_impl.cc.o CMakeFiles/ost_mol.dir/impl/torsion_impl.cc.o CMakeFiles/ost_mol.dir/impl/atom_prop.cc.o -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib: ../../../../stage/lib/libost_info.so.2.3.1 ../../../../stage/lib/libost_base.so.2.3.1 ../../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -7244,6 +7243,8 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/mask_image.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/mask_image.cc.o -MF CMakeFiles/ost_img_alg.dir/mask_image.cc.o.d -o CMakeFiles/ost_img_alg.dir/mask_image.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/mask_image.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -7269,25 +7270,22 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E cmake_symlink_library ../../../../stage/lib/libost_mol.so.2.3.1 ../../../../stage/lib/libost_mol.so.2.3 ../../../../stage/lib/libost_mol.so In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/stat.hh:30, - from /build/openstructure-2.3.1/modules/img/alg/src/highest_peak_search_3d.cc:4: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/extent.hh:34, + from /build/openstructure-2.3.1/modules/img/alg/src/line_iterator.hh:29, + from /build/openstructure-2.3.1/modules/img/alg/src/line_iterator.cc:25: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/ostream:38, - from /usr/include/c++/12/iostream:39, - from /build/openstructure-2.3.1/modules/img/alg/src/highest_peak_search_3d.cc:1: + from /usr/include/c++/12/stdexcept:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/extent.hh:30: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -7297,8 +7295,18 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/norm_linear.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/norm_linear.cc.o -MF CMakeFiles/ost_img_alg.dir/norm_linear.cc.o.d -o CMakeFiles/ost_img_alg.dir/norm_linear.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/norm_linear.cc +make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[ 20%] Built target ost_mol +make -f modules/seq/base/src/CMakeFiles/ost_seq.dir/build.make modules/seq/base/src/CMakeFiles/ost_seq.dir/depend +make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/seq/base/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src/CMakeFiles/ost_seq.dir/DependInfo.cmake --color= +make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +make -f modules/seq/base/src/CMakeFiles/ost_seq.dir/build.make modules/seq/base/src/CMakeFiles/ost_seq.dir/build +make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[ 20%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/impl/sequence_impl.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/c++ -DOST_MODULE_OST_SEQ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/base/src/CMakeFiles/ost_seq.dir/impl/sequence_impl.cc.o -MF CMakeFiles/ost_seq.dir/impl/sequence_impl.cc.o.d -o CMakeFiles/ost_seq.dir/impl/sequence_impl.cc.o -c /build/openstructure-2.3.1/modules/seq/base/src/impl/sequence_impl.cc +[ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/normalizer.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/normalizer.cc.o -MF CMakeFiles/ost_img_alg.dir/normalizer.cc.o.d -o CMakeFiles/ost_img_alg.dir/normalizer.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/normalizer.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -7306,15 +7314,15 @@ from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, - from /build/openstructure-2.3.1/modules/img/alg/src/stat.hh:30, - from /build/openstructure-2.3.1/modules/img/alg/src/histogram.cc:27: + from /build/openstructure-2.3.1/modules/img/alg/src/gaussian_laplacian.hh:28, + from /build/openstructure-2.3.1/modules/img/alg/src/gaussian_laplacian.cc:27: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/12/string:45, - from /usr/include/c++/12/stdexcept:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, - from /build/openstructure-2.3.1/modules/img/alg/src/histogram.cc:25: +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/bits/specfun.h:45, + from /usr/include/c++/12/cmath:1935, + from /build/openstructure-2.3.1/modules/img/alg/src/gaussian_laplacian.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -7324,6 +7332,8 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/normalizer_factory.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/normalizer_factory.cc.o -MF CMakeFiles/ost_img_alg.dir/normalizer_factory.cc.o.d -o CMakeFiles/ost_img_alg.dir/normalizer_factory.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/normalizer_factory.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -7331,15 +7341,18 @@ from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, - from /build/openstructure-2.3.1/modules/img/alg/src/gaussian_laplacian.hh:28, - from /build/openstructure-2.3.1/modules/img/alg/src/gaussian_laplacian.cc:27: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/stat.hh:30, + from /build/openstructure-2.3.1/modules/img/alg/src/highest_peak_search_3d.cc:4: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/specfun.h:45, - from /usr/include/c++/12/cmath:1935, - from /build/openstructure-2.3.1/modules/img/alg/src/gaussian_laplacian.cc:25: +In file included from /usr/include/c++/12/string:45, + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/ostream:38, + from /usr/include/c++/12/iostream:39, + from /build/openstructure-2.3.1/modules/img/alg/src/highest_peak_search_3d.cc:1: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -7354,16 +7367,17 @@ from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/extent.hh:34, - from /build/openstructure-2.3.1/modules/img/alg/src/line_iterator.hh:29, - from /build/openstructure-2.3.1/modules/img/alg/src/line_iterator.cc:25: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, + from /build/openstructure-2.3.1/modules/img/alg/src/stat.hh:30, + from /build/openstructure-2.3.1/modules/img/alg/src/histogram.cc:27: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/extent.hh:30: + from /build/openstructure-2.3.1/modules/img/alg/src/histogram.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -7373,6 +7387,10 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/norm_linear.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/norm_linear.cc.o -MF CMakeFiles/ost_img_alg.dir/norm_linear.cc.o.d -o CMakeFiles/ost_img_alg.dir/norm_linear.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/norm_linear.cc +[ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/norm_log.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/norm_log.cc.o -MF CMakeFiles/ost_img_alg.dir/norm_log.cc.o.d -o CMakeFiles/ost_img_alg.dir/norm_log.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/norm_log.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -7402,15 +7420,19 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/norm_od.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/norm_od.cc.o -MF CMakeFiles/ost_img_alg.dir/norm_od.cc.o.d -o CMakeFiles/ost_img_alg.dir/norm_od.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/norm_od.cc +[ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/power_spectrum.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/power_spectrum.cc.o -MF CMakeFiles/ost_img_alg.dir/power_spectrum.cc.o.d -o CMakeFiles/ost_img_alg.dir/power_spectrum.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/power_spectrum.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, - from /build/openstructure-2.3.1/modules/img/alg/src/normalizer.hh:28, - from /build/openstructure-2.3.1/modules/img/alg/src/normalizer.cc:26: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, + from /build/openstructure-2.3.1/modules/img/alg/src/mask_image.cc:25: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -7418,8 +7440,7 @@ from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/module_config.hh:23, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:31: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:30: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -7429,18 +7450,21 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 20%] Linking CXX shared library ../../../../stage/lib/libost_mol.so -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_mol.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libost_mol.so.2.3 -o ../../../../stage/lib/libost_mol.so.2.3.1 CMakeFiles/ost_mol.dir/atom_base.cc.o CMakeFiles/ost_mol.dir/atom_handle.cc.o CMakeFiles/ost_mol.dir/atom_view.cc.o CMakeFiles/ost_mol.dir/bond_handle.cc.o CMakeFiles/ost_mol.dir/chain_base.cc.o CMakeFiles/ost_mol.dir/chain_handle.cc.o CMakeFiles/ost_mol.dir/chain_view.cc.o CMakeFiles/ost_mol.dir/chain_type.cc.o CMakeFiles/ost_mol.dir/coord_frame.cc.o CMakeFiles/ost_mol.dir/coord_group.cc.o CMakeFiles/ost_mol.dir/editor_base.cc.o CMakeFiles/ost_mol.dir/entity_base.cc.o CMakeFiles/ost_mol.dir/entity_handle.cc.o CMakeFiles/ost_mol.dir/entity_observer.cc.o CMakeFiles/ost_mol.dir/entity_property_mapper.cc.o CMakeFiles/ost_mol.dir/entity_view.cc.o CMakeFiles/ost_mol.dir/entity_visitor.cc.o CMakeFiles/ost_mol.dir/ics_editor.cc.o CMakeFiles/ost_mol.dir/not_connected_error.cc.o CMakeFiles/ost_mol.dir/property_id.cc.o CMakeFiles/ost_mol.dir/query.cc.o CMakeFiles/ost_mol.dir/query_error.cc.o CMakeFiles/ost_mol.dir/query_state.cc.o CMakeFiles/ost_mol.dir/residue_base.cc.o CMakeFiles/ost_mol.dir/residue_handle.cc.o CMakeFiles/ost_mol.dir/residue_view.cc.o CMakeFiles/ost_mol.dir/surface_builder.cc.o CMakeFiles/ost_mol.dir/surface_handle.cc.o CMakeFiles/ost_mol.dir/transfer_connectivity.cc.o CMakeFiles/ost_mol.dir/torsion_handle.cc.o CMakeFiles/ost_mol.dir/query_view_wrapper.cc.o CMakeFiles/ost_mol.dir/view_op.cc.o CMakeFiles/ost_mol.dir/coord_source.cc.o CMakeFiles/ost_mol.dir/in_mem_coord_source.cc.o CMakeFiles/ost_mol.dir/bounding_box.cc.o CMakeFiles/ost_mol.dir/xcs_editor.cc.o CMakeFiles/ost_mol.dir/impl/atom_impl.cc.o CMakeFiles/ost_mol.dir/impl/chain_impl.cc.o CMakeFiles/ost_mol.dir/impl/connector_impl.cc.o CMakeFiles/ost_mol.dir/impl/dihedral.cc.o CMakeFiles/ost_mol.dir/impl/entity_impl.cc.o CMakeFiles/ost_mol.dir/impl/fragment_impl.cc.o CMakeFiles/ost_mol.dir/impl/query_ast.cc.o CMakeFiles/ost_mol.dir/impl/query_impl.cc.o CMakeFiles/ost_mol.dir/impl/residue_impl.cc.o CMakeFiles/ost_mol.dir/impl/surface_impl.cc.o CMakeFiles/ost_mol.dir/impl/torsion_impl.cc.o CMakeFiles/ost_mol.dir/impl/atom_prop.cc.o -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib: ../../../../stage/lib/libost_info.so.2.3.1 ../../../../stage/lib/libost_base.so.2.3.1 ../../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 +[ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/randomize.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/randomize.cc.o -MF CMakeFiles/ost_img_alg.dir/randomize.cc.o.d -o CMakeFiles/ost_img_alg.dir/randomize.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/randomize.cc +[ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/smooth_mask_image.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/smooth_mask_image.cc.o -MF CMakeFiles/ost_img_alg.dir/smooth_mask_image.cc.o.d -o CMakeFiles/ost_img_alg.dir/smooth_mask_image.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/smooth_mask_image.cc +[ 21%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/stat.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/stat.cc.o -MF CMakeFiles/ost_img_alg.dir/stat.cc.o.d -o CMakeFiles/ost_img_alg.dir/stat.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/stat.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, - from /build/openstructure-2.3.1/modules/img/alg/src/mask_image.cc:25: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/stat_min_max.hh:30, + from /build/openstructure-2.3.1/modules/img/alg/src/normalizer_factory.cc:27: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -7448,7 +7472,8 @@ from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:30: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/module_config.hh:23, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:31: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -7458,10 +7483,6 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/norm_log.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/norm_log.cc.o -MF CMakeFiles/ost_img_alg.dir/norm_log.cc.o.d -o CMakeFiles/ost_img_alg.dir/norm_log.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/norm_log.cc -[ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/norm_od.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/norm_od.cc.o -MF CMakeFiles/ost_img_alg.dir/norm_od.cc.o.d -o CMakeFiles/ost_img_alg.dir/norm_od.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/norm_od.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -7469,8 +7490,8 @@ from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/stat_min_max.hh:30, - from /build/openstructure-2.3.1/modules/img/alg/src/normalizer_factory.cc:27: + from /build/openstructure-2.3.1/modules/img/alg/src/normalizer.hh:28, + from /build/openstructure-2.3.1/modules/img/alg/src/normalizer.cc:26: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -7489,10 +7510,37 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/power_spectrum.cc.o -[ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/randomize.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/power_spectrum.cc.o -MF CMakeFiles/ost_img_alg.dir/power_spectrum.cc.o.d -o CMakeFiles/ost_img_alg.dir/power_spectrum.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/power_spectrum.cc -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/randomize.cc.o -MF CMakeFiles/ost_img_alg.dir/randomize.cc.o.d -o CMakeFiles/ost_img_alg.dir/randomize.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/randomize.cc +[ 21%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/stat_min_max.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/stat_min_max.cc.o -MF CMakeFiles/ost_img_alg.dir/stat_min_max.cc.o.d -o CMakeFiles/ost_img_alg.dir/stat_min_max.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/stat_min_max.cc +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/info_group.hh:33, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/info.hh:32, + from /build/openstructure-2.3.1/modules/seq/base/src/impl/sequence_impl.cc:26: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/vector:60, + from /usr/include/boost/format.hpp:17, + from /build/openstructure-2.3.1/modules/seq/base/src/impl/sequence_impl.cc:23: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 21%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/alg_transform.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/alg_transform.cc.o -MF CMakeFiles/ost_img_alg.dir/alg_transform.cc.o.d -o CMakeFiles/ost_img_alg.dir/alg_transform.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/alg_transform.cc +[ 21%] Linking CXX shared module ../../../stage/lib/python3.11/dist-packages/ost/_ost_base.so +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_base.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -o ../../../stage/lib/python3.11/dist-packages/ost/_ost_base.so CMakeFiles/_ost_base.dir/wrap_base.cc.o CMakeFiles/_ost_base.dir/export_logger.cc.o CMakeFiles/_ost_base.dir/export_range.cc.o CMakeFiles/_ost_base.dir/export_units.cc.o -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib: ../../../stage/lib/libost_base.so.2.3.1 /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so ../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so +[ 21%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/alg_mirror.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/alg_mirror.cc.o -MF CMakeFiles/ost_img_alg.dir/alg_mirror.cc.o.d -o CMakeFiles/ost_img_alg.dir/alg_mirror.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/alg_mirror.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -7523,29 +7571,10 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/smooth_mask_image.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/smooth_mask_image.cc.o -MF CMakeFiles/ost_img_alg.dir/smooth_mask_image.cc.o.d -o CMakeFiles/ost_img_alg.dir/smooth_mask_image.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/smooth_mask_image.cc -[ 21%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/stat.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/stat.cc.o -MF CMakeFiles/ost_img_alg.dir/stat.cc.o.d -o CMakeFiles/ost_img_alg.dir/stat.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/stat.cc -[ 21%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/stat_min_max.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/stat_min_max.cc.o -MF CMakeFiles/ost_img_alg.dir/stat_min_max.cc.o.d -o CMakeFiles/ost_img_alg.dir/stat_min_max.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/stat_min_max.cc -[ 21%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/alg_transform.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/alg_transform.cc.o -MF CMakeFiles/ost_img_alg.dir/alg_transform.cc.o.d -o CMakeFiles/ost_img_alg.dir/alg_transform.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/alg_transform.cc -[ 21%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/alg_mirror.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/alg_mirror.cc.o -MF CMakeFiles/ost_img_alg.dir/alg_mirror.cc.o.d -o CMakeFiles/ost_img_alg.dir/alg_mirror.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/alg_mirror.cc -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E cmake_symlink_library ../../../../stage/lib/libost_mol.so.2.3.1 ../../../../stage/lib/libost_mol.so.2.3 ../../../../stage/lib/libost_mol.so [ 21%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/alg_shift.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/alg_shift.cc.o -MF CMakeFiles/ost_img_alg.dir/alg_shift.cc.o.d -o CMakeFiles/ost_img_alg.dir/alg_shift.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/alg_shift.cc -make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 21%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/threshold.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/threshold.cc.o -MF CMakeFiles/ost_img_alg.dir/threshold.cc.o.d -o CMakeFiles/ost_img_alg.dir/threshold.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/threshold.cc -[ 21%] Built target ost_mol -[ 21%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/discrete_shrink.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/discrete_shrink.cc.o -MF CMakeFiles/ost_img_alg.dir/discrete_shrink.cc.o.d -o CMakeFiles/ost_img_alg.dir/discrete_shrink.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/discrete_shrink.cc -[ 21%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/transformation_base.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/transformation_base.cc.o -MF CMakeFiles/ost_img_alg.dir/transformation_base.cc.o.d -o CMakeFiles/ost_img_alg.dir/transformation_base.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/transformation_base.cc -[ 21%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/transformations.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/transformations.cc.o -MF CMakeFiles/ost_img_alg.dir/transformations.cc.o.d -o CMakeFiles/ost_img_alg.dir/transformations.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/transformations.cc +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/base/pymod/settings.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/./settings.pyc\",\"settings.py\",doraise=True)" +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/base/pymod/stutil.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/./stutil.pyc\",\"stutil.py\",doraise=True)" In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -7555,8 +7584,8 @@ from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/normalizer_impl.hh:32, - from /build/openstructure-2.3.1/modules/img/alg/src/norm_od.hh:28, - from /build/openstructure-2.3.1/modules/img/alg/src/norm_od.cc:24: + from /build/openstructure-2.3.1/modules/img/alg/src/norm_log.hh:28, + from /build/openstructure-2.3.1/modules/img/alg/src/norm_log.cc:25: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -7576,8 +7605,8 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 21%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/fractional_shift.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/fractional_shift.cc.o -MF CMakeFiles/ost_img_alg.dir/fractional_shift.cc.o.d -o CMakeFiles/ost_img_alg.dir/fractional_shift.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/fractional_shift.cc +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/base/pymod/table.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/./table.pyc\",\"table.py\",doraise=True)" +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/base/pymod/table_selector.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/./table_selector.pyc\",\"table_selector.py\",doraise=True)" In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -7587,8 +7616,8 @@ from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/normalizer_impl.hh:32, - from /build/openstructure-2.3.1/modules/img/alg/src/norm_log.hh:28, - from /build/openstructure-2.3.1/modules/img/alg/src/norm_log.cc:25: + from /build/openstructure-2.3.1/modules/img/alg/src/norm_od.hh:28, + from /build/openstructure-2.3.1/modules/img/alg/src/norm_od.cc:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -7608,6 +7637,22 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/base/pymod/xmlrunner.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/./xmlrunner.pyc\",\"xmlrunner.py\",doraise=True)" +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/base/pymod/testutils.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/./testutils.pyc\",\"testutils.py\",doraise=True)" +make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[ 21%] Built target _ost_base +make -f modules/info/pymod/CMakeFiles/_ost_info.dir/build.make modules/info/pymod/CMakeFiles/_ost_info.dir/depend +make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/info/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/pymod/CMakeFiles/_ost_info.dir/DependInfo.cmake --color= +make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +make -f modules/info/pymod/CMakeFiles/_ost_info.dir/build.make modules/info/pymod/CMakeFiles/_ost_info.dir/build +make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[ 21%] Building CXX object modules/info/pymod/CMakeFiles/_ost_info.dir/wrap_info.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_info_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/info/pymod/CMakeFiles/_ost_info.dir/wrap_info.cc.o -MF CMakeFiles/_ost_info.dir/wrap_info.cc.o.d -o CMakeFiles/_ost_info.dir/wrap_info.cc.o -c /build/openstructure-2.3.1/modules/info/pymod/wrap_info.cc +[ 21%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/threshold.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/threshold.cc.o -MF CMakeFiles/ost_img_alg.dir/threshold.cc.o.d -o CMakeFiles/ost_img_alg.dir/threshold.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/threshold.cc +[ 21%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/discrete_shrink.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/discrete_shrink.cc.o -MF CMakeFiles/ost_img_alg.dir/discrete_shrink.cc.o.d -o CMakeFiles/ost_img_alg.dir/discrete_shrink.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/discrete_shrink.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -7687,21 +7732,26 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 21%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/polar.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/polar.cc.o -MF CMakeFiles/ost_img_alg.dir/polar.cc.o.d -o CMakeFiles/ost_img_alg.dir/polar.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/polar.cc +[ 21%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/transformation_base.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/transformation_base.cc.o -MF CMakeFiles/ost_img_alg.dir/transformation_base.cc.o.d -o CMakeFiles/ost_img_alg.dir/transformation_base.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/transformation_base.cc +[ 21%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/transformations.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/transformations.cc.o -MF CMakeFiles/ost_img_alg.dir/transformations.cc.o.d -o CMakeFiles/ost_img_alg.dir/transformations.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/transformations.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/openstructure-2.3.1/modules/img/alg/src/transformation_base.hh:32, - from /build/openstructure-2.3.1/modules/img/alg/src/transformation_base.cc:25: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, + from /build/openstructure-2.3.1/modules/img/alg/src/stat_min_max.hh:30, + from /build/openstructure-2.3.1/modules/img/alg/src/stat_min_max.cc:32: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, - from /build/openstructure-2.3.1/modules/img/alg/src/transformation_base.hh:30: + from /build/openstructure-2.3.1/modules/img/alg/src/stat_min_max.cc:26: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -7715,18 +7765,20 @@ from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, - from /build/openstructure-2.3.1/modules/img/alg/src/stat.hh:30, - from /build/openstructure-2.3.1/modules/img/alg/src/stat.cc:32: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, + from /build/openstructure-2.3.1/modules/img/alg/src/alg_mirror.hh:24, + from /build/openstructure-2.3.1/modules/img/alg/src/alg_mirror.cc:21: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, - from /build/openstructure-2.3.1/modules/img/alg/src/stat.cc:26: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:30: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -7736,20 +7788,24 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 21%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/fractional_shift.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/fractional_shift.cc.o -MF CMakeFiles/ost_img_alg.dir/fractional_shift.cc.o.d -o CMakeFiles/ost_img_alg.dir/fractional_shift.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/fractional_shift.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/openstructure-2.3.1/modules/img/alg/src/transformation_base.hh:32, - from /build/openstructure-2.3.1/modules/img/alg/src/transformations.hh:31, - from /build/openstructure-2.3.1/modules/img/alg/src/transformations.cc:29: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, + from /build/openstructure-2.3.1/modules/img/alg/src/stat.hh:30, + from /build/openstructure-2.3.1/modules/img/alg/src/stat.cc:32: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/12/string:45, - from /usr/include/c++/12/stdexcept:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, - from /build/openstructure-2.3.1/modules/img/alg/src/transformations.cc:27: +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/bits/specfun.h:45, + from /usr/include/c++/12/cmath:1935, + from /build/openstructure-2.3.1/modules/img/alg/src/stat.cc:26: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -7767,8 +7823,8 @@ from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, - from /build/openstructure-2.3.1/modules/img/alg/src/alg_mirror.hh:24, - from /build/openstructure-2.3.1/modules/img/alg/src/alg_mirror.cc:21: + from /build/openstructure-2.3.1/modules/img/alg/src/alg_transform.hh:24, + from /build/openstructure-2.3.1/modules/img/alg/src/alg_transform.cc:21: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -7786,21 +7842,28 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 21%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/polar.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/polar.cc.o -MF CMakeFiles/ost_img_alg.dir/polar.cc.o.d -o CMakeFiles/ost_img_alg.dir/polar.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/polar.cc +[ 23%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/rscrosscorr.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/rscrosscorr.cc.o -MF CMakeFiles/ost_img_alg.dir/rscrosscorr.cc.o.d -o CMakeFiles/ost_img_alg.dir/rscrosscorr.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/rscrosscorr.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, - from /build/openstructure-2.3.1/modules/img/alg/src/discrete_shrink.hh:24, - from /build/openstructure-2.3.1/modules/img/alg/src/discrete_shrink.cc:24: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, + from /build/openstructure-2.3.1/modules/img/alg/src/alg_shift.hh:24, + from /build/openstructure-2.3.1/modules/img/alg/src/alg_shift.cc:21: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/12/string:45, - from /usr/include/c++/12/stdexcept:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, - from /build/openstructure-2.3.1/modules/img/alg/src/discrete_shrink.cc:21: +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/bits/specfun.h:45, + from /usr/include/c++/12/cmath:1935, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:30: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -7810,8 +7873,6 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 23%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/rscrosscorr.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/rscrosscorr.cc.o -MF CMakeFiles/ost_img_alg.dir/rscrosscorr.cc.o.d -o CMakeFiles/ost_img_alg.dir/rscrosscorr.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/rscrosscorr.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -7843,20 +7904,15 @@ from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, - from /build/openstructure-2.3.1/modules/img/alg/src/alg_shift.hh:24, - from /build/openstructure-2.3.1/modules/img/alg/src/alg_shift.cc:21: + from /build/openstructure-2.3.1/modules/img/alg/src/transformation_base.hh:32, + from /build/openstructure-2.3.1/modules/img/alg/src/transformation_base.cc:25: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:30: + from /build/openstructure-2.3.1/modules/img/alg/src/transformation_base.hh:30: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -7866,22 +7922,25 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 23%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/line_average.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/line_average.cc.o -MF CMakeFiles/ost_img_alg.dir/line_average.cc.o.d -o CMakeFiles/ost_img_alg.dir/line_average.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/line_average.cc +[ 23%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/impl/sequence_list_impl.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/c++ -DOST_MODULE_OST_SEQ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/base/src/CMakeFiles/ost_seq.dir/impl/sequence_list_impl.cc.o -MF CMakeFiles/ost_seq.dir/impl/sequence_list_impl.cc.o.d -o CMakeFiles/ost_seq.dir/impl/sequence_list_impl.cc.o -c /build/openstructure-2.3.1/modules/seq/base/src/impl/sequence_list_impl.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, - from /build/openstructure-2.3.1/modules/img/alg/src/stat_min_max.hh:30, - from /build/openstructure-2.3.1/modules/img/alg/src/stat_min_max.cc:32: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, + from /build/openstructure-2.3.1/modules/img/alg/src/discrete_shrink.hh:24, + from /build/openstructure-2.3.1/modules/img/alg/src/discrete_shrink.cc:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/specfun.h:45, - from /usr/include/c++/12/cmath:1935, - from /build/openstructure-2.3.1/modules/img/alg/src/stat_min_max.cc:26: +In file included from /usr/include/c++/12/string:45, + from /usr/include/c++/12/stdexcept:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, + from /build/openstructure-2.3.1/modules/img/alg/src/discrete_shrink.cc:21: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -7891,26 +7950,20 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 23%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/line_average.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/line_average.cc.o -MF CMakeFiles/ost_img_alg.dir/line_average.cc.o.d -o CMakeFiles/ost_img_alg.dir/line_average.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/line_average.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, - from /build/openstructure-2.3.1/modules/img/alg/src/alg_transform.hh:24, - from /build/openstructure-2.3.1/modules/img/alg/src/alg_transform.cc:21: + from /build/openstructure-2.3.1/modules/img/alg/src/transformation_base.hh:32, + from /build/openstructure-2.3.1/modules/img/alg/src/transformations.hh:31, + from /build/openstructure-2.3.1/modules/img/alg/src/transformations.cc:29: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/specfun.h:45, - from /usr/include/c++/12/cmath:1935, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:30: +In file included from /usr/include/c++/12/string:45, + from /usr/include/c++/12/stdexcept:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, + from /build/openstructure-2.3.1/modules/img/alg/src/transformations.cc:27: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -7920,18 +7973,18 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -make -f modules/seq/base/src/CMakeFiles/ost_seq.dir/build.make modules/seq/base/src/CMakeFiles/ost_seq.dir/depend -make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/seq/base/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src/CMakeFiles/ost_seq.dir/DependInfo.cmake --color= -make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/seq/base/src/CMakeFiles/ost_seq.dir/build.make modules/seq/base/src/CMakeFiles/ost_seq.dir/build -make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 23%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/impl/sequence_impl.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/c++ -DOST_MODULE_OST_SEQ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/base/src/CMakeFiles/ost_seq.dir/impl/sequence_impl.cc.o -MF CMakeFiles/ost_seq.dir/impl/sequence_impl.cc.o.d -o CMakeFiles/ost_seq.dir/impl/sequence_impl.cc.o -c /build/openstructure-2.3.1/modules/seq/base/src/impl/sequence_impl.cc -[ 23%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/impl/sequence_list_impl.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/c++ -DOST_MODULE_OST_SEQ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/base/src/CMakeFiles/ost_seq.dir/impl/sequence_list_impl.cc.o -MF CMakeFiles/ost_seq.dir/impl/sequence_list_impl.cc.o.d -o CMakeFiles/ost_seq.dir/impl/sequence_list_impl.cc.o -c /build/openstructure-2.3.1/modules/seq/base/src/impl/sequence_list_impl.cc [ 23%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/sequence_handle.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/c++ -DOST_MODULE_OST_SEQ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/base/src/CMakeFiles/ost_seq.dir/sequence_handle.cc.o -MF CMakeFiles/ost_seq.dir/sequence_handle.cc.o.d -o CMakeFiles/ost_seq.dir/sequence_handle.cc.o -c /build/openstructure-2.3.1/modules/seq/base/src/sequence_handle.cc +[ 23%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/aligned_region.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/c++ -DOST_MODULE_OST_SEQ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/base/src/CMakeFiles/ost_seq.dir/aligned_region.cc.o -MF CMakeFiles/ost_seq.dir/aligned_region.cc.o.d -o CMakeFiles/ost_seq.dir/aligned_region.cc.o -c /build/openstructure-2.3.1/modules/seq/base/src/aligned_region.cc +[ 23%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/aligned_column.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/c++ -DOST_MODULE_OST_SEQ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/base/src/CMakeFiles/ost_seq.dir/aligned_column.cc.o -MF CMakeFiles/ost_seq.dir/aligned_column.cc.o.d -o CMakeFiles/ost_seq.dir/aligned_column.cc.o -c /build/openstructure-2.3.1/modules/seq/base/src/aligned_column.cc +[ 23%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/sequence_list.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/c++ -DOST_MODULE_OST_SEQ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/base/src/CMakeFiles/ost_seq.dir/sequence_list.cc.o -MF CMakeFiles/ost_seq.dir/sequence_list.cc.o.d -o CMakeFiles/ost_seq.dir/sequence_list.cc.o -c /build/openstructure-2.3.1/modules/seq/base/src/sequence_list.cc +[ 23%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/alignment_handle.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/c++ -DOST_MODULE_OST_SEQ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/base/src/CMakeFiles/ost_seq.dir/alignment_handle.cc.o -MF CMakeFiles/ost_seq.dir/alignment_handle.cc.o.d -o CMakeFiles/ost_seq.dir/alignment_handle.cc.o -c /build/openstructure-2.3.1/modules/seq/base/src/alignment_handle.cc +[ 23%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/sequence_op.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/c++ -DOST_MODULE_OST_SEQ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/base/src/CMakeFiles/ost_seq.dir/sequence_op.cc.o -MF CMakeFiles/ost_seq.dir/sequence_op.cc.o.d -o CMakeFiles/ost_seq.dir/sequence_op.cc.o -c /build/openstructure-2.3.1/modules/seq/base/src/sequence_op.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -7958,12 +8011,6 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 23%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/aligned_region.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/c++ -DOST_MODULE_OST_SEQ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/base/src/CMakeFiles/ost_seq.dir/aligned_region.cc.o -MF CMakeFiles/ost_seq.dir/aligned_region.cc.o.d -o CMakeFiles/ost_seq.dir/aligned_region.cc.o -c /build/openstructure-2.3.1/modules/seq/base/src/aligned_region.cc -[ 23%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/aligned_column.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/c++ -DOST_MODULE_OST_SEQ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/base/src/CMakeFiles/ost_seq.dir/aligned_column.cc.o -MF CMakeFiles/ost_seq.dir/aligned_column.cc.o.d -o CMakeFiles/ost_seq.dir/aligned_column.cc.o -c /build/openstructure-2.3.1/modules/seq/base/src/aligned_column.cc -[ 23%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/sequence_list.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/c++ -DOST_MODULE_OST_SEQ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/base/src/CMakeFiles/ost_seq.dir/sequence_list.cc.o -MF CMakeFiles/ost_seq.dir/sequence_list.cc.o.d -o CMakeFiles/ost_seq.dir/sequence_list.cc.o -c /build/openstructure-2.3.1/modules/seq/base/src/sequence_list.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -7990,14 +8037,8 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 23%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/alignment_handle.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/c++ -DOST_MODULE_OST_SEQ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/base/src/CMakeFiles/ost_seq.dir/alignment_handle.cc.o -MF CMakeFiles/ost_seq.dir/alignment_handle.cc.o.d -o CMakeFiles/ost_seq.dir/alignment_handle.cc.o -c /build/openstructure-2.3.1/modules/seq/base/src/alignment_handle.cc -[ 23%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/sequence_op.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/c++ -DOST_MODULE_OST_SEQ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/base/src/CMakeFiles/ost_seq.dir/sequence_op.cc.o -MF CMakeFiles/ost_seq.dir/sequence_op.cc.o.d -o CMakeFiles/ost_seq.dir/sequence_op.cc.o -c /build/openstructure-2.3.1/modules/seq/base/src/sequence_op.cc [ 23%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/views_from_sequences.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/c++ -DOST_MODULE_OST_SEQ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/base/src/CMakeFiles/ost_seq.dir/views_from_sequences.cc.o -MF CMakeFiles/ost_seq.dir/views_from_sequences.cc.o.d -o CMakeFiles/ost_seq.dir/views_from_sequences.cc.o -c /build/openstructure-2.3.1/modules/seq/base/src/views_from_sequences.cc -[ 23%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/profile_handle.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/c++ -DOST_MODULE_OST_SEQ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/base/src/CMakeFiles/ost_seq.dir/profile_handle.cc.o -MF CMakeFiles/ost_seq.dir/profile_handle.cc.o.d -o CMakeFiles/ost_seq.dir/profile_handle.cc.o -c /build/openstructure-2.3.1/modules/seq/base/src/profile_handle.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -8024,6 +8065,26 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/openstructure-2.3.1/modules/info/pymod/wrap_info.cc:27: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -8051,31 +8112,6 @@ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, - from /build/openstructure-2.3.1/modules/seq/base/src/sequence_handle.cc:25: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/12/string:45, - from /usr/include/c++/12/stdexcept:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/invalid_handle.hh:22, - from /build/openstructure-2.3.1/modules/seq/base/src/sequence_handle.cc:24: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/extent.hh:34, @@ -8097,19 +8133,30 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 23%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/profile_handle.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/c++ -DOST_MODULE_OST_SEQ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/base/src/CMakeFiles/ost_seq.dir/profile_handle.cc.o -MF CMakeFiles/ost_seq.dir/profile_handle.cc.o.d -o CMakeFiles/ost_seq.dir/profile_handle.cc.o -c /build/openstructure-2.3.1/modules/seq/base/src/profile_handle.cc +In file included from /usr/include/boost/bind.hpp:30, + from /build/openstructure-2.3.1/modules/seq/base/src/sequence_op.cc:22: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/info_group.hh:33, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/info.hh:32, - from /build/openstructure-2.3.1/modules/seq/base/src/impl/sequence_impl.cc:26: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_column.hh:26, + from /build/openstructure-2.3.1/modules/seq/base/src/aligned_column.cc:19: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, - from /usr/include/boost/format.hpp:17, - from /build/openstructure-2.3.1/modules/seq/base/src/impl/sequence_impl.cc:23: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_impl_fw.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:27: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -8119,11 +8166,6 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /usr/include/boost/bind.hpp:30, - from /build/openstructure-2.3.1/modules/seq/base/src/sequence_op.cc:22: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -8151,7 +8193,40 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, + from /build/openstructure-2.3.1/modules/seq/base/src/sequence_handle.cc:25: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/12/string:45, + from /usr/include/c++/12/stdexcept:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/invalid_handle.hh:22, + from /build/openstructure-2.3.1/modules/seq/base/src/sequence_handle.cc:24: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 32 | : public std::iterator{ + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ @@ -8169,6 +8244,33 @@ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/info_group.hh:33, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/info.hh:32, + from /build/openstructure-2.3.1/modules/info/pymod/wrap_info.cc:29: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/bits/specfun.h:45, + from /usr/include/c++/12/cmath:1935, + from /usr/include/c++/12/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, @@ -8210,20 +8312,17 @@ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_column.hh:26, - from /build/openstructure-2.3.1/modules/seq/base/src/aligned_column.cc:19: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/info_group.hh:33, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/info.hh:32, + from /build/openstructure-2.3.1/modules/seq/base/src/sequence_list.cc:27: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/vector:60, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_impl_fw.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:27: +In file included from /usr/include/c++/12/string:45, + from /usr/include/c++/12/stdexcept:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/invalid_handle.hh:22, + from /build/openstructure-2.3.1/modules/seq/base/src/sequence_list.cc:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -8233,14 +8332,6 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 32 | : public std::iterator{ - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -8268,6 +8359,14 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, + from /build/openstructure-2.3.1/modules/seq/base/src/sequence_list.cc:31: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 32 | : public std::iterator{ + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -8303,56 +8402,6 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/info_group.hh:33, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/info.hh:32, - from /build/openstructure-2.3.1/modules/seq/base/src/sequence_list.cc:27: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/12/string:45, - from /usr/include/c++/12/stdexcept:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/invalid_handle.hh:22, - from /build/openstructure-2.3.1/modules/seq/base/src/sequence_list.cc:24: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -[ 23%] Linking CXX shared module ../../../stage/lib/python3.11/dist-packages/ost/_ost_base.so -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_base.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -o ../../../stage/lib/python3.11/dist-packages/ost/_ost_base.so CMakeFiles/_ost_base.dir/wrap_base.cc.o CMakeFiles/_ost_base.dir/export_logger.cc.o CMakeFiles/_ost_base.dir/export_range.cc.o CMakeFiles/_ost_base.dir/export_units.cc.o -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib: ../../../stage/lib/libost_base.so.2.3.1 /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so ../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/base/pymod/settings.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/./settings.pyc\",\"settings.py\",doraise=True)" -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/base/pymod/stutil.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/./stutil.pyc\",\"stutil.py\",doraise=True)" -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/base/pymod/table.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/./table.pyc\",\"table.py\",doraise=True)" -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/base/pymod/table_selector.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/./table_selector.pyc\",\"table_selector.py\",doraise=True)" -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/base/pymod/xmlrunner.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/./xmlrunner.pyc\",\"xmlrunner.py\",doraise=True)" -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, - from /build/openstructure-2.3.1/modules/seq/base/src/sequence_list.cc:31: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 32 | : public std::iterator{ - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/base/pymod/testutils.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/./testutils.pyc\",\"testutils.py\",doraise=True)" -make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 23%] Built target _ost_base -make -f modules/info/pymod/CMakeFiles/_ost_info.dir/build.make modules/info/pymod/CMakeFiles/_ost_info.dir/depend -make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/info/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/pymod/CMakeFiles/_ost_info.dir/DependInfo.cmake --color= -make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/info/pymod/CMakeFiles/_ost_info.dir/build.make modules/info/pymod/CMakeFiles/_ost_info.dir/build -make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 23%] Building CXX object modules/info/pymod/CMakeFiles/_ost_info.dir/wrap_info.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_info_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/info/pymod/CMakeFiles/_ost_info.dir/wrap_info.cc.o -MF CMakeFiles/_ost_info.dir/wrap_info.cc.o.d -o CMakeFiles/_ost_info.dir/wrap_info.cc.o -c /build/openstructure-2.3.1/modules/info/pymod/wrap_info.cc [ 23%] Linking CXX shared library ../../../../stage/lib/libost_img_alg.so cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_img_alg.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libost_img_alg.so.2.3 -o ../../../../stage/lib/libost_img_alg.so.2.3.1 CMakeFiles/ost_img_alg.dir/anisotropic.cc.o CMakeFiles/ost_img_alg.dir/auto_correlate.cc.o CMakeFiles/ost_img_alg.dir/convolute.cc.o CMakeFiles/ost_img_alg.dir/correlate.cc.o CMakeFiles/ost_img_alg.dir/cross_correlate.cc.o CMakeFiles/ost_img_alg.dir/density_slice.cc.o CMakeFiles/ost_img_alg.dir/dft.cc.o CMakeFiles/ost_img_alg.dir/fft.cc.o CMakeFiles/ost_img_alg.dir/fourier_filters.cc.o CMakeFiles/ost_img_alg.dir/gaussian.cc.o CMakeFiles/ost_img_alg.dir/gaussian_gradient_magnitude.cc.o CMakeFiles/ost_img_alg.dir/gaussian_laplacian.cc.o CMakeFiles/ost_img_alg.dir/highest_peak_search_3d.cc.o CMakeFiles/ost_img_alg.dir/histogram.cc.o CMakeFiles/ost_img_alg.dir/line_iterator.cc.o CMakeFiles/ost_img_alg.dir/local_sigma_threshold.cc.o CMakeFiles/ost_img_alg.dir/mask_image.cc.o CMakeFiles/ost_img_alg.dir/normalizer.cc.o CMakeFiles/ost_img_alg.dir/normalizer_factory.cc.o CMakeFiles/ost_img_alg.dir/norm_linear.cc.o CMakeFiles/ost_img_alg.dir/norm_log.cc.o CMakeFiles/ost_img_alg.dir/norm_od.cc.o CMakeFiles/ost_img_alg.dir/power_spectrum.cc.o CMakeFiles/ost_img_alg.dir/randomize.cc.o CMakeFiles/ost_img_alg.dir/smooth_mask_image.cc.o CMakeFiles/ost_img_alg.dir/stat.cc.o CMakeFiles/ost_img_alg.dir/stat_min_max.cc.o CMakeFiles/ost_img_alg.dir/alg_transform.cc.o CMakeFiles/ost_img_alg.dir/alg_mirror.cc.o CMakeFiles/ost_img_alg.dir/alg_shift.cc.o CMakeFiles/ost_img_alg.dir/threshold.cc.o CMakeFiles/ost_img_alg.dir/discrete_shrink.cc.o CMakeFiles/ost_img_alg.dir/transformation_base.cc.o CMakeFiles/ost_img_alg.dir/transformations.cc.o CMakeFiles/ost_img_alg.dir/fractional_shift.cc.o CMakeFiles/ost_img_alg.dir/polar.cc.o CMakeFiles/ost_img_alg.dir/rscrosscorr.cc.o CMakeFiles/ost_img_alg.dir/line_average.cc.o -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib: /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libfftw3f_threads.so ../../../../stage/lib/libost_img.so.2.3.1 ../../../../stage/lib/libost_info.so.2.3.1 ../../../../stage/lib/libost_base.so.2.3.1 ../../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 @@ -8366,104 +8415,53 @@ make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 24%] Built target ost_seq make -f modules/bindings/src/CMakeFiles/ost_bindings.dir/build.make modules/bindings/src/CMakeFiles/ost_bindings.dir/depend -make -f modules/db/src/CMakeFiles/ost_db.dir/build.make modules/db/src/CMakeFiles/ost_db.dir/depend make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/bindings/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/src/CMakeFiles/ost_bindings.dir/DependInfo.cmake --color= -make -f modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/build.make modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/depend +make -f modules/db/src/CMakeFiles/ost_db.dir/build.make modules/db/src/CMakeFiles/ost_db.dir/depend make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/db/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/src/CMakeFiles/ost_db.dir/DependInfo.cmake --color= +make -f modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/build.make modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/depend make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/seq/alg/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/bindings/src/CMakeFiles/ost_bindings.dir/build.make modules/bindings/src/CMakeFiles/ost_bindings.dir/build +make -f modules/db/src/CMakeFiles/ost_db.dir/build.make modules/db/src/CMakeFiles/ost_db.dir/build make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/db/src/CMakeFiles/ost_db.dir/build.make modules/db/src/CMakeFiles/ost_db.dir/build +make -f modules/bindings/src/CMakeFiles/ost_bindings.dir/build.make modules/bindings/src/CMakeFiles/ost_bindings.dir/build make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[ 24%] Building CXX object modules/db/src/CMakeFiles/ost_db.dir/sqlite_wrap.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/src && /usr/bin/c++ -DOST_MODULE_OST_DB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -DSQLITE_OMIT_LOAD_EXTENSION -Dost_db_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/db/src/CMakeFiles/ost_db.dir/sqlite_wrap.cc.o -MF CMakeFiles/ost_db.dir/sqlite_wrap.cc.o.d -o CMakeFiles/ost_db.dir/sqlite_wrap.cc.o -c /build/openstructure-2.3.1/modules/db/src/sqlite_wrap.cc make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/build.make modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/build -make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 24%] Building CXX object modules/bindings/src/CMakeFiles/ost_bindings.dir/wrap_tmalign.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/src && /usr/bin/c++ -DOST_MODULE_OST_BINDINGS -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_bindings_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/bindings/src/CMakeFiles/ost_bindings.dir/wrap_tmalign.cc.o -MF CMakeFiles/ost_bindings.dir/wrap_tmalign.cc.o.d -o CMakeFiles/ost_bindings.dir/wrap_tmalign.cc.o -c /build/openstructure-2.3.1/modules/bindings/src/wrap_tmalign.cc [ 24%] Building CXX object modules/db/src/CMakeFiles/ost_db.dir/linear_indexer.cc.o -[ 24%] Building CXX object modules/db/src/CMakeFiles/ost_db.dir/sqlite_wrap.cc.o +make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/src && /usr/bin/c++ -DOST_MODULE_OST_DB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -DSQLITE_OMIT_LOAD_EXTENSION -Dost_db_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/db/src/CMakeFiles/ost_db.dir/linear_indexer.cc.o -MF CMakeFiles/ost_db.dir/linear_indexer.cc.o.d -o CMakeFiles/ost_db.dir/linear_indexer.cc.o -c /build/openstructure-2.3.1/modules/db/src/linear_indexer.cc -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/src && /usr/bin/c++ -DOST_MODULE_OST_DB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -DSQLITE_OMIT_LOAD_EXTENSION -Dost_db_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/db/src/CMakeFiles/ost_db.dir/sqlite_wrap.cc.o -MF CMakeFiles/ost_db.dir/sqlite_wrap.cc.o.d -o CMakeFiles/ost_db.dir/sqlite_wrap.cc.o -c /build/openstructure-2.3.1/modules/db/src/sqlite_wrap.cc -[ 24%] Building CXX object modules/db/src/CMakeFiles/ost_db.dir/binary_container.cc.o [ 24%] Building CXX object modules/db/src/CMakeFiles/ost_db.dir/extract_data_helper.cc.o +[ 24%] Building CXX object modules/bindings/src/CMakeFiles/ost_bindings.dir/wrap_tmalign.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/src && /usr/bin/c++ -DOST_MODULE_OST_DB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -DSQLITE_OMIT_LOAD_EXTENSION -Dost_db_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/db/src/CMakeFiles/ost_db.dir/extract_data_helper.cc.o -MF CMakeFiles/ost_db.dir/extract_data_helper.cc.o.d -o CMakeFiles/ost_db.dir/extract_data_helper.cc.o -c /build/openstructure-2.3.1/modules/db/src/extract_data_helper.cc -[ 24%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/clip_alignment.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/src && /usr/bin/c++ -DOST_MODULE_OST_BINDINGS -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_bindings_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/bindings/src/CMakeFiles/ost_bindings.dir/wrap_tmalign.cc.o -MF CMakeFiles/ost_bindings.dir/wrap_tmalign.cc.o.d -o CMakeFiles/ost_bindings.dir/wrap_tmalign.cc.o -c /build/openstructure-2.3.1/modules/bindings/src/wrap_tmalign.cc +[ 24%] Building CXX object modules/db/src/CMakeFiles/ost_db.dir/binary_container.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/src && /usr/bin/c++ -DOST_MODULE_OST_DB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -DSQLITE_OMIT_LOAD_EXTENSION -Dost_db_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/db/src/CMakeFiles/ost_db.dir/binary_container.cc.o -MF CMakeFiles/ost_db.dir/binary_container.cc.o.d -o CMakeFiles/ost_db.dir/binary_container.cc.o -c /build/openstructure-2.3.1/modules/db/src/binary_container.cc [ 24%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/conservation.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/c++ -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/clip_alignment.cc.o -MF CMakeFiles/ost_seq_alg.dir/clip_alignment.cc.o.d -o CMakeFiles/ost_seq_alg.dir/clip_alignment.cc.o -c /build/openstructure-2.3.1/modules/seq/alg/src/clip_alignment.cc cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/c++ -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/conservation.cc.o -MF CMakeFiles/ost_seq_alg.dir/conservation.cc.o.d -o CMakeFiles/ost_seq_alg.dir/conservation.cc.o -c /build/openstructure-2.3.1/modules/seq/alg/src/conservation.cc -[ 24%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/contact_weight_matrix.cc.o +[ 24%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/clip_alignment.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/c++ -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/clip_alignment.cc.o -MF CMakeFiles/ost_seq_alg.dir/clip_alignment.cc.o.d -o CMakeFiles/ost_seq_alg.dir/clip_alignment.cc.o -c /build/openstructure-2.3.1/modules/seq/alg/src/clip_alignment.cc [ 24%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/contact_prediction_score.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/c++ -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/contact_prediction_score.cc.o -MF CMakeFiles/ost_seq_alg.dir/contact_prediction_score.cc.o.d -o CMakeFiles/ost_seq_alg.dir/contact_prediction_score.cc.o -c /build/openstructure-2.3.1/modules/seq/alg/src/contact_prediction_score.cc +[ 24%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/contact_weight_matrix.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/c++ -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/contact_weight_matrix.cc.o -MF CMakeFiles/ost_seq_alg.dir/contact_weight_matrix.cc.o.d -o CMakeFiles/ost_seq_alg.dir/contact_weight_matrix.cc.o -c /build/openstructure-2.3.1/modules/seq/alg/src/contact_weight_matrix.cc [ 24%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/distance_map.cc.o -[ 24%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/entropy.cc.o -[ 24%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/global_align.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/c++ -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/contact_prediction_score.cc.o -MF CMakeFiles/ost_seq_alg.dir/contact_prediction_score.cc.o.d -o CMakeFiles/ost_seq_alg.dir/contact_prediction_score.cc.o -c /build/openstructure-2.3.1/modules/seq/alg/src/contact_prediction_score.cc -[ 24%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/ins_del.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/c++ -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/distance_map.cc.o -MF CMakeFiles/ost_seq_alg.dir/distance_map.cc.o.d -o CMakeFiles/ost_seq_alg.dir/distance_map.cc.o -c /build/openstructure-2.3.1/modules/seq/alg/src/distance_map.cc -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/c++ -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/entropy.cc.o -MF CMakeFiles/ost_seq_alg.dir/entropy.cc.o.d -o CMakeFiles/ost_seq_alg.dir/entropy.cc.o -c /build/openstructure-2.3.1/modules/seq/alg/src/entropy.cc +[ 24%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/global_align.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/c++ -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/global_align.cc.o -MF CMakeFiles/ost_seq_alg.dir/global_align.cc.o.d -o CMakeFiles/ost_seq_alg.dir/global_align.cc.o -c /build/openstructure-2.3.1/modules/seq/alg/src/global_align.cc +[ 24%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/entropy.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/c++ -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/entropy.cc.o -MF CMakeFiles/ost_seq_alg.dir/entropy.cc.o.d -o CMakeFiles/ost_seq_alg.dir/entropy.cc.o -c /build/openstructure-2.3.1/modules/seq/alg/src/entropy.cc +[ 24%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/ins_del.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/c++ -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/ins_del.cc.o -MF CMakeFiles/ost_seq_alg.dir/ins_del.cc.o.d -o CMakeFiles/ost_seq_alg.dir/ins_del.cc.o -c /build/openstructure-2.3.1/modules/seq/alg/src/ins_del.cc [ 24%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/local_align.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/c++ -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/local_align.cc.o -MF CMakeFiles/ost_seq_alg.dir/local_align.cc.o.d -o CMakeFiles/ost_seq_alg.dir/local_align.cc.o -c /build/openstructure-2.3.1/modules/seq/alg/src/local_align.cc [ 24%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/merge_pairwise_alignments.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/c++ -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/merge_pairwise_alignments.cc.o -MF CMakeFiles/ost_seq_alg.dir/merge_pairwise_alignments.cc.o.d -o CMakeFiles/ost_seq_alg.dir/merge_pairwise_alignments.cc.o -c /build/openstructure-2.3.1/modules/seq/alg/src/merge_pairwise_alignments.cc -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/info/pymod/wrap_info.cc:27: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/info_group.hh:33, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/info.hh:32, - from /build/openstructure-2.3.1/modules/info/pymod/wrap_info.cc:29: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/specfun.h:45, - from /usr/include/c++/12/cmath:1935, - from /usr/include/c++/12/math.h:36, - from /usr/include/python3.11/pyport.h:218, - from /usr/include/python3.11/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -[ 25%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/pair_subst_weight_matrix.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/c++ -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/pair_subst_weight_matrix.cc.o -MF CMakeFiles/ost_seq_alg.dir/pair_subst_weight_matrix.cc.o.d -o CMakeFiles/ost_seq_alg.dir/pair_subst_weight_matrix.cc.o -c /build/openstructure-2.3.1/modules/seq/alg/src/pair_subst_weight_matrix.cc -[ 25%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/semiglobal_align.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/c++ -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/semiglobal_align.cc.o -MF CMakeFiles/ost_seq_alg.dir/semiglobal_align.cc.o.d -o CMakeFiles/ost_seq_alg.dir/semiglobal_align.cc.o -c /build/openstructure-2.3.1/modules/seq/alg/src/semiglobal_align.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -8473,7 +8471,8 @@ from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_column.hh:26, - from /build/openstructure-2.3.1/modules/seq/alg/src/conservation.cc:20: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_column_iterator.hh:22, + from /build/openstructure-2.3.1/modules/seq/alg/src/ins_del.cc:23: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -8490,35 +8489,6 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, - from /build/openstructure-2.3.1/modules/seq/alg/src/impl/align_impl.hh:22, - from /build/openstructure-2.3.1/modules/seq/alg/src/local_align.cc:20: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/12/string:45, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/ostream:38, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, - from /build/openstructure-2.3.1/modules/seq/alg/src/local_align.cc:19: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] @@ -8527,6 +8497,14 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_column_iterator.hh:29:43: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 29 | class AlignedColumnIterator : public std::iterator struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/12/string:45, - from /usr/include/c++/12/stdexcept:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec3.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/db/extract_data_helper.hh:23: +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/vector:60, + from /build/openstructure-2.3.1/modules/seq/alg/src/clip_alignment.cc:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -8557,17 +8535,18 @@ from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, - from /build/openstructure-2.3.1/modules/seq/alg/src/entropy.hh:24, - from /build/openstructure-2.3.1/modules/seq/alg/src/entropy.cc:21: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, + from /build/openstructure-2.3.1/modules/seq/alg/src/distance_map.cc:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/vector:60, - from /build/openstructure-2.3.1/modules/seq/alg/src/entropy.hh:22: + from /usr/include/c++/12/bits/specfun.h:45, + from /usr/include/c++/12/cmath:1935, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -8593,14 +8572,15 @@ from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/clip_alignment.hh:27, - from /build/openstructure-2.3.1/modules/seq/alg/src/clip_alignment.cc:25: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_column.hh:26, + from /build/openstructure-2.3.1/modules/seq/alg/src/conservation.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, - from /build/openstructure-2.3.1/modules/seq/alg/src/clip_alignment.cc:24: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_impl_fw.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:27: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -8611,20 +8591,15 @@ 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/distance_map.hh:33, + from /build/openstructure-2.3.1/modules/seq/alg/src/distance_map.cc:25: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/openstructure-2.3.1/modules/seq/alg/src/entropy.cc:24: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_column_iterator.hh:29:43: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 29 | class AlignedColumnIterator : public std::iterator struct std::iterator' is deprecated [-Wdeprecated-declarations] @@ -8638,18 +8613,17 @@ from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, - from /build/openstructure-2.3.1/modules/seq/alg/src/distance_map.cc:24: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/db/extract_data_helper.hh:24, + from /build/openstructure-2.3.1/modules/db/src/extract_data_helper.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/specfun.h:45, - from /usr/include/c++/12/cmath:1935, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: +In file included from /usr/include/c++/12/string:45, + from /usr/include/c++/12/stdexcept:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec3.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/db/extract_data_helper.hh:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -8659,19 +8633,34 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/db/extract_data_helper.hh:27: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 32 | : public std::iterator{ - | ^~~~~~~~ +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_column.hh:26, + from /build/openstructure-2.3.1/modules/seq/alg/src/contact_prediction_score.cc:20: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/vector:60, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_impl_fw.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:27: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/distance_map.hh:33, - from /build/openstructure-2.3.1/modules/seq/alg/src/distance_map.cc:25: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ @@ -8686,15 +8675,14 @@ from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_column.hh:26, - from /build/openstructure-2.3.1/modules/seq/alg/src/contact_prediction_score.cc:20: + from /build/openstructure-2.3.1/modules/seq/alg/src/entropy.hh:24, + from /build/openstructure-2.3.1/modules/seq/alg/src/entropy.cc:21: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_impl_fw.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:27: + from /build/openstructure-2.3.1/modules/seq/alg/src/entropy.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -8712,8 +8700,8 @@ from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, - from /build/openstructure-2.3.1/modules/seq/alg/src/merge_pairwise_alignments.hh:22, - from /build/openstructure-2.3.1/modules/seq/alg/src/merge_pairwise_alignments.cc:25: + from /build/openstructure-2.3.1/modules/seq/alg/src/impl/align_impl.hh:22, + from /build/openstructure-2.3.1/modules/seq/alg/src/global_align.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -8721,9 +8709,9 @@ from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/istream:38, - from /usr/include/c++/12/sstream:38, - from /build/openstructure-2.3.1/modules/seq/alg/src/merge_pairwise_alignments.cc:21: + from /usr/include/c++/12/ostream:38, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, + from /build/openstructure-2.3.1/modules/seq/alg/src/global_align.cc:19: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -8734,7 +8722,8 @@ 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/db/extract_data_helper.hh:27: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ @@ -8757,18 +8746,18 @@ from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/bindings/wrap_tmalign.hh:24, - from /build/openstructure-2.3.1/modules/bindings/src/wrap_tmalign.cc:24: + from /build/openstructure-2.3.1/modules/seq/alg/src/impl/align_impl.hh:22, + from /build/openstructure-2.3.1/modules/seq/alg/src/local_align.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/specfun.h:45, - from /usr/include/c++/12/cmath:1935, - from /usr/include/c++/12/math.h:36, - from /build/openstructure-2.3.1/modules/bindings/src/tmalign/param_set.h:6, - from /build/openstructure-2.3.1/modules/bindings/src/tmalign/TMalign.h:4, - from /build/openstructure-2.3.1/modules/bindings/src/wrap_tmalign.cc:20: +In file included from /usr/include/c++/12/string:45, + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/ostream:38, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, + from /build/openstructure-2.3.1/modules/seq/alg/src/local_align.cc:19: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -8778,6 +8767,21 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +In file included from /build/openstructure-2.3.1/modules/seq/alg/src/entropy.cc:24: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_column_iterator.hh:29:43: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 29 | class AlignedColumnIterator : public std::iterator struct std::iterator' is deprecated [-Wdeprecated-declarations] + 32 | : public std::iterator{ + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] @@ -8794,16 +8798,18 @@ from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_column.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_column_iterator.hh:22, - from /build/openstructure-2.3.1/modules/seq/alg/src/ins_del.cc:23: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/bindings/wrap_tmalign.hh:24, + from /build/openstructure-2.3.1/modules/bindings/src/wrap_tmalign.cc:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/vector:60, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_impl_fw.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:27: + from /usr/include/c++/12/bits/specfun.h:45, + from /usr/include/c++/12/cmath:1935, + from /usr/include/c++/12/math.h:36, + from /build/openstructure-2.3.1/modules/bindings/src/tmalign/param_set.h:6, + from /build/openstructure-2.3.1/modules/bindings/src/tmalign/TMalign.h:4, + from /build/openstructure-2.3.1/modules/bindings/src/wrap_tmalign.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -8821,12 +8827,10 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_column_iterator.hh:29:43: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 29 | class AlignedColumnIterator : public std::iterator struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -8844,9 +8848,9 @@ from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/ostream:38, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, - from /build/openstructure-2.3.1/modules/seq/alg/src/global_align.cc:19: + from /usr/include/c++/12/istream:38, + from /usr/include/c++/12/sstream:38, + from /build/openstructure-2.3.1/modules/seq/alg/src/merge_pairwise_alignments.cc:21: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -8962,8 +8966,6 @@ /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ -[ 25%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/sequence_identity.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/c++ -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/sequence_identity.cc.o -MF CMakeFiles/ost_seq_alg.dir/sequence_identity.cc.o.d -o CMakeFiles/ost_seq_alg.dir/sequence_identity.cc.o -c /build/openstructure-2.3.1/modules/seq/alg/src/sequence_identity.cc [ 25%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/sequence_similarity.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/c++ -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/sequence_similarity.cc.o -MF CMakeFiles/ost_seq_alg.dir/sequence_similarity.cc.o.d -o CMakeFiles/ost_seq_alg.dir/sequence_similarity.cc.o -c /build/openstructure-2.3.1/modules/seq/alg/src/sequence_similarity.cc [ 25%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/subst_weight_matrix.cc.o @@ -8987,12 +8989,12 @@ make -f modules/conop/src/CMakeFiles/ost_conop.dir/build.make modules/conop/src/CMakeFiles/ost_conop.dir/build make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 25%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/processor.cc.o +[ 25%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/amino_acids.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/c++ -DOST_MODULE_OST_CONOP -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_conop_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/src/CMakeFiles/ost_conop.dir/processor.cc.o -MF CMakeFiles/ost_conop.dir/processor.cc.o.d -o CMakeFiles/ost_conop.dir/processor.cc.o -c /build/openstructure-2.3.1/modules/conop/src/processor.cc +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/c++ -DOST_MODULE_OST_CONOP -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_conop_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/src/CMakeFiles/ost_conop.dir/amino_acids.cc.o -MF CMakeFiles/ost_conop.dir/amino_acids.cc.o.d -o CMakeFiles/ost_conop.dir/amino_acids.cc.o -c /build/openstructure-2.3.1/modules/conop/src/amino_acids.cc [ 25%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/conop.cc.o -[ 25%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/amino_acids.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/c++ -DOST_MODULE_OST_CONOP -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_conop_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/src/CMakeFiles/ost_conop.dir/conop.cc.o -MF CMakeFiles/ost_conop.dir/conop.cc.o.d -o CMakeFiles/ost_conop.dir/conop.cc.o -c /build/openstructure-2.3.1/modules/conop/src/conop.cc [ 25%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/minimal_compound_lib.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/c++ -DOST_MODULE_OST_CONOP -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_conop_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/src/CMakeFiles/ost_conop.dir/amino_acids.cc.o -MF CMakeFiles/ost_conop.dir/amino_acids.cc.o.d -o CMakeFiles/ost_conop.dir/amino_acids.cc.o -c /build/openstructure-2.3.1/modules/conop/src/amino_acids.cc +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/c++ -DOST_MODULE_OST_CONOP -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_conop_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/src/CMakeFiles/ost_conop.dir/conop.cc.o -MF CMakeFiles/ost_conop.dir/conop.cc.o.d -o CMakeFiles/ost_conop.dir/conop.cc.o -c /build/openstructure-2.3.1/modules/conop/src/conop.cc cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/c++ -DOST_MODULE_OST_CONOP -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_conop_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/src/CMakeFiles/ost_conop.dir/minimal_compound_lib.cc.o -MF CMakeFiles/ost_conop.dir/minimal_compound_lib.cc.o.d -o CMakeFiles/ost_conop.dir/minimal_compound_lib.cc.o -c /build/openstructure-2.3.1/modules/conop/src/minimal_compound_lib.cc [ 25%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/compound_lib_base.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/c++ -DOST_MODULE_OST_CONOP -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_conop_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/src/CMakeFiles/ost_conop.dir/compound_lib_base.cc.o -MF CMakeFiles/ost_conop.dir/compound_lib_base.cc.o.d -o CMakeFiles/ost_conop.dir/compound_lib_base.cc.o -c /build/openstructure-2.3.1/modules/conop/src/compound_lib_base.cc @@ -9025,8 +9027,6 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 25%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/heuristic.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/c++ -DOST_MODULE_OST_CONOP -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_conop_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/src/CMakeFiles/ost_conop.dir/heuristic.cc.o -MF CMakeFiles/ost_conop.dir/heuristic.cc.o.d -o CMakeFiles/ost_conop.dir/heuristic.cc.o -c /build/openstructure-2.3.1/modules/conop/src/heuristic.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] @@ -9035,6 +9035,8 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 25%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/heuristic.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/c++ -DOST_MODULE_OST_CONOP -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_conop_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/src/CMakeFiles/ost_conop.dir/heuristic.cc.o -MF CMakeFiles/ost_conop.dir/heuristic.cc.o.d -o CMakeFiles/ost_conop.dir/heuristic.cc.o -c /build/openstructure-2.3.1/modules/conop/src/heuristic.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -9103,22 +9105,6 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 32 | : public std::iterator{ - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_column_iterator.hh:29:43: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 29 | class AlignedColumnIterator : public std::iterator struct std::iterator' is deprecated [-Wdeprecated-declarations] + 32 | : public std::iterator{ + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_column_iterator.hh:29:43: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 29 | class AlignedColumnIterator : public std::iterator struct std::iterator' is deprecated [-Wdeprecated-declarations] @@ -9196,47 +9196,21 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 26%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/compound.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/c++ -DOST_MODULE_OST_CONOP -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_conop_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/src/CMakeFiles/ost_conop.dir/compound.cc.o -MF CMakeFiles/ost_conop.dir/compound.cc.o.d -o CMakeFiles/ost_conop.dir/compound.cc.o -c /build/openstructure-2.3.1/modules/conop/src/compound.cc -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/xcs_editor.hh:26, - from /build/openstructure-2.3.1/modules/conop/src/processor.cc:21: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/12/string:45, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/ostream:38, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, - from /build/openstructure-2.3.1/modules/conop/src/processor.cc:20: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, - from /build/openstructure-2.3.1/modules/conop/src/compound_lib_base.hh:5, - from /build/openstructure-2.3.1/modules/conop/src/compound_lib_base.cc:1: + from /build/openstructure-2.3.1/modules/conop/src/amino_acids.hh:26, + from /build/openstructure-2.3.1/modules/conop/src/amino_acids.cc:19: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/vector:60, - from /build/openstructure-2.3.1/modules/conop/src/compound.hh:22, - from /build/openstructure-2.3.1/modules/conop/src/compound_lib_base.hh:4: + from /usr/include/c++/12/bits/stl_tree.h:63, + from /usr/include/c++/12/set:60, + from /build/openstructure-2.3.1/modules/conop/src/amino_acids.hh:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -9246,12 +9220,17 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 26%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/compound_lib.cc.o +/build/openstructure-2.3.1/modules/conop/src/amino_acids.hh:61:42: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 61 | class AminoAcidSetIterator : public std::iterator struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -9261,7 +9240,7 @@ from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, - from /build/openstructure-2.3.1/modules/conop/src/heuristic.cc:20: + from /build/openstructure-2.3.1/modules/conop/src/processor.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -9271,7 +9250,6 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/c++ -DOST_MODULE_OST_CONOP -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_conop_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/src/CMakeFiles/ost_conop.dir/compound_lib.cc.o -MF CMakeFiles/ost_conop.dir/compound_lib.cc.o.d -o CMakeFiles/ost_conop.dir/compound_lib.cc.o -c /build/openstructure-2.3.1/modules/conop/src/compound_lib.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -9296,6 +9274,8 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 26%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/model_check.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/c++ -DOST_MODULE_OST_CONOP -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_conop_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/src/CMakeFiles/ost_conop.dir/model_check.cc.o -MF CMakeFiles/ost_conop.dir/model_check.cc.o.d -o CMakeFiles/ost_conop.dir/model_check.cc.o -c /build/openstructure-2.3.1/modules/conop/src/model_check.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -9321,21 +9301,23 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 26%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/compound.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/c++ -DOST_MODULE_OST_CONOP -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_conop_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/src/CMakeFiles/ost_conop.dir/compound.cc.o -MF CMakeFiles/ost_conop.dir/compound.cc.o.d -o CMakeFiles/ost_conop.dir/compound.cc.o -c /build/openstructure-2.3.1/modules/conop/src/compound.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, - from /build/openstructure-2.3.1/modules/conop/src/amino_acids.hh:26, - from /build/openstructure-2.3.1/modules/conop/src/amino_acids.cc:19: + from /build/openstructure-2.3.1/modules/conop/src/compound_lib_base.hh:5, + from /build/openstructure-2.3.1/modules/conop/src/compound_lib_base.cc:1: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/stl_tree.h:63, - from /usr/include/c++/12/set:60, - from /build/openstructure-2.3.1/modules/conop/src/amino_acids.hh:24: + from /usr/include/c++/12/vector:60, + from /build/openstructure-2.3.1/modules/conop/src/compound.hh:22, + from /build/openstructure-2.3.1/modules/conop/src/compound_lib_base.hh:4: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -9345,30 +9327,21 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -/build/openstructure-2.3.1/modules/conop/src/amino_acids.hh:61:42: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 61 | class AminoAcidSetIterator : public std::iterator struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/specfun.h:45, - from /usr/include/c++/12/cmath:1935, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/atom_handle.hh:22, - from /build/openstructure-2.3.1/modules/conop/src/diag.hh:22: +In file included from /usr/include/c++/12/string:45, + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/ostream:38, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, + from /build/openstructure-2.3.1/modules/conop/src/heuristic.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -9383,9 +9356,9 @@ from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, - from /build/openstructure-2.3.1/modules/conop/src/model_check.hh:4, - from /build/openstructure-2.3.1/modules/conop/src/model_check.cc:1: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, + from /build/openstructure-2.3.1/modules/conop/src/diag.hh:23, + from /build/openstructure-2.3.1/modules/conop/src/diag.cc:19: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -9394,7 +9367,8 @@ from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/atom_handle.hh:22, + from /build/openstructure-2.3.1/modules/conop/src/diag.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -9404,8 +9378,8 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 26%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/ring_finder.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/c++ -DOST_MODULE_OST_CONOP -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_conop_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/src/CMakeFiles/ost_conop.dir/ring_finder.cc.o -MF CMakeFiles/ost_conop.dir/ring_finder.cc.o.d -o CMakeFiles/ost_conop.dir/ring_finder.cc.o -c /build/openstructure-2.3.1/modules/conop/src/ring_finder.cc +[ 26%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/compound_lib.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/c++ -DOST_MODULE_OST_CONOP -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_conop_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/src/CMakeFiles/ost_conop.dir/compound_lib.cc.o -MF CMakeFiles/ost_conop.dir/compound_lib.cc.o.d -o CMakeFiles/ost_conop.dir/compound_lib.cc.o -c /build/openstructure-2.3.1/modules/conop/src/compound_lib.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -9430,32 +9404,25 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/openstructure-2.3.1/modules/conop/src/model_check.cc:2: -/build/openstructure-2.3.1/modules/conop/src/amino_acids.hh:61:42: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 61 | class AminoAcidSetIterator : public std::iterator struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/12/string:45, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/ostream:38, - from /usr/include/c++/12/iostream:39, - from /build/openstructure-2.3.1/modules/conop/src/compound_lib.cc:24: +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/bits/specfun.h:45, + from /usr/include/c++/12/cmath:1935, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -9465,6 +9432,13 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +In file included from /build/openstructure-2.3.1/modules/conop/src/model_check.cc:2: +/build/openstructure-2.3.1/modules/conop/src/amino_acids.hh:61:42: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 61 | class AminoAcidSetIterator : public std::iterator struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/12/string:45, + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/ostream:38, + from /usr/include/c++/12/iostream:39, + from /build/openstructure-2.3.1/modules/conop/src/compound_lib.cc:24: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ In file included from /usr/include/c++/12/string:53, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, @@ -9753,18 +9755,18 @@ /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ -[ 26%] Linking CXX shared library ../../../../stage/lib/libost_seq_alg.so -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_seq_alg.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libost_seq_alg.so.2.3 -o ../../../../stage/lib/libost_seq_alg.so.2.3.1 CMakeFiles/ost_seq_alg.dir/clip_alignment.cc.o CMakeFiles/ost_seq_alg.dir/conservation.cc.o CMakeFiles/ost_seq_alg.dir/contact_prediction_score.cc.o CMakeFiles/ost_seq_alg.dir/contact_weight_matrix.cc.o CMakeFiles/ost_seq_alg.dir/distance_map.cc.o CMakeFiles/ost_seq_alg.dir/entropy.cc.o CMakeFiles/ost_seq_alg.dir/global_align.cc.o CMakeFiles/ost_seq_alg.dir/ins_del.cc.o CMakeFiles/ost_seq_alg.dir/local_align.cc.o CMakeFiles/ost_seq_alg.dir/merge_pairwise_alignments.cc.o CMakeFiles/ost_seq_alg.dir/pair_subst_weight_matrix.cc.o CMakeFiles/ost_seq_alg.dir/semiglobal_align.cc.o CMakeFiles/ost_seq_alg.dir/sequence_identity.cc.o CMakeFiles/ost_seq_alg.dir/sequence_similarity.cc.o CMakeFiles/ost_seq_alg.dir/subst_weight_matrix.cc.o CMakeFiles/ost_seq_alg.dir/variance_map.cc.o CMakeFiles/ost_seq_alg.dir/hmm_pseudo_counts.cc.o CMakeFiles/ost_seq_alg.dir/hmm_score.cc.o -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib: ../../../../stage/lib/libost_seq.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so ../../../../stage/lib/libost_mol.so.2.3.1 ../../../../stage/lib/libost_info.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../../stage/lib/libost_base.so.2.3.1 ../../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E cmake_symlink_library ../../../../stage/lib/libost_seq_alg.so.2.3.1 ../../../../stage/lib/libost_seq_alg.so.2.3 ../../../../stage/lib/libost_seq_alg.so -make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 26%] Built target ost_seq_alg [ 26%] Linking CXX shared library ../../../stage/lib/libost_bindings.so cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_bindings.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libost_bindings.so.2.3 -o ../../../stage/lib/libost_bindings.so.2.3.1 CMakeFiles/ost_bindings.dir/wrap_tmalign.cc.o -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib: ../../../stage/lib/libost_seq.so.2.3.1 ../../../stage/lib/libost_mol.so.2.3.1 ../../../stage/lib/libost_info.so.2.3.1 ../../../stage/lib/libost_base.so.2.3.1 ../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/src && /usr/bin/cmake -E cmake_symlink_library ../../../stage/lib/libost_bindings.so.2.3.1 ../../../stage/lib/libost_bindings.so.2.3 ../../../stage/lib/libost_bindings.so make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 26%] Built target ost_bindings +[ 26%] Linking CXX shared library ../../../../stage/lib/libost_seq_alg.so +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_seq_alg.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libost_seq_alg.so.2.3 -o ../../../../stage/lib/libost_seq_alg.so.2.3.1 CMakeFiles/ost_seq_alg.dir/clip_alignment.cc.o CMakeFiles/ost_seq_alg.dir/conservation.cc.o CMakeFiles/ost_seq_alg.dir/contact_prediction_score.cc.o CMakeFiles/ost_seq_alg.dir/contact_weight_matrix.cc.o CMakeFiles/ost_seq_alg.dir/distance_map.cc.o CMakeFiles/ost_seq_alg.dir/entropy.cc.o CMakeFiles/ost_seq_alg.dir/global_align.cc.o CMakeFiles/ost_seq_alg.dir/ins_del.cc.o CMakeFiles/ost_seq_alg.dir/local_align.cc.o CMakeFiles/ost_seq_alg.dir/merge_pairwise_alignments.cc.o CMakeFiles/ost_seq_alg.dir/pair_subst_weight_matrix.cc.o CMakeFiles/ost_seq_alg.dir/semiglobal_align.cc.o CMakeFiles/ost_seq_alg.dir/sequence_identity.cc.o CMakeFiles/ost_seq_alg.dir/sequence_similarity.cc.o CMakeFiles/ost_seq_alg.dir/subst_weight_matrix.cc.o CMakeFiles/ost_seq_alg.dir/variance_map.cc.o CMakeFiles/ost_seq_alg.dir/hmm_pseudo_counts.cc.o CMakeFiles/ost_seq_alg.dir/hmm_score.cc.o -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib: ../../../../stage/lib/libost_seq.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so ../../../../stage/lib/libost_mol.so.2.3.1 ../../../../stage/lib/libost_info.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../../stage/lib/libost_base.so.2.3.1 ../../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E cmake_symlink_library ../../../../stage/lib/libost_seq_alg.so.2.3.1 ../../../../stage/lib/libost_seq_alg.so.2.3 ../../../../stage/lib/libost_seq_alg.so +make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[ 26%] Built target ost_seq_alg [ 26%] Linking CXX shared module ../../../stage/lib/python3.11/dist-packages/ost/info/_ost_info.so cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_info.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -o ../../../stage/lib/python3.11/dist-packages/ost/info/_ost_info.so CMakeFiles/_ost_info.dir/wrap_info.cc.o -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib: ../../../stage/lib/libost_info.so.2.3.1 /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 ../../../stage/lib/libost_base.so.2.3.1 ../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so @@ -9774,45 +9776,43 @@ make -f modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/build.make modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/depend make -f modules/img/base/pymod/CMakeFiles/_ost_img.dir/build.make modules/img/base/pymod/CMakeFiles/_ost_img.dir/depend make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/img/base/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/pymod/CMakeFiles/_ost_img.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/base/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/img/base/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/pymod/CMakeFiles/_ost_img.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/build.make modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/build -make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/img/base/pymod/CMakeFiles/_ost_img.dir/build.make modules/img/base/pymod/CMakeFiles/_ost_img.dir/build make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 26%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_atom.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_atom.cc.o -MF CMakeFiles/_ost_mol.dir/export_atom.cc.o.d -o CMakeFiles/_ost_mol.dir/export_atom.cc.o -c /build/openstructure-2.3.1/modules/mol/base/pymod/export_atom.cc -[ 26%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_bond.cc.o [ 26%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_atom_view.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_bond.cc.o -MF CMakeFiles/_ost_mol.dir/export_bond.cc.o.d -o CMakeFiles/_ost_mol.dir/export_bond.cc.o -c /build/openstructure-2.3.1/modules/mol/base/pymod/export_bond.cc -[ 26%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_data_algorithm.cc.o -[ 26%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_data.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_data_algorithm.cc.o -MF CMakeFiles/_ost_img.dir/export_data_algorithm.cc.o.d -o CMakeFiles/_ost_img.dir/export_data_algorithm.cc.o -c /build/openstructure-2.3.1/modules/img/base/pymod/export_data_algorithm.cc +[ 26%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_bond.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_atom_view.cc.o -MF CMakeFiles/_ost_mol.dir/export_atom_view.cc.o.d -o CMakeFiles/_ost_mol.dir/export_atom_view.cc.o -c /build/openstructure-2.3.1/modules/mol/base/pymod/export_atom_view.cc -[ 26%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_extent.cc.o -[ 26%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_image_handle.cc.o +[ 26%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_data.cc.o +[ 26%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_data_algorithm.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_bond.cc.o -MF CMakeFiles/_ost_mol.dir/export_bond.cc.o.d -o CMakeFiles/_ost_mol.dir/export_bond.cc.o -c /build/openstructure-2.3.1/modules/mol/base/pymod/export_bond.cc +[ 26%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_chain_view.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_data.cc.o -MF CMakeFiles/_ost_img.dir/export_data.cc.o.d -o CMakeFiles/_ost_img.dir/export_data.cc.o -c /build/openstructure-2.3.1/modules/img/base/pymod/export_data.cc [ 26%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_chain.cc.o -[ 26%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_chain_view.cc.o -[ 26%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_coord_frame.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_chain_view.cc.o -MF CMakeFiles/_ost_mol.dir/export_chain_view.cc.o.d -o CMakeFiles/_ost_mol.dir/export_chain_view.cc.o -c /build/openstructure-2.3.1/modules/mol/base/pymod/export_chain_view.cc -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_extent.cc.o -MF CMakeFiles/_ost_img.dir/export_extent.cc.o.d -o CMakeFiles/_ost_img.dir/export_extent.cc.o -c /build/openstructure-2.3.1/modules/img/base/pymod/export_extent.cc -[ 26%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_editors.cc.o -[ 26%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_phase.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_image_handle.cc.o -MF CMakeFiles/_ost_img.dir/export_image_handle.cc.o.d -o CMakeFiles/_ost_img.dir/export_image_handle.cc.o -c /build/openstructure-2.3.1/modules/img/base/pymod/export_image_handle.cc +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_data_algorithm.cc.o -MF CMakeFiles/_ost_img.dir/export_data_algorithm.cc.o.d -o CMakeFiles/_ost_img.dir/export_data_algorithm.cc.o -c /build/openstructure-2.3.1/modules/img/base/pymod/export_data_algorithm.cc +[ 26%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_extent.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_chain.cc.o -MF CMakeFiles/_ost_mol.dir/export_chain.cc.o.d -o CMakeFiles/_ost_mol.dir/export_chain.cc.o -c /build/openstructure-2.3.1/modules/mol/base/pymod/export_chain.cc [ 26%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_coord_group.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_chain_view.cc.o -MF CMakeFiles/_ost_mol.dir/export_chain_view.cc.o.d -o CMakeFiles/_ost_mol.dir/export_chain_view.cc.o -c /build/openstructure-2.3.1/modules/mol/base/pymod/export_chain_view.cc +[ 26%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_image_handle.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_extent.cc.o -MF CMakeFiles/_ost_img.dir/export_extent.cc.o.d -o CMakeFiles/_ost_img.dir/export_extent.cc.o -c /build/openstructure-2.3.1/modules/img/base/pymod/export_extent.cc [ 28%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_peak.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_peak.cc.o -MF CMakeFiles/_ost_img.dir/export_peak.cc.o.d -o CMakeFiles/_ost_img.dir/export_peak.cc.o -c /build/openstructure-2.3.1/modules/img/base/pymod/export_peak.cc +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_coord_group.cc.o -MF CMakeFiles/_ost_mol.dir/export_coord_group.cc.o.d -o CMakeFiles/_ost_mol.dir/export_coord_group.cc.o -c /build/openstructure-2.3.1/modules/mol/base/pymod/export_coord_group.cc +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_image_handle.cc.o -MF CMakeFiles/_ost_img.dir/export_image_handle.cc.o.d -o CMakeFiles/_ost_img.dir/export_image_handle.cc.o -c /build/openstructure-2.3.1/modules/img/base/pymod/export_image_handle.cc +[ 28%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_coord_frame.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_coord_frame.cc.o -MF CMakeFiles/_ost_mol.dir/export_coord_frame.cc.o.d -o CMakeFiles/_ost_mol.dir/export_coord_frame.cc.o -c /build/openstructure-2.3.1/modules/mol/base/pymod/export_coord_frame.cc +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_peak.cc.o -MF CMakeFiles/_ost_img.dir/export_peak.cc.o.d -o CMakeFiles/_ost_img.dir/export_peak.cc.o -c /build/openstructure-2.3.1/modules/img/base/pymod/export_peak.cc +[ 28%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_phase.cc.o +[ 28%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_editors.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_phase.cc.o -MF CMakeFiles/_ost_img.dir/export_phase.cc.o.d -o CMakeFiles/_ost_img.dir/export_phase.cc.o -c /build/openstructure-2.3.1/modules/img/base/pymod/export_phase.cc -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_coord_group.cc.o -MF CMakeFiles/_ost_mol.dir/export_coord_group.cc.o.d -o CMakeFiles/_ost_mol.dir/export_coord_group.cc.o -c /build/openstructure-2.3.1/modules/mol/base/pymod/export_coord_group.cc -[ 28%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_point.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_editors.cc.o -MF CMakeFiles/_ost_mol.dir/export_editors.cc.o.d -o CMakeFiles/_ost_mol.dir/export_editors.cc.o -c /build/openstructure-2.3.1/modules/mol/base/pymod/export_editors.cc -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_point.cc.o -MF CMakeFiles/_ost_img.dir/export_point.cc.o.d -o CMakeFiles/_ost_img.dir/export_point.cc.o -c /build/openstructure-2.3.1/modules/img/base/pymod/export_point.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -9826,13 +9826,39 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/img/base/pymod/export_peak.cc:25: + from /build/openstructure-2.3.1/modules/mol/base/pymod/export_coord_frame.cc:24: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/coord_frame.hh:27, + from /build/openstructure-2.3.1/modules/mol/base/pymod/export_coord_frame.cc:27: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/bits/specfun.h:45, + from /usr/include/c++/12/cmath:1935, + from /usr/include/c++/12/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -9846,10 +9872,13 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/mol/base/pymod/export_atom.cc:19: + from /build/openstructure-2.3.1/modules/img/base/pymod/export_image_handle.cc:25: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -9863,16 +9892,10 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/mol/base/pymod/export_bond.cc:19: + from /build/openstructure-2.3.1/modules/mol/base/pymod/export_atom.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -9886,13 +9909,16 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/mol/base/pymod/export_editors.cc:19: + from /build/openstructure-2.3.1/modules/mol/base/pymod/export_atom_view.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -9906,41 +9932,13 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/img/base/pymod/export_data_algorithm.cc:25: + from /build/openstructure-2.3.1/modules/img/base/pymod/export_phase.cc:25: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/peak.hh:31, - from /build/openstructure-2.3.1/modules/img/base/pymod/export_peak.cc:29: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/specfun.h:45, - from /usr/include/c++/12/cmath:1935, - from /usr/include/c++/12/math.h:36, - from /usr/include/python3.11/pyport.h:218, - from /usr/include/python3.11/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -9954,7 +9952,7 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/img/base/pymod/export_image_handle.cc:25: + from /build/openstructure-2.3.1/modules/mol/base/pymod/export_coord_group.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ @@ -9978,6 +9976,9 @@ /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -9991,16 +9992,13 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/mol/base/pymod/export_chain.cc:19: + from /build/openstructure-2.3.1/modules/mol/base/pymod/export_chain_view.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -10014,42 +10012,13 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/img/base/pymod/export_phase.cc:25: + from /build/openstructure-2.3.1/modules/img/base/pymod/export_data_algorithm.cc:25: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, - from /build/openstructure-2.3.1/modules/mol/base/pymod/export_atom.cc:24: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/specfun.h:45, - from /usr/include/c++/12/cmath:1935, - from /usr/include/c++/12/math.h:36, - from /usr/include/python3.11/pyport.h:218, - from /usr/include/python3.11/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -10063,7 +10032,7 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/img/base/pymod/export_point.cc:25: + from /build/openstructure-2.3.1/modules/img/base/pymod/export_peak.cc:25: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ @@ -10083,7 +10052,7 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/mol/base/pymod/export_chain_view.cc:19: + from /build/openstructure-2.3.1/modules/mol/base/pymod/export_editors.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ @@ -10103,7 +10072,7 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/img/base/pymod/export_data.cc:25: + from /build/openstructure-2.3.1/modules/mol/base/pymod/export_bond.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ @@ -10113,11 +10082,11 @@ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, - from /build/openstructure-2.3.1/modules/mol/base/pymod/export_bond.cc:24: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, + from /build/openstructure-2.3.1/modules/img/base/pymod/export_image_handle.cc:29: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -10144,9 +10113,9 @@ from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, - from /build/openstructure-2.3.1/modules/img/base/pymod/export_data_algorithm.cc:28: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/extent.hh:34, + from /build/openstructure-2.3.1/modules/img/base/pymod/wrap_extent_iterator.hh:34, + from /build/openstructure-2.3.1/modules/img/base/pymod/export_extent.cc:26: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -10168,6 +10137,26 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/openstructure-2.3.1/modules/img/base/pymod/export_data.cc:25: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -10175,7 +10164,7 @@ from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, - from /build/openstructure-2.3.1/modules/mol/base/pymod/export_editors.cc:24: + from /build/openstructure-2.3.1/modules/mol/base/pymod/export_atom_view.cc:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -10200,11 +10189,11 @@ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, - from /build/openstructure-2.3.1/modules/img/base/pymod/export_image_handle.cc:29: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, + from /build/openstructure-2.3.1/modules/mol/base/pymod/export_atom.cc:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -10220,27 +10209,13 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:41, - from /build/openstructure-2.3.1/modules/mol/base/pymod/export_editors.cc:25: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 27 | class pointer_it : public std::iterator{ - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point_list.hh:28, - from /build/openstructure-2.3.1/modules/img/base/pymod/export_point.cc:29: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/coord_frame.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/coord_source.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/coord_group.hh:29, + from /build/openstructure-2.3.1/modules/mol/base/pymod/export_coord_group.cc:23: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -10262,6 +10237,12 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -10275,20 +10256,18 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/mol/base/pymod/export_coord_frame.cc:24: + from /build/openstructure-2.3.1/modules/mol/base/pymod/export_chain.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, - from /build/openstructure-2.3.1/modules/img/base/pymod/export_data.cc:28: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, + from /build/openstructure-2.3.1/modules/mol/base/pymod/export_chain_view.cc:22: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -10310,34 +10289,14 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/mol/base/pymod/export_atom_view.cc:19: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/extent.hh:34, - from /build/openstructure-2.3.1/modules/img/base/pymod/wrap_extent_iterator.hh:34, - from /build/openstructure-2.3.1/modules/img/base/pymod/export_extent.cc:26: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, + from /build/openstructure-2.3.1/modules/img/base/pymod/export_data_algorithm.cc:28: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -10359,14 +10318,16 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, - from /build/openstructure-2.3.1/modules/mol/base/pymod/export_chain_view.cc:22: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/peak.hh:31, + from /build/openstructure-2.3.1/modules/img/base/pymod/export_peak.cc:29: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -10388,26 +10349,6 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/mol/base/pymod/export_coord_group.cc:19: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -10415,7 +10356,7 @@ from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, - from /build/openstructure-2.3.1/modules/mol/base/pymod/export_chain.cc:23: + from /build/openstructure-2.3.1/modules/mol/base/pymod/export_editors.cc:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -10437,6 +10378,14 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:41, + from /build/openstructure-2.3.1/modules/mol/base/pymod/export_editors.cc:25: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 27 | class pointer_it : public std::iterator{ + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -10444,7 +10393,7 @@ from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, - from /build/openstructure-2.3.1/modules/mol/base/pymod/export_atom_view.cc:24: + from /build/openstructure-2.3.1/modules/mol/base/pymod/export_bond.cc:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -10469,8 +10418,10 @@ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/coord_frame.hh:27, - from /build/openstructure-2.3.1/modules/mol/base/pymod/export_coord_frame.cc:27: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, + from /build/openstructure-2.3.1/modules/img/base/pymod/export_data.cc:28: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -10495,10 +10446,11 @@ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/coord_frame.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/coord_source.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/coord_group.hh:29, - from /build/openstructure-2.3.1/modules/mol/base/pymod/export_coord_group.cc:23: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, + from /build/openstructure-2.3.1/modules/mol/base/pymod/export_chain.cc:23: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -10520,28 +10472,18 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 28%] Linking CXX shared library ../../../stage/lib/libost_conop.so -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_conop.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libost_conop.so.2.3 -o ../../../stage/lib/libost_conop.so.2.3.1 CMakeFiles/ost_conop.dir/processor.cc.o CMakeFiles/ost_conop.dir/amino_acids.cc.o CMakeFiles/ost_conop.dir/conop.cc.o CMakeFiles/ost_conop.dir/minimal_compound_lib.cc.o CMakeFiles/ost_conop.dir/compound_lib_base.cc.o CMakeFiles/ost_conop.dir/heuristic.cc.o CMakeFiles/ost_conop.dir/diag.cc.o CMakeFiles/ost_conop.dir/rule_based.cc.o CMakeFiles/ost_conop.dir/model_check.cc.o CMakeFiles/ost_conop.dir/compound.cc.o CMakeFiles/ost_conop.dir/compound_lib.cc.o CMakeFiles/ost_conop.dir/ring_finder.cc.o -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib: ../../../stage/lib/libost_db.so.2.3.1 /usr/lib/x86_64-linux-gnu/libsqlite3.so ../../../stage/lib/libost_seq.so.2.3.1 ../../../stage/lib/libost_mol.so.2.3.1 ../../../stage/lib/libost_info.so.2.3.1 ../../../stage/lib/libost_base.so.2.3.1 ../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -[ 28%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_progress.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_progress.cc.o -MF CMakeFiles/_ost_img.dir/export_progress.cc.o.d -o CMakeFiles/_ost_img.dir/export_progress.cc.o -c /build/openstructure-2.3.1/modules/img/base/pymod/export_progress.cc -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E cmake_symlink_library ../../../stage/lib/libost_conop.so.2.3.1 ../../../stage/lib/libost_conop.so.2.3 ../../../stage/lib/libost_conop.so -make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 28%] Built target ost_conop -[ 28%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_raster_image.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_raster_image.cc.o -MF CMakeFiles/_ost_img.dir/export_raster_image.cc.o.d -o CMakeFiles/_ost_img.dir/export_raster_image.cc.o -c /build/openstructure-2.3.1/modules/img/base/pymod/export_raster_image.cc -[ 28%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_size.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_size.cc.o -MF CMakeFiles/_ost_img.dir/export_size.cc.o.d -o CMakeFiles/_ost_img.dir/export_size.cc.o -c /build/openstructure-2.3.1/modules/img/base/pymod/export_size.cc -[ 28%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_mask.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_mask.cc.o -MF CMakeFiles/_ost_img.dir/export_mask.cc.o.d -o CMakeFiles/_ost_img.dir/export_mask.cc.o -c /build/openstructure-2.3.1/modules/img/base/pymod/export_mask.cc -[ 28%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_image_list.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_image_list.cc.o -MF CMakeFiles/_ost_img.dir/export_image_list.cc.o.d -o CMakeFiles/_ost_img.dir/export_image_list.cc.o -c /build/openstructure-2.3.1/modules/img/base/pymod/export_image_list.cc +[ 28%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_point.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_point.cc.o -MF CMakeFiles/_ost_img.dir/export_point.cc.o.d -o CMakeFiles/_ost_img.dir/export_point.cc.o -c /build/openstructure-2.3.1/modules/img/base/pymod/export_point.cc [ 29%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_entity.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_entity.cc.o -MF CMakeFiles/_ost_mol.dir/export_entity.cc.o.d -o CMakeFiles/_ost_mol.dir/export_entity.cc.o -c /build/openstructure-2.3.1/modules/mol/base/pymod/export_entity.cc -[ 29%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_map.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_map.cc.o -MF CMakeFiles/_ost_img.dir/export_map.cc.o.d -o CMakeFiles/_ost_img.dir/export_map.cc.o -c /build/openstructure-2.3.1/modules/img/base/pymod/export_map.cc +[ 29%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_progress.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_progress.cc.o -MF CMakeFiles/_ost_img.dir/export_progress.cc.o.d -o CMakeFiles/_ost_img.dir/export_progress.cc.o -c /build/openstructure-2.3.1/modules/img/base/pymod/export_progress.cc [ 29%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_entity_view.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_entity_view.cc.o -MF CMakeFiles/_ost_mol.dir/export_entity_view.cc.o.d -o CMakeFiles/_ost_mol.dir/export_entity_view.cc.o -c /build/openstructure-2.3.1/modules/mol/base/pymod/export_entity_view.cc +[ 29%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_raster_image.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_raster_image.cc.o -MF CMakeFiles/_ost_img.dir/export_raster_image.cc.o.d -o CMakeFiles/_ost_img.dir/export_raster_image.cc.o -c /build/openstructure-2.3.1/modules/img/base/pymod/export_raster_image.cc +[ 29%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_size.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_size.cc.o -MF CMakeFiles/_ost_img.dir/export_size.cc.o.d -o CMakeFiles/_ost_img.dir/export_size.cc.o -c /build/openstructure-2.3.1/modules/img/base/pymod/export_size.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -10555,43 +10497,20 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/img/base/pymod/export_progress.cc:25: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 29%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_property_id.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_property_id.cc.o -MF CMakeFiles/_ost_mol.dir/export_property_id.cc.o.d -o CMakeFiles/_ost_mol.dir/export_property_id.cc.o -c /build/openstructure-2.3.1/modules/mol/base/pymod/export_property_id.cc -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/img/base/pymod/export_raster_image.cc:25: + from /build/openstructure-2.3.1/modules/img/base/pymod/export_point.cc:25: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 29%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/wrap_img.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/wrap_img.cc.o -MF CMakeFiles/_ost_img.dir/wrap_img.cc.o.d -o CMakeFiles/_ost_img.dir/wrap_img.cc.o -c /build/openstructure-2.3.1/modules/img/base/pymod/wrap_img.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/raster_image/raster_image.hh:31, - from /build/openstructure-2.3.1/modules/img/base/pymod/export_raster_image.cc:28: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point_list.hh:28, + from /build/openstructure-2.3.1/modules/img/base/pymod/export_point.cc:29: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -10626,23 +10545,20 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/img/base/pymod/export_size.cc:25: + from /build/openstructure-2.3.1/modules/mol/base/pymod/export_entity.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 29%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_query.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_query.cc.o -MF CMakeFiles/_ost_mol.dir/export_query.cc.o.d -o CMakeFiles/_ost_mol.dir/export_query.cc.o -c /build/openstructure-2.3.1/modules/mol/base/pymod/export_query.cc -[ 29%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_residue.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_residue.cc.o -MF CMakeFiles/_ost_mol.dir/export_residue.cc.o.d -o CMakeFiles/_ost_mol.dir/export_residue.cc.o -c /build/openstructure-2.3.1/modules/mol/base/pymod/export_residue.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/openstructure-2.3.1/modules/img/base/pymod/export_size.cc:27: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, + from /build/openstructure-2.3.1/modules/mol/base/pymod/export_entity.cc:23: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -10664,6 +10580,18 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:41, + from /build/openstructure-2.3.1/modules/mol/base/pymod/export_entity.cc:24: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 27 | class pointer_it : public std::iterator{ + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 29%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_property_id.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_property_id.cc.o -MF CMakeFiles/_ost_mol.dir/export_property_id.cc.o.d -o CMakeFiles/_ost_mol.dir/export_property_id.cc.o -c /build/openstructure-2.3.1/modules/mol/base/pymod/export_property_id.cc +[ 29%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_mask.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_mask.cc.o -MF CMakeFiles/_ost_img.dir/export_mask.cc.o.d -o CMakeFiles/_ost_img.dir/export_mask.cc.o -c /build/openstructure-2.3.1/modules/img/base/pymod/export_mask.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -10677,7 +10605,7 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/mol/base/pymod/export_entity.cc:19: + from /build/openstructure-2.3.1/modules/img/base/pymod/export_progress.cc:25: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ @@ -10697,21 +10625,13 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/img/base/pymod/export_mask.cc:25: + from /build/openstructure-2.3.1/modules/img/base/pymod/export_size.cc:25: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -make -f modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/build.make modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/depend -make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/alg/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/DependInfo.cmake --color= -make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/build.make modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/build -make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 29%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/svd_superpose.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/svd_superpose.cc.o -MF CMakeFiles/ost_mol_alg.dir/svd_superpose.cc.o.d -o CMakeFiles/ost_mol_alg.dir/svd_superpose.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/src/svd_superpose.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -10725,13 +10645,42 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/img/base/pymod/export_image_list.cc:25: + from /build/openstructure-2.3.1/modules/mol/base/pymod/export_entity_view.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 29%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_image_list.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_image_list.cc.o -MF CMakeFiles/_ost_img.dir/export_image_list.cc.o.d -o CMakeFiles/_ost_img.dir/export_image_list.cc.o -c /build/openstructure-2.3.1/modules/img/base/pymod/export_image_list.cc +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, + from /build/openstructure-2.3.1/modules/img/base/pymod/export_size.cc:27: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/bits/specfun.h:45, + from /usr/include/c++/12/cmath:1935, + from /usr/include/c++/12/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -10745,25 +10694,22 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/img/base/pymod/export_map.cc:20: + from /build/openstructure-2.3.1/modules/img/base/pymod/export_raster_image.cc:25: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/boost/bind.hpp:30, - from /build/openstructure-2.3.1/modules/mol/alg/src/svd_superpose.cc:22: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ +[ 29%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_query.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_query.cc.o -MF CMakeFiles/_ost_mol.dir/export_query.cc.o.d -o CMakeFiles/_ost_mol.dir/export_query.cc.o -c /build/openstructure-2.3.1/modules/mol/base/pymod/export_query.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, - from /build/openstructure-2.3.1/modules/mol/base/pymod/export_entity.cc:23: + from /build/openstructure-2.3.1/modules/mol/base/pymod/export_entity_view.cc:29: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -10785,21 +10731,12 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:41, - from /build/openstructure-2.3.1/modules/mol/base/pymod/export_entity.cc:24: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 27 | class pointer_it : public std::iterator{ - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/polygon_mask.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/mask.hh:29, - from /build/openstructure-2.3.1/modules/img/base/pymod/export_mask.cc:28: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/raster_image/raster_image.hh:31, + from /build/openstructure-2.3.1/modules/img/base/pymod/export_raster_image.cc:28: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -10821,14 +10758,38 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 29%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_residue.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_residue.cc.o -MF CMakeFiles/_ost_mol.dir/export_residue.cc.o.d -o CMakeFiles/_ost_mol.dir/export_residue.cc.o -c /build/openstructure-2.3.1/modules/mol/base/pymod/export_residue.cc +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/openstructure-2.3.1/modules/mol/base/pymod/export_property_id.cc:19: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 29%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_map.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_map.cc.o -MF CMakeFiles/_ost_img.dir/export_map.cc.o.d -o CMakeFiles/_ost_img.dir/export_map.cc.o -c /build/openstructure-2.3.1/modules/img/base/pymod/export_map.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, - from /build/openstructure-2.3.1/modules/img/base/pymod/export_image_list.cc:29: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, + from /build/openstructure-2.3.1/modules/mol/base/pymod/export_property_id.cc:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -10863,21 +10824,22 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/mol/base/pymod/export_entity_view.cc:19: + from /build/openstructure-2.3.1/modules/img/base/pymod/export_mask.cc:25: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 29%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/wrap_img.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/wrap_img.cc.o -MF CMakeFiles/_ost_img.dir/wrap_img.cc.o.d -o CMakeFiles/_ost_img.dir/wrap_img.cc.o -c /build/openstructure-2.3.1/modules/img/base/pymod/wrap_img.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/map.hh:22, - from /build/openstructure-2.3.1/modules/img/base/pymod/export_map.cc:23: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/polygon_mask.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/mask.hh:29, + from /build/openstructure-2.3.1/modules/img/base/pymod/export_mask.cc:28: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -10899,13 +10861,68 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 29%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_residue_view.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_residue_view.cc.o -MF CMakeFiles/_ost_mol.dir/export_residue_view.cc.o.d -o CMakeFiles/_ost_mol.dir/export_residue_view.cc.o -c /build/openstructure-2.3.1/modules/mol/base/pymod/export_residue_view.cc +[ 29%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_surface.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_surface.cc.o -MF CMakeFiles/_ost_mol.dir/export_surface.cc.o.d -o CMakeFiles/_ost_mol.dir/export_surface.cc.o -c /build/openstructure-2.3.1/modules/mol/base/pymod/export_surface.cc +[ 29%] Linking CXX shared library ../../../stage/lib/libost_conop.so +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_conop.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libost_conop.so.2.3 -o ../../../stage/lib/libost_conop.so.2.3.1 CMakeFiles/ost_conop.dir/processor.cc.o CMakeFiles/ost_conop.dir/amino_acids.cc.o CMakeFiles/ost_conop.dir/conop.cc.o CMakeFiles/ost_conop.dir/minimal_compound_lib.cc.o CMakeFiles/ost_conop.dir/compound_lib_base.cc.o CMakeFiles/ost_conop.dir/heuristic.cc.o CMakeFiles/ost_conop.dir/diag.cc.o CMakeFiles/ost_conop.dir/rule_based.cc.o CMakeFiles/ost_conop.dir/model_check.cc.o CMakeFiles/ost_conop.dir/compound.cc.o CMakeFiles/ost_conop.dir/compound_lib.cc.o CMakeFiles/ost_conop.dir/ring_finder.cc.o -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib: ../../../stage/lib/libost_db.so.2.3.1 /usr/lib/x86_64-linux-gnu/libsqlite3.so ../../../stage/lib/libost_seq.so.2.3.1 ../../../stage/lib/libost_mol.so.2.3.1 ../../../stage/lib/libost_info.so.2.3.1 ../../../stage/lib/libost_base.so.2.3.1 ../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/openstructure-2.3.1/modules/img/base/pymod/export_image_list.cc:25: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/openstructure-2.3.1/modules/mol/base/pymod/export_query.cc:19: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E cmake_symlink_library ../../../stage/lib/libost_conop.so.2.3.1 ../../../stage/lib/libost_conop.so.2.3 ../../../stage/lib/libost_conop.so +[ 29%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_bounding_box.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_bounding_box.cc.o -MF CMakeFiles/_ost_mol.dir/export_bounding_box.cc.o.d -o CMakeFiles/_ost_mol.dir/export_bounding_box.cc.o -c /build/openstructure-2.3.1/modules/mol/base/pymod/export_bounding_box.cc +make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[ 29%] Built target ost_conop +[ 29%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_query_view_wrapper.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_query_view_wrapper.cc.o -MF CMakeFiles/_ost_mol.dir/export_query_view_wrapper.cc.o.d -o CMakeFiles/_ost_mol.dir/export_query_view_wrapper.cc.o -c /build/openstructure-2.3.1/modules/mol/base/pymod/export_query_view_wrapper.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, - from /build/openstructure-2.3.1/modules/mol/base/pymod/export_entity_view.cc:29: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, + from /build/openstructure-2.3.1/modules/img/base/pymod/export_image_list.cc:29: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -10927,45 +10944,24 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -make -f modules/gfx/src/CMakeFiles/ost_gfx.dir/build.make modules/gfx/src/CMakeFiles/ost_gfx.dir/depend -make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/gfx/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src/CMakeFiles/ost_gfx.dir/DependInfo.cmake --color= -make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/gfx/src/CMakeFiles/ost_gfx.dir/build.make modules/gfx/src/CMakeFiles/ost_gfx.dir/build -make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 29%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/bitmap_io.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/bitmap_io.cc.o -MF CMakeFiles/ost_gfx.dir/bitmap_io.cc.o.d -o CMakeFiles/ost_gfx.dir/bitmap_io.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/bitmap_io.cc -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/mol/base/pymod/export_property_id.cc:19: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/svd_superpose.hh:27, - from /build/openstructure-2.3.1/modules/mol/alg/src/svd_superpose.cc:30: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/openstructure-2.3.1/modules/mol/base/pymod/export_query.cc:23: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/12/string:45, - from /usr/include/c++/12/stdexcept:39, - from /build/openstructure-2.3.1/modules/mol/alg/src/svd_superpose.cc:20: +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/bits/specfun.h:45, + from /usr/include/c++/12/cmath:1935, + from /usr/include/c++/12/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -10988,10 +10984,15 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/mol/base/pymod/export_query.cc:19: + from /build/openstructure-2.3.1/modules/mol/base/pymod/export_residue.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 29%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_torsion.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_torsion.cc.o -MF CMakeFiles/_ost_mol.dir/export_torsion.cc.o.d -o CMakeFiles/_ost_mol.dir/export_torsion.cc.o -c /build/openstructure-2.3.1/modules/mol/base/pymod/export_torsion.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -11005,18 +11006,13 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/img/base/pymod/wrap_img.cc:27: + from /build/openstructure-2.3.1/modules/img/base/pymod/export_map.cc:20: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 29%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/exporter.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/exporter.cc.o -MF CMakeFiles/ost_gfx.dir/exporter.cc.o.d -o CMakeFiles/ost_gfx.dir/exporter.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/exporter.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -11024,7 +11020,38 @@ from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, - from /build/openstructure-2.3.1/modules/mol/base/pymod/export_property_id.cc:24: + from /build/openstructure-2.3.1/modules/mol/base/pymod/export_residue.cc:25: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/bits/specfun.h:45, + from /usr/include/c++/12/cmath:1935, + from /usr/include/c++/12/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 30%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_visitor.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_visitor.cc.o -MF CMakeFiles/_ost_mol.dir/export_visitor.cc.o.d -o CMakeFiles/_ost_mol.dir/export_visitor.cc.o -c /build/openstructure-2.3.1/modules/mol/base/pymod/export_visitor.cc +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/map.hh:22, + from /build/openstructure-2.3.1/modules/img/base/pymod/export_map.cc:23: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -11046,6 +11073,28 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 30%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/wrap_mol.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/wrap_mol.cc.o -MF CMakeFiles/_ost_mol.dir/wrap_mol.cc.o.d -o CMakeFiles/_ost_mol.dir/wrap_mol.cc.o -c /build/openstructure-2.3.1/modules/mol/base/pymod/wrap_mol.cc +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/openstructure-2.3.1/modules/img/base/pymod/wrap_img.cc:27: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -11075,12 +11124,70 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/openstructure-2.3.1/modules/mol/base/pymod/export_surface.cc:19: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/openstructure-2.3.1/modules/mol/base/pymod/export_residue_view.cc:19: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 30%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_entity_property_mapper.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_entity_property_mapper.cc.o -MF CMakeFiles/_ost_mol.dir/export_entity_property_mapper.cc.o.d -o CMakeFiles/_ost_mol.dir/export_entity_property_mapper.cc.o -c /build/openstructure-2.3.1/modules/mol/base/pymod/export_entity_property_mapper.cc +make -f modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/build.make modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/depend +make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/alg/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/DependInfo.cmake --color= +make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +make -f modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/build.make modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/build +make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[ 30%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/svd_superpose.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/svd_superpose.cc.o -MF CMakeFiles/ost_mol_alg.dir/svd_superpose.cc.o.d -o CMakeFiles/ost_mol_alg.dir/svd_superpose.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/src/svd_superpose.cc +make -f modules/gfx/src/CMakeFiles/ost_gfx.dir/build.make modules/gfx/src/CMakeFiles/ost_gfx.dir/depend +make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/gfx/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src/CMakeFiles/ost_gfx.dir/DependInfo.cmake --color= +make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +make -f modules/gfx/src/CMakeFiles/ost_gfx.dir/build.make modules/gfx/src/CMakeFiles/ost_gfx.dir/build +make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[ 30%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/bitmap_io.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/bitmap_io.cc.o -MF CMakeFiles/ost_gfx.dir/bitmap_io.cc.o.d -o CMakeFiles/ost_gfx.dir/bitmap_io.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/bitmap_io.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/modules/mol/base/pymod/export_query.cc:23: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/surface_prop.hh:25, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/surface_handle.hh:24, + from /build/openstructure-2.3.1/modules/mol/base/pymod/export_surface.cc:23: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -11102,10 +11209,6 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 29%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/clash_score.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/clash_score.cc.o -MF CMakeFiles/ost_mol_alg.dir/clash_score.cc.o.d -o CMakeFiles/ost_mol_alg.dir/clash_score.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/src/clash_score.cc -[ 30%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/collada_exporter.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/collada_exporter.cc.o -MF CMakeFiles/ost_gfx.dir/collada_exporter.cc.o.d -o CMakeFiles/ost_gfx.dir/collada_exporter.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/collada_exporter.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -11119,23 +11222,33 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/mol/base/pymod/export_residue.cc:19: + from /build/openstructure-2.3.1/modules/mol/base/pymod/export_bounding_box.cc:19: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/openstructure-2.3.1/modules/mol/base/pymod/export_query_view_wrapper.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 30%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_residue_view.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_residue_view.cc.o -MF CMakeFiles/_ost_mol.dir/export_residue_view.cc.o.d -o CMakeFiles/_ost_mol.dir/export_residue_view.cc.o -c /build/openstructure-2.3.1/modules/mol/base/pymod/export_residue_view.cc -[ 30%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/color.cc.o -MF CMakeFiles/ost_gfx.dir/color.cc.o.d -o CMakeFiles/ost_gfx.dir/color.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/color.cc -[ 30%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/primitives.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/primitives.cc.o -MF CMakeFiles/ost_gfx.dir/primitives.cc.o.d -o CMakeFiles/ost_gfx.dir/primitives.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/primitives.cc -[ 30%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_surface.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_surface.cc.o -MF CMakeFiles/_ost_mol.dir/export_surface.cc.o.d -o CMakeFiles/_ost_mol.dir/export_surface.cc.o -c /build/openstructure-2.3.1/modules/mol/base/pymod/export_surface.cc -[ 30%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_bounding_box.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_bounding_box.cc.o -MF CMakeFiles/_ost_mol.dir/export_bounding_box.cc.o.d -o CMakeFiles/_ost_mol.dir/export_bounding_box.cc.o -c /build/openstructure-2.3.1/modules/mol/base/pymod/export_bounding_box.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -11143,7 +11256,7 @@ from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, - from /build/openstructure-2.3.1/modules/mol/base/pymod/export_residue.cc:25: + from /build/openstructure-2.3.1/modules/mol/base/pymod/export_residue_view.cc:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -11165,22 +11278,32 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 30%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/exporter.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/exporter.cc.o -MF CMakeFiles/ost_gfx.dir/exporter.cc.o.d -o CMakeFiles/ost_gfx.dir/exporter.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/exporter.cc +In file included from /usr/include/boost/bind.hpp:30, + from /build/openstructure-2.3.1/modules/mol/alg/src/svd_superpose.cc:22: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, - from /build/openstructure-2.3.1/modules/mol/alg/src/clash_score.cc:19: + from /build/openstructure-2.3.1/modules/mol/base/pymod/export_bounding_box.cc:23: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:24: + from /usr/include/c++/12/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -11190,21 +11313,25 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 30%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_query_view_wrapper.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_query_view_wrapper.cc.o -MF CMakeFiles/_ost_mol.dir/export_query_view_wrapper.cc.o.d -o CMakeFiles/_ost_mol.dir/export_query_view_wrapper.cc.o -c /build/openstructure-2.3.1/modules/mol/base/pymod/export_query_view_wrapper.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/primitives.hh:22, - from /build/openstructure-2.3.1/modules/gfx/src/primitives.cc:27: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, + from /build/openstructure-2.3.1/modules/mol/base/pymod/export_query_view_wrapper.cc:22: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/12/string:45, - from /usr/include/c++/12/stdexcept:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec3.hh:22, - from /build/openstructure-2.3.1/modules/gfx/src/gl_helper.hh:36, - from /build/openstructure-2.3.1/modules/gfx/src/primitives.cc:23: +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/bits/specfun.h:45, + from /usr/include/c++/12/cmath:1935, + from /usr/include/c++/12/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -11214,19 +11341,57 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/openstructure-2.3.1/modules/mol/base/pymod/export_torsion.cc:19: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/openstructure-2.3.1/modules/mol/base/pymod/export_visitor.cc:19: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color.hh:31, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/scene.hh:37, - from /build/openstructure-2.3.1/modules/gfx/src/exporter.cc:20: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/svd_superpose.hh:27, + from /build/openstructure-2.3.1/modules/mol/alg/src/svd_superpose.cc:30: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/stl_tree.h:63, - from /usr/include/c++/12/map:60, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/scene.hh:26: +In file included from /usr/include/c++/12/string:45, + from /usr/include/c++/12/stdexcept:39, + from /build/openstructure-2.3.1/modules/mol/alg/src/svd_superpose.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -11236,20 +11401,21 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 32%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/collada_exporter.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/collada_exporter.cc.o -MF CMakeFiles/ost_gfx.dir/collada_exporter.cc.o.d -o CMakeFiles/ost_gfx.dir/collada_exporter.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/collada_exporter.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/modules/gfx/src/color.hh:31, - from /build/openstructure-2.3.1/modules/gfx/src/color.cc:25: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color.hh:31, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/scene.hh:37, + from /build/openstructure-2.3.1/modules/gfx/src/exporter.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/12/string:45, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/ostream:38, - from /build/openstructure-2.3.1/modules/gfx/src/color.cc:23: +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/bits/stl_tree.h:63, + from /usr/include/c++/12/map:60, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/scene.hh:26: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -11259,30 +11425,26 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 30%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_torsion.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_torsion.cc.o -MF CMakeFiles/_ost_mol.dir/export_torsion.cc.o.d -o CMakeFiles/_ost_mol.dir/export_torsion.cc.o -c /build/openstructure-2.3.1/modules/mol/base/pymod/export_torsion.cc -[ 30%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/sec_structure_segments.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/sec_structure_segments.cc.o -MF CMakeFiles/ost_mol_alg.dir/sec_structure_segments.cc.o.d -o CMakeFiles/ost_mol_alg.dir/sec_structure_segments.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/src/sec_structure_segments.cc -[ 30%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/entity.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/entity.cc.o -MF CMakeFiles/ost_gfx.dir/entity.cc.o.d -o CMakeFiles/ost_gfx.dir/entity.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/entity.cc -[ 30%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/symmetry_node.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/symmetry_node.cc.o -MF CMakeFiles/ost_gfx.dir/symmetry_node.cc.o.d -o CMakeFiles/ost_gfx.dir/symmetry_node.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/symmetry_node.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/modules/gfx/src/color.hh:31, - from /build/openstructure-2.3.1/modules/gfx/src/scene.hh:37, - from /build/openstructure-2.3.1/modules/gfx/src/collada_exporter.cc:28: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, + from /build/openstructure-2.3.1/modules/mol/base/pymod/export_visitor.cc:22: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/12/string:45, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/istream:38, - from /usr/include/c++/12/sstream:38, - from /build/openstructure-2.3.1/modules/gfx/src/collada_exporter.cc:24: +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/bits/specfun.h:45, + from /usr/include/c++/12/cmath:1935, + from /usr/include/c++/12/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -11292,8 +11454,8 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 30%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/gfx_node.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/gfx_node.cc.o -MF CMakeFiles/ost_gfx.dir/gfx_node.cc.o.d -o CMakeFiles/ost_gfx.dir/gfx_node.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/gfx_node.cc +[ 32%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/color.cc.o -MF CMakeFiles/ost_gfx.dir/color.cc.o.d -o CMakeFiles/ost_gfx.dir/color.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/color.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -11307,7 +11469,7 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/mol/base/pymod/export_bounding_box.cc:19: + from /build/openstructure-2.3.1/modules/mol/base/pymod/wrap_mol.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ @@ -11327,20 +11489,20 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/mol/base/pymod/export_residue_view.cc:19: + from /build/openstructure-2.3.1/modules/mol/base/pymod/export_entity_property_mapper.cc:1: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 32%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/primitives.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/primitives.cc.o -MF CMakeFiles/ost_gfx.dir/primitives.cc.o.d -o CMakeFiles/ost_gfx.dir/primitives.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/primitives.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, - from /build/openstructure-2.3.1/modules/mol/base/pymod/export_bounding_box.cc:23: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/editor_base.hh:27, + from /build/openstructure-2.3.1/modules/mol/base/pymod/wrap_mol.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -11369,16 +11531,20 @@ from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, - from /build/openstructure-2.3.1/modules/mol/alg/src/sec_structure_segments.cc:19: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_property_mapper.hh:29, + from /build/openstructure-2.3.1/modules/mol/base/pymod/export_entity_property_mapper.cc:3: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: + from /usr/include/c++/12/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -11388,39 +11554,81 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /usr/include/boost/bind.hpp:30, - from /build/openstructure-2.3.1/modules/gfx/src/gfx_node.cc:19: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/mol/base/pymod/export_surface.cc:19: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 30%] Linking CXX shared module ../../../../stage/lib/python3.11/dist-packages/ost/img/_ost_img.so +[ 32%] Linking CXX shared module ../../../../stage/lib/python3.11/dist-packages/ost/img/_ost_img.so cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_img.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -o ../../../../stage/lib/python3.11/dist-packages/ost/img/_ost_img.so CMakeFiles/_ost_img.dir/export_data.cc.o CMakeFiles/_ost_img.dir/export_data_algorithm.cc.o CMakeFiles/_ost_img.dir/export_extent.cc.o CMakeFiles/_ost_img.dir/export_image_handle.cc.o CMakeFiles/_ost_img.dir/export_peak.cc.o CMakeFiles/_ost_img.dir/export_phase.cc.o CMakeFiles/_ost_img.dir/export_point.cc.o CMakeFiles/_ost_img.dir/export_progress.cc.o CMakeFiles/_ost_img.dir/export_raster_image.cc.o CMakeFiles/_ost_img.dir/export_size.cc.o CMakeFiles/_ost_img.dir/export_mask.cc.o CMakeFiles/_ost_img.dir/export_image_list.cc.o CMakeFiles/_ost_img.dir/export_map.cc.o CMakeFiles/_ost_img.dir/wrap_img.cc.o -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib: ../../../../stage/lib/libost_img.so.2.3.1 /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so ../../../../stage/lib/libost_info.so.2.3.1 ../../../../stage/lib/libost_base.so.2.3.1 ../../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/modules/gfx/src/symmetry_node.hh:22, - from /build/openstructure-2.3.1/modules/gfx/src/symmetry_node.cc:21: + from /build/openstructure-2.3.1/modules/gfx/src/color.hh:31, + from /build/openstructure-2.3.1/modules/gfx/src/scene.hh:37, + from /build/openstructure-2.3.1/modules/gfx/src/collada_exporter.cc:28: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/12/string:45, + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/istream:38, + from /usr/include/c++/12/sstream:38, + from /build/openstructure-2.3.1/modules/gfx/src/collada_exporter.cc:24: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/openstructure-2.3.1/modules/gfx/src/color.hh:31, + from /build/openstructure-2.3.1/modules/gfx/src/color.cc:25: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/12/string:45, + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/ostream:38, + from /build/openstructure-2.3.1/modules/gfx/src/color.cc:23: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/img/base/pymod/__init__.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/img/./__init__.pyc\",\"__init__.py\",doraise=True)" +make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[ 32%] Built target _ost_img +make -f modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/build.make modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/depend +make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/img/alg/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/DependInfo.cmake --color= +make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +make -f modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/build.make modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/build +make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[ 33%] Building CXX object modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/wrap_alg.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/wrap_alg.cc.o -MF CMakeFiles/_ost_img_alg.dir/wrap_alg.cc.o.d -o CMakeFiles/_ost_img_alg.dir/wrap_alg.cc.o -c /build/openstructure-2.3.1/modules/img/alg/pymod/wrap_alg.cc +[ 33%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/entity.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/entity.cc.o -MF CMakeFiles/ost_gfx.dir/entity.cc.o.d -o CMakeFiles/ost_gfx.dir/entity.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/entity.cc +[ 33%] Building CXX object modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/export_filter.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/export_filter.cc.o -MF CMakeFiles/_ost_img_alg.dir/export_filter.cc.o.d -o CMakeFiles/_ost_img_alg.dir/export_filter.cc.o -c /build/openstructure-2.3.1/modules/img/alg/pymod/export_filter.cc +[ 33%] Building CXX object modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/export_normalizer.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/export_normalizer.cc.o -MF CMakeFiles/_ost_img_alg.dir/export_normalizer.cc.o.d -o CMakeFiles/_ost_img_alg.dir/export_normalizer.cc.o -c /build/openstructure-2.3.1/modules/img/alg/pymod/export_normalizer.cc +[ 33%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/symmetry_node.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/symmetry_node.cc.o -MF CMakeFiles/ost_gfx.dir/symmetry_node.cc.o.d -o CMakeFiles/ost_gfx.dir/symmetry_node.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/symmetry_node.cc +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/primitives.hh:22, + from /build/openstructure-2.3.1/modules/gfx/src/primitives.cc:27: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -11428,7 +11636,7 @@ from /usr/include/c++/12/stdexcept:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec3.hh:22, from /build/openstructure-2.3.1/modules/gfx/src/gl_helper.hh:36, - from /build/openstructure-2.3.1/modules/gfx/src/symmetry_node.cc:20: + from /build/openstructure-2.3.1/modules/gfx/src/primitives.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -11438,19 +11646,27 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 33%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/gfx_node.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/gfx_node.cc.o -MF CMakeFiles/ost_gfx.dir/gfx_node.cc.o.d -o CMakeFiles/ost_gfx.dir/gfx_node.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/gfx_node.cc +[ 33%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/gfx_object.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/gfx_object.cc.o -MF CMakeFiles/ost_gfx.dir/gfx_object.cc.o.d -o CMakeFiles/ost_gfx.dir/gfx_object.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/gfx_object.cc +[ 33%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/gfx_prim.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/gfx_prim.cc.o -MF CMakeFiles/ost_gfx.dir/gfx_prim.cc.o.d -o CMakeFiles/ost_gfx.dir/gfx_prim.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/gfx_prim.cc +[ 33%] Building CXX object modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/export_transcendentals.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/export_transcendentals.cc.o -MF CMakeFiles/_ost_img_alg.dir/export_transcendentals.cc.o.d -o CMakeFiles/_ost_img_alg.dir/export_transcendentals.cc.o -c /build/openstructure-2.3.1/modules/img/alg/pymod/export_transcendentals.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/modules/gfx/src/entity.cc:36: + from /build/openstructure-2.3.1/modules/gfx/src/symmetry_node.hh:22, + from /build/openstructure-2.3.1/modules/gfx/src/symmetry_node.cc:21: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/specfun.h:45, - from /usr/include/c++/12/cmath:1935, - from /build/openstructure-2.3.1/modules/gfx/src/entity.cc:23: +In file included from /usr/include/c++/12/string:45, + from /usr/include/c++/12/stdexcept:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec3.hh:22, + from /build/openstructure-2.3.1/modules/gfx/src/gl_helper.hh:36, + from /build/openstructure-2.3.1/modules/gfx/src/symmetry_node.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -11465,21 +11681,14 @@ from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, - from /build/openstructure-2.3.1/modules/mol/base/pymod/export_residue_view.cc:24: + from /build/openstructure-2.3.1/modules/gfx/src/entity.cc:36: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, - from /usr/include/c++/12/math.h:36, - from /usr/include/python3.11/pyport.h:218, - from /usr/include/python3.11/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8: + from /build/openstructure-2.3.1/modules/gfx/src/entity.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -11489,37 +11698,22 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/img/base/pymod/__init__.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/img/./__init__.pyc\",\"__init__.py\",doraise=True)" -make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 30%] Built target _ost_img -make -f modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/build.make modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/depend -make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/img/alg/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/DependInfo.cmake --color= -make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/build.make modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/build -make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 32%] Building CXX object modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/wrap_alg.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/wrap_alg.cc.o -MF CMakeFiles/_ost_img_alg.dir/wrap_alg.cc.o.d -o CMakeFiles/_ost_img_alg.dir/wrap_alg.cc.o -c /build/openstructure-2.3.1/modules/img/alg/pymod/wrap_alg.cc -[ 33%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_visitor.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_visitor.cc.o -MF CMakeFiles/_ost_mol.dir/export_visitor.cc.o.d -o CMakeFiles/_ost_mol.dir/export_visitor.cc.o -c /build/openstructure-2.3.1/modules/mol/base/pymod/export_visitor.cc +In file included from /usr/include/boost/bind.hpp:30, + from /build/openstructure-2.3.1/modules/gfx/src/gfx_node.cc:19: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/surface_prop.hh:25, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/surface_handle.hh:24, - from /build/openstructure-2.3.1/modules/mol/base/pymod/export_surface.cc:23: + from /build/openstructure-2.3.1/modules/gfx/src/gfx_prim.hh:28, + from /build/openstructure-2.3.1/modules/gfx/src/gfx_prim.cc:23: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/specfun.h:45, - from /usr/include/c++/12/cmath:1935, - from /usr/include/c++/12/math.h:36, - from /usr/include/python3.11/pyport.h:218, - from /usr/include/python3.11/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8: + from /usr/include/c++/12/vector:60, + from /build/openstructure-2.3.1/modules/gfx/src/gfx_prim.hh:26: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -11529,10 +11723,8 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 33%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/gfx_object.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/gfx_object.cc.o -MF CMakeFiles/ost_gfx.dir/gfx_object.cc.o.d -o CMakeFiles/ost_gfx.dir/gfx_object.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/gfx_object.cc -[ 33%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/local_dist_diff_test.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/local_dist_diff_test.cc.o -MF CMakeFiles/ost_mol_alg.dir/local_dist_diff_test.cc.o.d -o CMakeFiles/ost_mol_alg.dir/local_dist_diff_test.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/src/local_dist_diff_test.cc +[ 33%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/gfx_test_object.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/gfx_test_object.cc.o -MF CMakeFiles/ost_gfx.dir/gfx_test_object.cc.o.d -o CMakeFiles/ost_gfx.dir/gfx_test_object.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/gfx_test_object.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -11546,13 +11738,15 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/mol/base/pymod/export_query_view_wrapper.cc:19: + from /build/openstructure-2.3.1/modules/img/alg/pymod/export_filter.cc:27: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 33%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/input.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/input.cc.o -MF CMakeFiles/ost_gfx.dir/input.cc.o.d -o CMakeFiles/ost_gfx.dir/input.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/input.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -11579,36 +11773,6 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 33%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/gfx_prim.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/gfx_prim.cc.o -MF CMakeFiles/ost_gfx.dir/gfx_prim.cc.o.d -o CMakeFiles/ost_gfx.dir/gfx_prim.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/gfx_prim.cc -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, - from /build/openstructure-2.3.1/modules/mol/base/pymod/export_query_view_wrapper.cc:22: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/specfun.h:45, - from /usr/include/c++/12/cmath:1935, - from /usr/include/c++/12/math.h:36, - from /usr/include/python3.11/pyport.h:218, - from /usr/include/python3.11/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -11622,15 +11786,13 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/mol/base/pymod/export_torsion.cc:19: + from /build/openstructure-2.3.1/modules/img/alg/pymod/wrap_alg.cc:25: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 33%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/wrap_mol.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/wrap_mol.cc.o -MF CMakeFiles/_ost_mol.dir/wrap_mol.cc.o.d -o CMakeFiles/_ost_mol.dir/wrap_mol.cc.o -c /build/openstructure-2.3.1/modules/mol/base/pymod/wrap_mol.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -11638,45 +11800,18 @@ from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, - from /build/openstructure-2.3.1/modules/mol/alg/src/local_dist_diff_test.cc:4: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_property_mapper.hh:29, + from /build/openstructure-2.3.1/modules/gfx/src/gfx_object.cc:27: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/iomanip:40, - from /build/openstructure-2.3.1/modules/mol/alg/src/local_dist_diff_test.cc:1: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, - from /build/openstructure-2.3.1/modules/mol/alg/src/local_dist_diff_test.hh:24, - from /build/openstructure-2.3.1/modules/mol/alg/src/local_dist_diff_test.cc:6: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 32 | : public std::iterator{ - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/modules/gfx/src/gfx_prim.hh:28, - from /build/openstructure-2.3.1/modules/gfx/src/gfx_prim.cc:23: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/vector:60, - from /build/openstructure-2.3.1/modules/gfx/src/gfx_prim.hh:26: + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/ostream:38, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, + from /build/openstructure-2.3.1/modules/gfx/src/gfx_object.cc:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -11686,6 +11821,8 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 33%] Building CXX object modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/export_polar.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/export_polar.cc.o -MF CMakeFiles/_ost_img_alg.dir/export_polar.cc.o.d -o CMakeFiles/_ost_img_alg.dir/export_polar.cc.o -c /build/openstructure-2.3.1/modules/img/alg/pymod/export_polar.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -11699,7 +11836,7 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/mol/base/pymod/export_visitor.cc:19: + from /build/openstructure-2.3.1/modules/img/alg/pymod/export_normalizer.cc:27: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ @@ -11709,22 +11846,25 @@ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_property_mapper.hh:29, - from /build/openstructure-2.3.1/modules/gfx/src/gfx_object.cc:27: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/gaussian.hh:36, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/filter.hh:30, + from /build/openstructure-2.3.1/modules/img/alg/pymod/export_filter.cc:30: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/12/string:45, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/ostream:38, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, - from /build/openstructure-2.3.1/modules/gfx/src/gfx_object.cc:24: +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/bits/specfun.h:45, + from /usr/include/c++/12/cmath:1935, + from /usr/include/c++/12/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -11734,18 +11874,20 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 33%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/gfx_test_object.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/gfx_test_object.cc.o -MF CMakeFiles/ost_gfx.dir/gfx_test_object.cc.o.d -o CMakeFiles/ost_gfx.dir/gfx_test_object.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/gfx_test_object.cc -[ 33%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/input.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/input.cc.o -MF CMakeFiles/ost_gfx.dir/input.cc.o.d -o CMakeFiles/ost_gfx.dir/input.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/input.cc +[ 33%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/prim_list.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/prim_list.cc.o -MF CMakeFiles/ost_gfx.dir/prim_list.cc.o.d -o CMakeFiles/ost_gfx.dir/prim_list.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/prim_list.cc +[ 33%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/clash_score.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/clash_score.cc.o -MF CMakeFiles/ost_mol_alg.dir/clash_score.cc.o.d -o CMakeFiles/ost_mol_alg.dir/clash_score.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/src/clash_score.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, - from /build/openstructure-2.3.1/modules/mol/base/pymod/export_visitor.cc:22: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/auto_correlate.hh:24, + from /build/openstructure-2.3.1/modules/img/alg/pymod/wrap_alg.cc:26: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -11767,32 +11909,8 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/img/alg/pymod/wrap_alg.cc:25: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 33%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/prim_list.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/prim_list.cc.o -MF CMakeFiles/ost_gfx.dir/prim_list.cc.o.d -o CMakeFiles/ost_gfx.dir/prim_list.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/prim_list.cc -[ 34%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/scene.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/scene.cc.o -MF CMakeFiles/ost_gfx.dir/scene.cc.o.d -o CMakeFiles/ost_gfx.dir/scene.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/scene.cc -[ 34%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_entity_property_mapper.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_entity_property_mapper.cc.o -MF CMakeFiles/_ost_mol.dir/export_entity_property_mapper.cc.o.d -o CMakeFiles/_ost_mol.dir/export_entity_property_mapper.cc.o -c /build/openstructure-2.3.1/modules/mol/base/pymod/export_entity_property_mapper.cc +[ 33%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/sec_structure_segments.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/sec_structure_segments.cc.o -MF CMakeFiles/ost_mol_alg.dir/sec_structure_segments.cc.o.d -o CMakeFiles/ost_mol_alg.dir/sec_structure_segments.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/src/sec_structure_segments.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -11801,8 +11919,10 @@ from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/auto_correlate.hh:24, - from /build/openstructure-2.3.1/modules/img/alg/pymod/wrap_alg.cc:26: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/normalizer_impl.hh:32, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/norm_linear.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/norm.hh:30, + from /build/openstructure-2.3.1/modules/img/alg/pymod/export_normalizer.cc:30: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -11824,8 +11944,26 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 34%] Building CXX object modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/export_filter.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/export_filter.cc.o -MF CMakeFiles/_ost_img_alg.dir/export_filter.cc.o.d -o CMakeFiles/_ost_img_alg.dir/export_filter.cc.o -c /build/openstructure-2.3.1/modules/img/alg/pymod/export_filter.cc +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/openstructure-2.3.1/modules/img/alg/pymod/export_transcendentals.cc:25: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -11855,40 +11993,14 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /usr/include/boost/bind.hpp:30, - from /build/openstructure-2.3.1/modules/gfx/src/scene.cc:33: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/mol/base/pymod/wrap_mol.cc:19: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 34%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/selection.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/selection.cc.o -MF CMakeFiles/ost_gfx.dir/selection.cc.o.d -o CMakeFiles/ost_gfx.dir/selection.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/selection.cc -[ 34%] Building CXX object modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/export_normalizer.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/export_normalizer.cc.o -MF CMakeFiles/_ost_img_alg.dir/export_normalizer.cc.o.d -o CMakeFiles/_ost_img_alg.dir/export_normalizer.cc.o -c /build/openstructure-2.3.1/modules/img/alg/pymod/export_normalizer.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/editor_base.hh:27, - from /build/openstructure-2.3.1/modules/mol/base/pymod/wrap_mol.cc:20: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/transcendentals.hh:34, + from /build/openstructure-2.3.1/modules/img/alg/pymod/export_transcendentals.cc:28: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -11913,14 +12025,20 @@ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/modules/gfx/src/scene.cc:40: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, + from /build/openstructure-2.3.1/modules/mol/alg/src/sec_structure_segments.cc:19: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/12/string:45, - from /usr/include/c++/12/stdexcept:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, - from /build/openstructure-2.3.1/modules/gfx/src/scene.cc:23: +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/bits/specfun.h:45, + from /usr/include/c++/12/cmath:1935, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -11933,9 +12051,10 @@ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/modules/gfx/src/color.hh:31, - from /build/openstructure-2.3.1/modules/gfx/src/scene.hh:37, - from /build/openstructure-2.3.1/modules/gfx/src/prim_list.cc:25: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, + from /build/openstructure-2.3.1/modules/mol/alg/src/clash_score.cc:19: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -11944,8 +12063,7 @@ from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/atom_handle.hh:22, - from /build/openstructure-2.3.1/modules/gfx/src/prim_list.cc:23: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -11955,19 +12073,12 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 34%] Building CXX object modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/export_transcendentals.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/export_transcendentals.cc.o -MF CMakeFiles/_ost_img_alg.dir/export_transcendentals.cc.o.d -o CMakeFiles/_ost_img_alg.dir/export_transcendentals.cc.o -c /build/openstructure-2.3.1/modules/img/alg/pymod/export_transcendentals.cc -[ 34%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/surface.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/surface.cc.o -MF CMakeFiles/ost_gfx.dir/surface.cc.o.d -o CMakeFiles/ost_gfx.dir/surface.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/surface.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, - from /build/openstructure-2.3.1/modules/gfx/src/selection.hh:26, - from /build/openstructure-2.3.1/modules/gfx/src/selection.cc:19: + from /build/openstructure-2.3.1/modules/gfx/src/color.hh:31, + from /build/openstructure-2.3.1/modules/gfx/src/scene.hh:37, + from /build/openstructure-2.3.1/modules/gfx/src/prim_list.cc:25: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -11976,7 +12087,8 @@ from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/atom_handle.hh:22, + from /build/openstructure-2.3.1/modules/gfx/src/prim_list.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -11986,30 +12098,16 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/mol/base/pymod/export_entity_property_mapper.cc:1: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 34%] Building CXX object modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/export_polar.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/export_polar.cc.o -MF CMakeFiles/_ost_img_alg.dir/export_polar.cc.o.d -o CMakeFiles/_ost_img_alg.dir/export_polar.cc.o -c /build/openstructure-2.3.1/modules/img/alg/pymod/export_polar.cc +[ 33%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/local_dist_diff_test.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/local_dist_diff_test.cc.o -MF CMakeFiles/ost_mol_alg.dir/local_dist_diff_test.cc.o.d -o CMakeFiles/ost_mol_alg.dir/local_dist_diff_test.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/src/local_dist_diff_test.cc +[ 34%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/scene.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/scene.cc.o -MF CMakeFiles/ost_gfx.dir/scene.cc.o.d -o CMakeFiles/ost_gfx.dir/scene.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/scene.cc [ 34%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/distance_test_common.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/distance_test_common.cc.o -MF CMakeFiles/ost_mol_alg.dir/distance_test_common.cc.o.d -o CMakeFiles/ost_mol_alg.dir/distance_test_common.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/src/distance_test_common.cc +[ 34%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/selection.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/selection.cc.o -MF CMakeFiles/ost_gfx.dir/selection.cc.o.d -o CMakeFiles/ost_gfx.dir/selection.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/selection.cc +[ 34%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/distance_rmsd_test.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/distance_rmsd_test.cc.o -MF CMakeFiles/ost_mol_alg.dir/distance_rmsd_test.cc.o.d -o CMakeFiles/ost_mol_alg.dir/distance_rmsd_test.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/src/distance_rmsd_test.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -12023,13 +12121,15 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/img/alg/pymod/export_filter.cc:27: + from /build/openstructure-2.3.1/modules/img/alg/pymod/export_polar.cc:24: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 34%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/surface.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/surface.cc.o -MF CMakeFiles/ost_gfx.dir/surface.cc.o.d -o CMakeFiles/ost_gfx.dir/surface.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/surface.cc [ 34%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/gradient.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/gradient.cc.o -MF CMakeFiles/ost_gfx.dir/gradient.cc.o.d -o CMakeFiles/ost_gfx.dir/gradient.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/gradient.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, @@ -12039,39 +12139,8 @@ from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/gaussian.hh:36, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/filter.hh:30, - from /build/openstructure-2.3.1/modules/img/alg/pymod/export_filter.cc:30: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/specfun.h:45, - from /usr/include/c++/12/cmath:1935, - from /usr/include/c++/12/math.h:36, - from /usr/include/python3.11/pyport.h:218, - from /usr/include/python3.11/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_property_mapper.hh:29, - from /build/openstructure-2.3.1/modules/mol/base/pymod/export_entity_property_mapper.cc:3: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/polar.hh:24, + from /build/openstructure-2.3.1/modules/img/alg/pymod/export_polar.cc:25: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -12095,28 +12164,11 @@ | ^~~~~~~~ [ 34%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/gradient_manager.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/gradient_manager.cc.o -MF CMakeFiles/ost_gfx.dir/gradient_manager.cc.o.d -o CMakeFiles/ost_gfx.dir/gradient_manager.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/gradient_manager.cc -[ 34%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/vertex_array.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/vertex_array.cc.o -MF CMakeFiles/ost_gfx.dir/vertex_array.cc.o.d -o CMakeFiles/ost_gfx.dir/vertex_array.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/vertex_array.cc -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/img/alg/pymod/export_normalizer.cc:27: +In file included from /usr/include/boost/bind.hpp:30, + from /build/openstructure-2.3.1/modules/gfx/src/scene.cc:33: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -12124,14 +12176,15 @@ from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, - from /build/openstructure-2.3.1/modules/gfx/src/surface.cc:26: + from /build/openstructure-2.3.1/modules/mol/alg/src/local_dist_diff_test.cc:4: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/stl_tree.h:63, - from /usr/include/c++/12/map:60, - from /build/openstructure-2.3.1/modules/gfx/src/surface.cc:23: +In file included from /usr/include/c++/12/string:45, + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/iomanip:40, + from /build/openstructure-2.3.1/modules/mol/alg/src/local_dist_diff_test.cc:1: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -12141,32 +12194,33 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 34%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/vertex_array_helper.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/vertex_array_helper.cc.o -MF CMakeFiles/ost_gfx.dir/vertex_array_helper.cc.o.d -o CMakeFiles/ost_gfx.dir/vertex_array_helper.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/vertex_array_helper.cc +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, + from /build/openstructure-2.3.1/modules/mol/alg/src/local_dist_diff_test.hh:24, + from /build/openstructure-2.3.1/modules/mol/alg/src/local_dist_diff_test.cc:6: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 32 | : public std::iterator{ + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/normalizer_impl.hh:32, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/norm_linear.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/norm.hh:30, - from /build/openstructure-2.3.1/modules/img/alg/pymod/export_normalizer.cc:30: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/distance_test_common.hh:22, + from /build/openstructure-2.3.1/modules/mol/alg/src/distance_test_common.cc:1: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, - from /usr/include/c++/12/math.h:36, - from /usr/include/python3.11/pyport.h:218, - from /usr/include/python3.11/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -12181,9 +12235,10 @@ from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/distance_test_common.hh:22, - from /build/openstructure-2.3.1/modules/mol/alg/src/distance_test_common.cc:1: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, + from /build/openstructure-2.3.1/modules/gfx/src/selection.hh:26, + from /build/openstructure-2.3.1/modules/gfx/src/selection.cc:19: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -12192,7 +12247,7 @@ from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:24: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -12202,40 +12257,17 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 34%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/distance_rmsd_test.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/distance_rmsd_test.cc.o -MF CMakeFiles/ost_mol_alg.dir/distance_rmsd_test.cc.o.d -o CMakeFiles/ost_mol_alg.dir/distance_rmsd_test.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/src/distance_rmsd_test.cc -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/img/alg/pymod/export_transcendentals.cc:25: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/modules/gfx/src/color.hh:31, - from /build/openstructure-2.3.1/modules/gfx/src/gradient.hh:28, - from /build/openstructure-2.3.1/modules/gfx/src/gradient.cc:19: + from /build/openstructure-2.3.1/modules/gfx/src/scene.cc:40: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/vector:60, - from /build/openstructure-2.3.1/modules/gfx/src/gradient.hh:26: +In file included from /usr/include/c++/12/string:45, + from /usr/include/c++/12/stdexcept:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, + from /build/openstructure-2.3.1/modules/gfx/src/scene.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -12248,23 +12280,21 @@ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/transcendentals.hh:34, - from /build/openstructure-2.3.1/modules/img/alg/pymod/export_transcendentals.cc:28: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, + from /build/openstructure-2.3.1/modules/mol/alg/src/distance_rmsd_test.cc:2: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/specfun.h:45, - from /usr/include/c++/12/cmath:1935, - from /usr/include/c++/12/math.h:36, - from /usr/include/python3.11/pyport.h:218, - from /usr/include/python3.11/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8: +In file included from /usr/include/c++/12/string:45, + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/ostream:38, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, + from /build/openstructure-2.3.1/modules/mol/alg/src/distance_rmsd_test.cc:1: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -12274,20 +12304,33 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 34%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/superpose_frames.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/superpose_frames.cc.o -MF CMakeFiles/ost_mol_alg.dir/superpose_frames.cc.o.d -o CMakeFiles/ost_mol_alg.dir/superpose_frames.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/src/superpose_frames.cc +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/local_dist_diff_test.hh:24, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/distance_rmsd_test.hh:24, + from /build/openstructure-2.3.1/modules/mol/alg/src/distance_rmsd_test.cc:3: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 32 | : public std::iterator{ + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 34%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/vertex_array.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/vertex_array.cc.o -MF CMakeFiles/ost_gfx.dir/vertex_array.cc.o.d -o CMakeFiles/ost_gfx.dir/vertex_array.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/vertex_array.cc +[ 34%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/vertex_array_helper.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/vertex_array_helper.cc.o -MF CMakeFiles/ost_gfx.dir/vertex_array_helper.cc.o.d -o CMakeFiles/ost_gfx.dir/vertex_array_helper.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/vertex_array_helper.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/modules/gfx/src/vertex_array.hh:34, - from /build/openstructure-2.3.1/modules/gfx/src/vertex_array.cc:25: + from /build/openstructure-2.3.1/modules/gfx/src/color.hh:31, + from /build/openstructure-2.3.1/modules/gfx/src/gradient.hh:28, + from /build/openstructure-2.3.1/modules/gfx/src/gradient.cc:19: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, - from /usr/include/boost/format.hpp:17, - from /build/openstructure-2.3.1/modules/gfx/src/vertex_array.cc:23: + from /build/openstructure-2.3.1/modules/gfx/src/gradient.hh:26: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -12297,6 +12340,8 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 34%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/superpose_frames.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/superpose_frames.cc.o -MF CMakeFiles/ost_mol_alg.dir/superpose_frames.cc.o.d -o CMakeFiles/ost_mol_alg.dir/superpose_frames.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/src/superpose_frames.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -12325,6 +12370,34 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 34%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/material.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/material.cc.o -MF CMakeFiles/ost_gfx.dir/material.cc.o.d -o CMakeFiles/ost_gfx.dir/material.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/material.cc +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, + from /build/openstructure-2.3.1/modules/gfx/src/surface.cc:26: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/bits/stl_tree.h:63, + from /usr/include/c++/12/map:60, + from /build/openstructure-2.3.1/modules/gfx/src/surface.cc:23: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 34%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/povray.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/povray.cc.o -MF CMakeFiles/ost_gfx.dir/povray.cc.o.d -o CMakeFiles/ost_gfx.dir/povray.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/povray.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -12347,24 +12420,22 @@ | ^~~~~~~~ [ 34%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/filter_clashes.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/filter_clashes.cc.o -MF CMakeFiles/ost_mol_alg.dir/filter_clashes.cc.o.d -o CMakeFiles/ost_mol_alg.dir/filter_clashes.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/src/filter_clashes.cc +[ 34%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/gost_exporter.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/gost_exporter.cc.o -MF CMakeFiles/ost_gfx.dir/gost_exporter.cc.o.d -o CMakeFiles/ost_gfx.dir/gost_exporter.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/gost_exporter.cc +[ 34%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/construct_cbeta.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/construct_cbeta.cc.o -MF CMakeFiles/ost_mol_alg.dir/construct_cbeta.cc.o.d -o CMakeFiles/ost_mol_alg.dir/construct_cbeta.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/src/construct_cbeta.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, - from /build/openstructure-2.3.1/modules/mol/alg/src/distance_rmsd_test.cc:2: + from /build/openstructure-2.3.1/modules/gfx/src/color.hh:31, + from /build/openstructure-2.3.1/modules/gfx/src/material.hh:22, + from /build/openstructure-2.3.1/modules/gfx/src/material.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/12/string:45, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/ostream:38, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, - from /build/openstructure-2.3.1/modules/mol/alg/src/distance_rmsd_test.cc:1: +In file included from /usr/include/c++/12/iterator:61, + from /usr/include/boost/operators.hpp:98, + from /build/openstructure-2.3.1/modules/gfx/src/color.hh:28: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -12374,70 +12445,43 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/local_dist_diff_test.hh:24, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/distance_rmsd_test.hh:24, - from /build/openstructure-2.3.1/modules/mol/alg/src/distance_rmsd_test.cc:3: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 32 | : public std::iterator{ - | ^~~~~~~~ +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/openstructure-2.3.1/modules/gfx/src/vertex_array.hh:34, + from /build/openstructure-2.3.1/modules/gfx/src/vertex_array.cc:25: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/vector:60, + from /usr/include/boost/format.hpp:17, + from /build/openstructure-2.3.1/modules/gfx/src/vertex_array.cc:23: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/img/alg/pymod/export_polar.cc:24: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -/build/openstructure-2.3.1/modules/gfx/src/vertex_array.cc:1311:8: warning: 'geom::Vec3 ost::gfx::{anonymous}::make_aaline_edge(const geom::Vec2&, const geom::Vec2&, float)' defined but not used [-Wunused-function] - 1311 | Vec3 make_aaline_edge(const Vec2& c1, const Vec2& c0, float s) - | ^~~~~~~~~~~~~~~~ -/build/openstructure-2.3.1/modules/gfx/src/vertex_array.cc:1239:8: warning: 'void ost::gfx::{anonymous}::render_aalines(AALineList&, float, float)' defined but not used [-Wunused-function] - 1239 | void render_aalines(AALineList& line_list, float w, float r) - | ^~~~~~~~~~~~~~ -[ 34%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/material.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/material.cc.o -MF CMakeFiles/ost_gfx.dir/material.cc.o.d -o CMakeFiles/ost_gfx.dir/material.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/material.cc -[ 34%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/povray.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/povray.cc.o -MF CMakeFiles/ost_gfx.dir/povray.cc.o.d -o CMakeFiles/ost_gfx.dir/povray.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/povray.cc -[ 34%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/gost_exporter.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/gost_exporter.cc.o -MF CMakeFiles/ost_gfx.dir/gost_exporter.cc.o.d -o CMakeFiles/ost_gfx.dir/gost_exporter.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/gost_exporter.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/polar.hh:24, - from /build/openstructure-2.3.1/modules/img/alg/pymod/export_polar.cc:25: + from /build/openstructure-2.3.1/modules/gfx/src/color.hh:31, + from /build/openstructure-2.3.1/modules/gfx/src/povray.hh:31, + from /build/openstructure-2.3.1/modules/gfx/src/povray.cc:27: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/specfun.h:45, - from /usr/include/c++/12/cmath:1935, - from /usr/include/c++/12/math.h:36, - from /usr/include/python3.11/pyport.h:218, - from /usr/include/python3.11/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8: +In file included from /usr/include/c++/12/string:45, + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/istream:38, + from /usr/include/c++/12/sstream:38, + from /build/openstructure-2.3.1/modules/gfx/src/povray.cc:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -12487,17 +12531,14 @@ from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, - from /build/openstructure-2.3.1/modules/mol/alg/src/superpose_frames.cc:22: + from /build/openstructure-2.3.1/modules/mol/alg/src/construct_cbeta.cc:4: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, - from /usr/include/eigen3/Eigen/src/Core/util/Macros.h:679, - from /usr/include/eigen3/Eigen/Core:19, - from /usr/include/eigen3/Eigen/Eigenvalues:11, - from /build/openstructure-2.3.1/modules/mol/alg/src/superpose_frames.cc:20: + from /build/openstructure-2.3.1/modules/mol/alg/src/construct_cbeta.cc:1: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -12510,15 +12551,21 @@ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/modules/gfx/src/color.hh:31, - from /build/openstructure-2.3.1/modules/gfx/src/material.hh:22, - from /build/openstructure-2.3.1/modules/gfx/src/material.cc:20: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, + from /build/openstructure-2.3.1/modules/mol/alg/src/superpose_frames.cc:22: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/12/iterator:61, - from /usr/include/boost/operators.hpp:98, - from /build/openstructure-2.3.1/modules/gfx/src/color.hh:28: +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/bits/specfun.h:45, + from /usr/include/c++/12/cmath:1935, + from /usr/include/eigen3/Eigen/src/Core/util/Macros.h:679, + from /usr/include/eigen3/Eigen/Core:19, + from /usr/include/eigen3/Eigen/Eigenvalues:11, + from /build/openstructure-2.3.1/modules/mol/alg/src/superpose_frames.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -12530,60 +12577,12 @@ | ^~~~~~~~ [ 35%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/by_chain_color_op.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/by_chain_color_op.cc.o -MF CMakeFiles/ost_gfx.dir/color_ops/by_chain_color_op.cc.o.d -o CMakeFiles/ost_gfx.dir/color_ops/by_chain_color_op.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/color_ops/by_chain_color_op.cc -[ 35%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/uniform_color_op.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/uniform_color_op.cc.o -MF CMakeFiles/ost_gfx.dir/color_ops/uniform_color_op.cc.o.d -o CMakeFiles/ost_gfx.dir/color_ops/uniform_color_op.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/color_ops/uniform_color_op.cc -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/modules/gfx/src/color.hh:31, - from /build/openstructure-2.3.1/modules/gfx/src/povray.hh:31, - from /build/openstructure-2.3.1/modules/gfx/src/povray.cc:27: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/12/string:45, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/istream:38, - from /usr/include/c++/12/sstream:38, - from /build/openstructure-2.3.1/modules/gfx/src/povray.cc:24: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -[ 35%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/gradient_color_op.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/gradient_color_op.cc.o -MF CMakeFiles/ost_gfx.dir/color_ops/gradient_color_op.cc.o.d -o CMakeFiles/ost_gfx.dir/color_ops/gradient_color_op.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/color_ops/gradient_color_op.cc -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/modules/gfx/src/color.hh:31, - from /build/openstructure-2.3.1/modules/gfx/src/scene.hh:37, - from /build/openstructure-2.3.1/modules/gfx/src/gost_exporter.cc:27: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/12/string:45, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/istream:38, - from /usr/include/c++/12/sstream:38, - from /build/openstructure-2.3.1/modules/gfx/src/gost_exporter.cc:24: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ +/build/openstructure-2.3.1/modules/gfx/src/vertex_array.cc:1311:8: warning: 'geom::Vec3 ost::gfx::{anonymous}::make_aaline_edge(const geom::Vec2&, const geom::Vec2&, float)' defined but not used [-Wunused-function] + 1311 | Vec3 make_aaline_edge(const Vec2& c1, const Vec2& c0, float s) + | ^~~~~~~~~~~~~~~~ +/build/openstructure-2.3.1/modules/gfx/src/vertex_array.cc:1239:8: warning: 'void ost::gfx::{anonymous}::render_aalines(AALineList&, float, float)' defined but not used [-Wunused-function] + 1239 | void render_aalines(AALineList& line_list, float w, float r) + | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:53: In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:866:17, @@ -12843,22 +12842,24 @@ /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ -[ 35%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/entity_view_color_op.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/entity_view_color_op.cc.o -MF CMakeFiles/ost_gfx.dir/color_ops/entity_view_color_op.cc.o.d -o CMakeFiles/ost_gfx.dir/color_ops/entity_view_color_op.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/color_ops/entity_view_color_op.cc +[ 35%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/uniform_color_op.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/uniform_color_op.cc.o -MF CMakeFiles/ost_gfx.dir/color_ops/uniform_color_op.cc.o.d -o CMakeFiles/ost_gfx.dir/color_ops/uniform_color_op.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/color_ops/uniform_color_op.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/color_op.hh:24, - from /build/openstructure-2.3.1/modules/gfx/src/color_ops/color_op.cc:20: + from /build/openstructure-2.3.1/modules/gfx/src/color.hh:31, + from /build/openstructure-2.3.1/modules/gfx/src/scene.hh:37, + from /build/openstructure-2.3.1/modules/gfx/src/gost_exporter.cc:27: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/color_op.hh:22: + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/istream:38, + from /usr/include/c++/12/sstream:38, + from /build/openstructure-2.3.1/modules/gfx/src/gost_exporter.cc:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -12868,23 +12869,20 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 35%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/basic_gradient_color_op.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/basic_gradient_color_op.cc.o -MF CMakeFiles/ost_gfx.dir/color_ops/basic_gradient_color_op.cc.o.d -o CMakeFiles/ost_gfx.dir/color_ops/basic_gradient_color_op.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/color_ops/basic_gradient_color_op.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/info_group.hh:33, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/info.hh:32, - from /build/openstructure-2.3.1/modules/gfx/src/color_ops/by_chain_color_op.hh:23, - from /build/openstructure-2.3.1/modules/gfx/src/color_ops/by_chain_color_op.cc:21: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/color_op.hh:24, + from /build/openstructure-2.3.1/modules/gfx/src/color_ops/color_op.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/specfun.h:45, - from /usr/include/c++/12/cmath:1935, - from /usr/include/c++/12/math.h:36, - from /build/openstructure-2.3.1/modules/gfx/src/color_ops/by_chain_color_op.cc:19: +In file included from /usr/include/c++/12/string:45, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/color_op.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -12894,6 +12892,10 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 37%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/trajectory_analysis.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/trajectory_analysis.cc.o -MF CMakeFiles/ost_mol_alg.dir/trajectory_analysis.cc.o.d -o CMakeFiles/ost_mol_alg.dir/trajectory_analysis.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/src/trajectory_analysis.cc +[ 37%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/structure_analysis.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/structure_analysis.cc.o -MF CMakeFiles/ost_mol_alg.dir/structure_analysis.cc.o.d -o CMakeFiles/ost_mol_alg.dir/structure_analysis.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/src/structure_analysis.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -12920,28 +12922,21 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 35%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/gradient_level_color_op.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/gradient_level_color_op.cc.o -MF CMakeFiles/ost_gfx.dir/color_ops/gradient_level_color_op.cc.o.d -o CMakeFiles/ost_gfx.dir/color_ops/gradient_level_color_op.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/color_ops/gradient_level_color_op.cc -[ 35%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/construct_cbeta.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/construct_cbeta.cc.o -MF CMakeFiles/ost_mol_alg.dir/construct_cbeta.cc.o.d -o CMakeFiles/ost_mol_alg.dir/construct_cbeta.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/src/construct_cbeta.cc -[ 35%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/entity_renderer.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/entity_renderer.cc.o -MF CMakeFiles/ost_gfx.dir/impl/entity_renderer.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/entity_renderer.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/impl/entity_renderer.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:29, - from /build/openstructure-2.3.1/modules/gfx/src/color_ops/uniform_color_op.cc:22: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/info_group.hh:33, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/info.hh:32, + from /build/openstructure-2.3.1/modules/gfx/src/color_ops/by_chain_color_op.hh:23, + from /build/openstructure-2.3.1/modules/gfx/src/color_ops/by_chain_color_op.cc:21: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/memory:63, - from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, - from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, - from /usr/include/boost/shared_ptr.hpp:17, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/dyn_cast.hh:22, - from /build/openstructure-2.3.1/modules/gfx/src/color_ops/uniform_color_op.cc:20: + from /usr/include/c++/12/bits/specfun.h:45, + from /usr/include/c++/12/cmath:1935, + from /usr/include/c++/12/math.h:36, + from /build/openstructure-2.3.1/modules/gfx/src/color_ops/by_chain_color_op.cc:19: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -12951,17 +12946,22 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 37%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/gradient_color_op.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/gradient_color_op.cc.o -MF CMakeFiles/ost_gfx.dir/color_ops/gradient_color_op.cc.o.d -o CMakeFiles/ost_gfx.dir/color_ops/gradient_color_op.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/color_ops/gradient_color_op.cc +[ 37%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/entity_view_color_op.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/entity_view_color_op.cc.o -MF CMakeFiles/ost_gfx.dir/color_ops/entity_view_color_op.cc.o.d -o CMakeFiles/ost_gfx.dir/color_ops/entity_view_color_op.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/color_ops/entity_view_color_op.cc +[ 37%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/basic_gradient_color_op.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/basic_gradient_color_op.cc.o -MF CMakeFiles/ost_gfx.dir/color_ops/basic_gradient_color_op.cc.o.d -o CMakeFiles/ost_gfx.dir/color_ops/basic_gradient_color_op.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/color_ops/basic_gradient_color_op.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:29, - from /build/openstructure-2.3.1/modules/gfx/src/color_ops/gradient_color_op.cc:20: + from /build/openstructure-2.3.1/modules/mol/alg/src/trajectory_analysis.cc:27: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/vector:60, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:25: +In file included from /usr/include/c++/12/string:45, + from /usr/include/c++/12/stdexcept:39, + from /build/openstructure-2.3.1/modules/mol/alg/src/trajectory_analysis.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -12971,22 +12971,22 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 37%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/trajectory_analysis.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/trajectory_analysis.cc.o -MF CMakeFiles/ost_mol_alg.dir/trajectory_analysis.cc.o.d -o CMakeFiles/ost_mol_alg.dir/trajectory_analysis.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/src/trajectory_analysis.cc -[ 37%] Linking CXX shared module ../../../../stage/lib/python3.11/dist-packages/ost/mol/_ost_mol.so -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_mol.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -o ../../../../stage/lib/python3.11/dist-packages/ost/mol/_ost_mol.so CMakeFiles/_ost_mol.dir/export_atom.cc.o CMakeFiles/_ost_mol.dir/export_atom_view.cc.o CMakeFiles/_ost_mol.dir/export_bond.cc.o CMakeFiles/_ost_mol.dir/export_chain.cc.o CMakeFiles/_ost_mol.dir/export_chain_view.cc.o CMakeFiles/_ost_mol.dir/export_coord_group.cc.o CMakeFiles/_ost_mol.dir/export_coord_frame.cc.o CMakeFiles/_ost_mol.dir/export_editors.cc.o CMakeFiles/_ost_mol.dir/export_entity.cc.o CMakeFiles/_ost_mol.dir/export_entity_view.cc.o CMakeFiles/_ost_mol.dir/export_property_id.cc.o CMakeFiles/_ost_mol.dir/export_query.cc.o CMakeFiles/_ost_mol.dir/export_residue.cc.o CMakeFiles/_ost_mol.dir/export_residue_view.cc.o CMakeFiles/_ost_mol.dir/export_surface.cc.o CMakeFiles/_ost_mol.dir/export_bounding_box.cc.o CMakeFiles/_ost_mol.dir/export_query_view_wrapper.cc.o CMakeFiles/_ost_mol.dir/export_torsion.cc.o CMakeFiles/_ost_mol.dir/export_visitor.cc.o CMakeFiles/_ost_mol.dir/wrap_mol.cc.o CMakeFiles/_ost_mol.dir/export_entity_property_mapper.cc.o -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib: ../../../../stage/lib/libost_mol.so.2.3.1 /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so ../../../../stage/lib/libost_info.so.2.3.1 ../../../../stage/lib/libost_base.so.2.3.1 ../../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:29, - from /build/openstructure-2.3.1/modules/gfx/src/color_ops/entity_view_color_op.cc:21: + from /build/openstructure-2.3.1/modules/gfx/src/color_ops/uniform_color_op.cc:22: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/vector:60, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:25: + from /usr/include/c++/12/memory:63, + from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, + from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, + from /usr/include/boost/shared_ptr.hpp:17, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/dyn_cast.hh:22, + from /build/openstructure-2.3.1/modules/gfx/src/color_ops/uniform_color_op.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -12996,15 +12996,16 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 37%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/entity_detail.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/entity_detail.cc.o -MF CMakeFiles/ost_gfx.dir/impl/entity_detail.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/entity_detail.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/impl/entity_detail.cc +[ 37%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/gradient_level_color_op.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/gradient_level_color_op.cc.o -MF CMakeFiles/ost_gfx.dir/color_ops/gradient_level_color_op.cc.o.d -o CMakeFiles/ost_gfx.dir/color_ops/gradient_level_color_op.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/color_ops/gradient_level_color_op.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/info_group.hh:33, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/info.hh:32, - from /build/openstructure-2.3.1/modules/gfx/src/color_ops/basic_gradient_color_op.hh:22, - from /build/openstructure-2.3.1/modules/gfx/src/color_ops/basic_gradient_color_op.cc:20: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, + from /build/openstructure-2.3.1/modules/mol/alg/src/structure_analysis.cc:25: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -13012,8 +13013,7 @@ from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/info_handle.hh:31, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/info.hh:31: + from /build/openstructure-2.3.1/modules/mol/alg/src/structure_analysis.cc:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -13023,25 +13023,21 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 38%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/cartoon_renderer.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/cartoon_renderer.cc.o -MF CMakeFiles/ost_gfx.dir/impl/cartoon_renderer.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/cartoon_renderer.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/impl/cartoon_renderer.cc -[ 38%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/custom_renderer.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/custom_renderer.cc.o -MF CMakeFiles/ost_gfx.dir/impl/custom_renderer.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/custom_renderer.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/impl/custom_renderer.cc +[ 37%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/consistency_checks.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/consistency_checks.cc.o -MF CMakeFiles/ost_mol_alg.dir/consistency_checks.cc.o.d -o CMakeFiles/ost_mol_alg.dir/consistency_checks.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/src/consistency_checks.cc +[ 37%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/entity_renderer.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/entity_renderer.cc.o -MF CMakeFiles/ost_gfx.dir/impl/entity_renderer.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/entity_renderer.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/impl/entity_renderer.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, - from /build/openstructure-2.3.1/modules/mol/alg/src/construct_cbeta.cc:4: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:29, + from /build/openstructure-2.3.1/modules/gfx/src/color_ops/gradient_color_op.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/specfun.h:45, - from /usr/include/c++/12/cmath:1935, - from /build/openstructure-2.3.1/modules/mol/alg/src/construct_cbeta.cc:1: + from /usr/include/c++/12/vector:60, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -13054,13 +13050,19 @@ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/modules/mol/alg/src/trajectory_analysis.cc:27: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/info_group.hh:33, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/info.hh:32, + from /build/openstructure-2.3.1/modules/gfx/src/color_ops/basic_gradient_color_op.hh:22, + from /build/openstructure-2.3.1/modules/gfx/src/color_ops/basic_gradient_color_op.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/12/string:45, - from /usr/include/c++/12/stdexcept:39, - from /build/openstructure-2.3.1/modules/mol/alg/src/trajectory_analysis.cc:23: +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/bits/specfun.h:45, + from /usr/include/c++/12/cmath:1935, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/info_handle.hh:31, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/info.hh:31: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -13070,24 +13072,17 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 38%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/cpk_renderer.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/cpk_renderer.cc.o -MF CMakeFiles/ost_gfx.dir/impl/cpk_renderer.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/cpk_renderer.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/impl/cpk_renderer.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/view_op.hh:29, - from /build/openstructure-2.3.1/modules/gfx/src/impl/entity_renderer.cc:25: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:29, + from /build/openstructure-2.3.1/modules/gfx/src/color_ops/entity_view_color_op.cc:21: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/12/string:45, - from /usr/include/c++/12/stdexcept:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec3.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gl_helper.hh:36, - from /build/openstructure-2.3.1/modules/gfx/src/impl/entity_renderer.cc:23: +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/vector:60, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -13097,8 +13092,12 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 38%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/debug_renderer.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/debug_renderer.cc.o -MF CMakeFiles/ost_gfx.dir/impl/debug_renderer.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/debug_renderer.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/impl/debug_renderer.cc +[ 37%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/entity_detail.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/entity_detail.cc.o -MF CMakeFiles/ost_gfx.dir/impl/entity_detail.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/entity_detail.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/impl/entity_detail.cc +[ 38%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/cartoon_renderer.cc.o +[ 38%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/pdbize.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/cartoon_renderer.cc.o -MF CMakeFiles/ost_gfx.dir/impl/cartoon_renderer.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/cartoon_renderer.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/impl/cartoon_renderer.cc +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/pdbize.cc.o -MF CMakeFiles/ost_mol_alg.dir/pdbize.cc.o.d -o CMakeFiles/ost_mol_alg.dir/pdbize.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/src/pdbize.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -13124,84 +13123,21 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/mol/base/pymod/__init__.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/./__init__.pyc\",\"__init__.py\",doraise=True)" -make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 38%] Built target _ost_mol -[ 38%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/simple_renderer.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/simple_renderer.cc.o -MF CMakeFiles/ost_gfx.dir/impl/simple_renderer.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/simple_renderer.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/impl/simple_renderer.cc -[ 38%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/structure_analysis.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/structure_analysis.cc.o -MF CMakeFiles/ost_mol_alg.dir/structure_analysis.cc.o.d -o CMakeFiles/ost_mol_alg.dir/structure_analysis.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/src/structure_analysis.cc -[ 38%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/sline_renderer.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/sline_renderer.cc.o -MF CMakeFiles/ost_gfx.dir/impl/sline_renderer.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/sline_renderer.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/impl/sline_renderer.cc -[ 38%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/consistency_checks.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/consistency_checks.cc.o -MF CMakeFiles/ost_mol_alg.dir/consistency_checks.cc.o.d -o CMakeFiles/ost_mol_alg.dir/consistency_checks.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/src/consistency_checks.cc -[ 38%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/line_trace_renderer.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/line_trace_renderer.cc.o -MF CMakeFiles/ost_gfx.dir/impl/line_trace_renderer.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/line_trace_renderer.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/impl/line_trace_renderer.cc -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/modules/gfx/src/impl/cartoon_renderer.hh:27, - from /build/openstructure-2.3.1/modules/gfx/src/impl/cartoon_renderer.cc:24: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -[ 38%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/backbone_trace.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/backbone_trace.cc.o -MF CMakeFiles/ost_gfx.dir/impl/backbone_trace.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/backbone_trace.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/impl/backbone_trace.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/entity_detail.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/connect_renderer_base.hh:23, - from /build/openstructure-2.3.1/modules/gfx/src/impl/custom_renderer.hh:22, - from /build/openstructure-2.3.1/modules/gfx/src/impl/custom_renderer.cc:19: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/chain_view.hh:23, + from /build/openstructure-2.3.1/modules/mol/alg/src/consistency_checks.cc:21: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/specfun.h:45, - from /usr/include/c++/12/cmath:1935, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/module_config.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/connect_renderer_base.hh:22: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, - from /usr/include/c++/12/stdexcept:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec2.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec.hh:24, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:24: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color.hh:31, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/scene.hh:37, - from /build/openstructure-2.3.1/modules/gfx/src/impl/entity_detail.cc:22: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/specfun.h:45, - from /usr/include/c++/12/cmath:1935, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/atom_view.hh:25, - from /build/openstructure-2.3.1/modules/gfx/src/impl/entity_detail.cc:20: + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/ostream:38, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, + from /build/openstructure-2.3.1/modules/mol/alg/src/consistency_checks.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -13211,27 +13147,28 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 38%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/connect_renderer_base.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/connect_renderer_base.cc.o -MF CMakeFiles/ost_gfx.dir/impl/connect_renderer_base.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/connect_renderer_base.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/impl/connect_renderer_base.cc -[ 38%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/pdbize.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/pdbize.cc.o -MF CMakeFiles/ost_mol_alg.dir/pdbize.cc.o.d -o CMakeFiles/ost_mol_alg.dir/pdbize.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/src/pdbize.cc +[ 38%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/adjacency_bitmap.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/adjacency_bitmap.cc.o -MF CMakeFiles/ost_mol_alg.dir/adjacency_bitmap.cc.o.d -o CMakeFiles/ost_mol_alg.dir/adjacency_bitmap.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/src/adjacency_bitmap.cc +[ 38%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/custom_renderer.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/custom_renderer.cc.o -MF CMakeFiles/ost_gfx.dir/impl/custom_renderer.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/custom_renderer.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/impl/custom_renderer.cc +[ 38%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/cpk_renderer.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/cpk_renderer.cc.o -MF CMakeFiles/ost_gfx.dir/impl/cpk_renderer.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/cpk_renderer.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/impl/cpk_renderer.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer.hh:32, - from /build/openstructure-2.3.1/modules/gfx/src/impl/cpk_renderer.hh:24, - from /build/openstructure-2.3.1/modules/gfx/src/impl/cpk_renderer.cc:19: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/view_op.hh:29, + from /build/openstructure-2.3.1/modules/gfx/src/impl/entity_renderer.cc:25: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec3.hh:22, - from /build/openstructure-2.3.1/modules/gfx/src/impl/cpk_renderer.hh:22: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gl_helper.hh:36, + from /build/openstructure-2.3.1/modules/gfx/src/impl/entity_renderer.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -13241,17 +13178,19 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 38%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/debug_renderer.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/debug_renderer.cc.o -MF CMakeFiles/ost_gfx.dir/impl/debug_renderer.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/debug_renderer.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/impl/debug_renderer.cc +[ 38%] Linking CXX shared module ../../../../stage/lib/python3.11/dist-packages/ost/mol/_ost_mol.so +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_mol.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -o ../../../../stage/lib/python3.11/dist-packages/ost/mol/_ost_mol.so CMakeFiles/_ost_mol.dir/export_atom.cc.o CMakeFiles/_ost_mol.dir/export_atom_view.cc.o CMakeFiles/_ost_mol.dir/export_bond.cc.o CMakeFiles/_ost_mol.dir/export_chain.cc.o CMakeFiles/_ost_mol.dir/export_chain_view.cc.o CMakeFiles/_ost_mol.dir/export_coord_group.cc.o CMakeFiles/_ost_mol.dir/export_coord_frame.cc.o CMakeFiles/_ost_mol.dir/export_editors.cc.o CMakeFiles/_ost_mol.dir/export_entity.cc.o CMakeFiles/_ost_mol.dir/export_entity_view.cc.o CMakeFiles/_ost_mol.dir/export_property_id.cc.o CMakeFiles/_ost_mol.dir/export_query.cc.o CMakeFiles/_ost_mol.dir/export_residue.cc.o CMakeFiles/_ost_mol.dir/export_residue_view.cc.o CMakeFiles/_ost_mol.dir/export_surface.cc.o CMakeFiles/_ost_mol.dir/export_bounding_box.cc.o CMakeFiles/_ost_mol.dir/export_query_view_wrapper.cc.o CMakeFiles/_ost_mol.dir/export_torsion.cc.o CMakeFiles/_ost_mol.dir/export_visitor.cc.o CMakeFiles/_ost_mol.dir/wrap_mol.cc.o CMakeFiles/_ost_mol.dir/export_entity_property_mapper.cc.o -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib: ../../../../stage/lib/libost_mol.so.2.3.1 /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so ../../../../stage/lib/libost_info.so.2.3.1 ../../../../stage/lib/libost_base.so.2.3.1 ../../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer.hh:32, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/trace_renderer_base.hh:27, - from /build/openstructure-2.3.1/modules/gfx/src/impl/debug_renderer.hh:22, - from /build/openstructure-2.3.1/modules/gfx/src/impl/debug_renderer.cc:19: + from /build/openstructure-2.3.1/modules/mol/alg/src/pdbize.hh:22, + from /build/openstructure-2.3.1/modules/mol/alg/src/pdbize.cc:19: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -13259,8 +13198,8 @@ from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/module_config.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/trace_renderer_base.hh:26: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -13270,14 +13209,24 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, + from /build/openstructure-2.3.1/modules/mol/alg/src/pdbize.hh:25: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 32 | : public std::iterator{ + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 38%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/simple_renderer.cc.o +[ 38%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/contact_overlap.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/simple_renderer.cc.o -MF CMakeFiles/ost_gfx.dir/impl/simple_renderer.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/simple_renderer.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/impl/simple_renderer.cc +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/contact_overlap.cc.o -MF CMakeFiles/ost_mol_alg.dir/contact_overlap.cc.o.d -o CMakeFiles/ost_mol_alg.dir/contact_overlap.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/src/contact_overlap.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, - from /build/openstructure-2.3.1/modules/mol/alg/src/structure_analysis.cc:25: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color.hh:31, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/scene.hh:37, + from /build/openstructure-2.3.1/modules/gfx/src/impl/entity_detail.cc:22: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -13285,7 +13234,9 @@ from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/openstructure-2.3.1/modules/mol/alg/src/structure_analysis.cc:24: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/atom_view.hh:25, + from /build/openstructure-2.3.1/modules/gfx/src/impl/entity_detail.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -13298,18 +13249,16 @@ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/chain_view.hh:23, - from /build/openstructure-2.3.1/modules/mol/alg/src/consistency_checks.cc:21: + from /build/openstructure-2.3.1/modules/gfx/src/impl/cartoon_renderer.hh:27, + from /build/openstructure-2.3.1/modules/gfx/src/impl/cartoon_renderer.cc:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/ostream:38, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, - from /build/openstructure-2.3.1/modules/mol/alg/src/consistency_checks.cc:20: + from /usr/include/c++/12/stdexcept:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec2.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec.hh:24, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -13319,17 +13268,16 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 38%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/trace_renderer_base.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/trace_renderer_base.cc.o -MF CMakeFiles/ost_gfx.dir/impl/trace_renderer_base.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/trace_renderer_base.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/impl/trace_renderer_base.cc +[ 38%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/domain_find.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/domain_find.cc.o -MF CMakeFiles/ost_mol_alg.dir/domain_find.cc.o.d -o CMakeFiles/ost_mol_alg.dir/domain_find.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/src/domain_find.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/backbone_trace.hh:26, - from /build/openstructure-2.3.1/modules/gfx/src/impl/line_trace_renderer.hh:29, - from /build/openstructure-2.3.1/modules/gfx/src/impl/line_trace_renderer.cc:24: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/extent.hh:34, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_factory.hh:32, + from /build/openstructure-2.3.1/modules/mol/alg/src/adjacency_bitmap.cc:19: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -13337,37 +13285,8 @@ from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:24: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/backbone_trace.hh:26, - from /build/openstructure-2.3.1/modules/gfx/src/impl/sline_renderer.hh:29, - from /build/openstructure-2.3.1/modules/gfx/src/impl/sline_renderer.cc:24: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/memory:63, - from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, - from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, - from /usr/include/boost/shared_ptr.hpp:17, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity_fw.hh:22, - from /build/openstructure-2.3.1/modules/gfx/src/impl/sline_renderer.hh:27: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/module_config.hh:23, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_factory.hh:31: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -13377,17 +13296,24 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 38%] Linking CXX shared module ../../../../stage/lib/python3.11/dist-packages/ost/img/alg/_ost_img_alg.so -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_img_alg.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -o ../../../../stage/lib/python3.11/dist-packages/ost/img/alg/_ost_img_alg.so CMakeFiles/_ost_img_alg.dir/wrap_alg.cc.o CMakeFiles/_ost_img_alg.dir/export_filter.cc.o CMakeFiles/_ost_img_alg.dir/export_normalizer.cc.o CMakeFiles/_ost_img_alg.dir/export_transcendentals.cc.o CMakeFiles/_ost_img_alg.dir/export_polar.cc.o -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib: ../../../../stage/lib/libost_img_alg.so.2.3.1 /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libfftw3f_threads.so ../../../../stage/lib/libost_img.so.2.3.1 ../../../../stage/lib/libost_info.so.2.3.1 ../../../../stage/lib/libost_base.so.2.3.1 ../../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 -[ 38%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/adjacency_bitmap.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/adjacency_bitmap.cc.o -MF CMakeFiles/ost_mol_alg.dir/adjacency_bitmap.cc.o.d -o CMakeFiles/ost_mol_alg.dir/adjacency_bitmap.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/src/adjacency_bitmap.cc -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/img/alg/pymod/__init__.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/img/alg/./__init__.pyc\",\"__init__.py\",doraise=True)" +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/mol/base/pymod/__init__.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/./__init__.pyc\",\"__init__.py\",doraise=True)" +[ 38%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/sline_renderer.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/sline_renderer.cc.o -MF CMakeFiles/ost_gfx.dir/impl/sline_renderer.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/sline_renderer.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/impl/sline_renderer.cc make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 38%] Built target _ost_img_alg +[ 38%] Built target _ost_mol make -f modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/build.make modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/depend make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/seq/base/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/DependInfo.cmake --color= +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, + from /build/openstructure-2.3.1/modules/mol/alg/src/adjacency_bitmap.hh:9, + from /build/openstructure-2.3.1/modules/mol/alg/src/adjacency_bitmap.cc:24: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 32 | : public std::iterator{ + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/build.make modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/build make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' @@ -13396,34 +13322,10 @@ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color.hh:31, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/scene.hh:37, - from /build/openstructure-2.3.1/modules/gfx/src/impl/simple_renderer.cc:25: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/12/string:45, - from /usr/include/c++/12/stdexcept:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec3.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gl_helper.hh:36, - from /build/openstructure-2.3.1/modules/gfx/src/impl/simple_renderer.cc:24: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, - from /build/openstructure-2.3.1/modules/gfx/src/impl/backbone_trace.cc:20: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/entity_detail.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/connect_renderer_base.hh:23, + from /build/openstructure-2.3.1/modules/gfx/src/impl/custom_renderer.hh:22, + from /build/openstructure-2.3.1/modules/gfx/src/impl/custom_renderer.cc:19: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -13431,8 +13333,8 @@ from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/module_config.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/connect_renderer_base.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -13442,21 +13344,25 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 38%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/mapped_property.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/mapped_property.cc.o -MF CMakeFiles/ost_gfx.dir/impl/mapped_property.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/mapped_property.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/impl/mapped_property.cc +[ 38%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/line_trace_renderer.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/line_trace_renderer.cc.o -MF CMakeFiles/ost_gfx.dir/impl/line_trace_renderer.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/line_trace_renderer.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/impl/line_trace_renderer.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color.hh:31, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/scene.hh:37, - from /build/openstructure-2.3.1/modules/gfx/src/impl/connect_renderer_base.cc:23: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer.hh:32, + from /build/openstructure-2.3.1/modules/gfx/src/impl/cpk_renderer.hh:24, + from /build/openstructure-2.3.1/modules/gfx/src/impl/cpk_renderer.cc:19: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/stl_tree.h:63, - from /usr/include/c++/12/map:60, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/scene.hh:26: +In file included from /usr/include/c++/12/string:45, + from /usr/include/c++/12/stdexcept:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec3.hh:22, + from /build/openstructure-2.3.1/modules/gfx/src/impl/cpk_renderer.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -13466,25 +13372,24 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 39%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/tabulated_trig.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/tabulated_trig.cc.o -MF CMakeFiles/ost_gfx.dir/impl/tabulated_trig.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/tabulated_trig.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/impl/tabulated_trig.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, - from /build/openstructure-2.3.1/modules/mol/alg/src/pdbize.hh:22, - from /build/openstructure-2.3.1/modules/mol/alg/src/pdbize.cc:19: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, + from /build/openstructure-2.3.1/modules/mol/alg/src/contact_overlap.cc:2: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/specfun.h:45, - from /usr/include/c++/12/cmath:1935, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:24: +In file included from /usr/include/c++/12/string:45, + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/ostream:38, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, + from /build/openstructure-2.3.1/modules/mol/alg/src/contact_overlap.cc:1: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -13494,26 +13399,28 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 39%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/contact_overlap.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/contact_overlap.cc.o -MF CMakeFiles/ost_mol_alg.dir/contact_overlap.cc.o.d -o CMakeFiles/ost_mol_alg.dir/contact_overlap.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/src/contact_overlap.cc +[ 38%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/similarity_matrix.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/similarity_matrix.cc.o -MF CMakeFiles/ost_mol_alg.dir/similarity_matrix.cc.o.d -o CMakeFiles/ost_mol_alg.dir/similarity_matrix.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/src/similarity_matrix.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, - from /build/openstructure-2.3.1/modules/mol/alg/src/pdbize.hh:25: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, + from /build/openstructure-2.3.1/modules/mol/alg/src/contact_overlap.cc:3: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 39%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/trace_renderer.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/trace_renderer.cc.o -MF CMakeFiles/ost_gfx.dir/impl/trace_renderer.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/trace_renderer.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/impl/trace_renderer.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/extent.hh:34, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_factory.hh:32, - from /build/openstructure-2.3.1/modules/mol/alg/src/adjacency_bitmap.cc:19: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer.hh:32, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/trace_renderer_base.hh:27, + from /build/openstructure-2.3.1/modules/gfx/src/impl/debug_renderer.hh:22, + from /build/openstructure-2.3.1/modules/gfx/src/impl/debug_renderer.cc:19: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -13521,8 +13428,8 @@ from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/module_config.hh:23, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_factory.hh:31: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/module_config.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/trace_renderer_base.hh:26: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -13532,21 +13439,23 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 39%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/fast_spheres.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/fast_spheres.cc.o -MF CMakeFiles/ost_gfx.dir/impl/fast_spheres.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/fast_spheres.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/impl/fast_spheres.cc +[ 38%] Linking CXX shared module ../../../../stage/lib/python3.11/dist-packages/ost/img/alg/_ost_img_alg.so +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_img_alg.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -o ../../../../stage/lib/python3.11/dist-packages/ost/img/alg/_ost_img_alg.so CMakeFiles/_ost_img_alg.dir/wrap_alg.cc.o CMakeFiles/_ost_img_alg.dir/export_filter.cc.o CMakeFiles/_ost_img_alg.dir/export_normalizer.cc.o CMakeFiles/_ost_img_alg.dir/export_transcendentals.cc.o CMakeFiles/_ost_img_alg.dir/export_polar.cc.o -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib: ../../../../stage/lib/libost_img_alg.so.2.3.1 /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libfftw3f_threads.so ../../../../stage/lib/libost_img.so.2.3.1 ../../../../stage/lib/libost_info.so.2.3.1 ../../../../stage/lib/libost_base.so.2.3.1 ../../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color.hh:31, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/scene.hh:37, - from /build/openstructure-2.3.1/modules/gfx/src/impl/trace_renderer_base.cc:24: + from /build/openstructure-2.3.1/modules/gfx/src/impl/simple_renderer.cc:25: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/stl_tree.h:63, - from /usr/include/c++/12/map:60, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/scene.hh:26: +In file included from /usr/include/c++/12/string:45, + from /usr/include/c++/12/stdexcept:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec3.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gl_helper.hh:36, + from /build/openstructure-2.3.1/modules/gfx/src/impl/simple_renderer.cc:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -13556,37 +13465,29 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 39%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/render_options.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/render_options.cc.o -MF CMakeFiles/ost_gfx.dir/render_options/render_options.cc.o.d -o CMakeFiles/ost_gfx.dir/render_options/render_options.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/render_options/render_options.cc -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, - from /build/openstructure-2.3.1/modules/mol/alg/src/adjacency_bitmap.hh:9, - from /build/openstructure-2.3.1/modules/mol/alg/src/adjacency_bitmap.cc:24: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 32 | : public std::iterator{ - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -[ 39%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/domain_find.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/domain_find.cc.o -MF CMakeFiles/ost_mol_alg.dir/domain_find.cc.o.d -o CMakeFiles/ost_mol_alg.dir/domain_find.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/src/domain_find.cc -[ 39%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/line_render_options.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/line_render_options.cc.o -MF CMakeFiles/ost_gfx.dir/render_options/line_render_options.cc.o.d -o CMakeFiles/ost_gfx.dir/render_options/line_render_options.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/render_options/line_render_options.cc +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/img/alg/pymod/__init__.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/img/alg/./__init__.pyc\",\"__init__.py\",doraise=True)" +make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[ 38%] Built target _ost_img_alg In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_property_mapper.hh:29, - from /build/openstructure-2.3.1/modules/gfx/src/impl/mapped_property.cc:20: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/backbone_trace.hh:26, + from /build/openstructure-2.3.1/modules/gfx/src/impl/sline_renderer.hh:29, + from /build/openstructure-2.3.1/modules/gfx/src/impl/sline_renderer.cc:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/vector:60, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_property_mapper.hh:28: + from /usr/include/c++/12/memory:63, + from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, + from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, + from /usr/include/boost/shared_ptr.hpp:17, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity_fw.hh:22, + from /build/openstructure-2.3.1/modules/gfx/src/impl/sline_renderer.hh:27: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -13596,18 +13497,18 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 39%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/custom_render_options.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/custom_render_options.cc.o -MF CMakeFiles/ost_gfx.dir/render_options/custom_render_options.cc.o.d -o CMakeFiles/ost_gfx.dir/render_options/custom_render_options.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/render_options/custom_render_options.cc -[ 39%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/similarity_matrix.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/similarity_matrix.cc.o -MF CMakeFiles/ost_mol_alg.dir/similarity_matrix.cc.o.d -o CMakeFiles/ost_mol_alg.dir/similarity_matrix.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/src/similarity_matrix.cc +[ 38%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/backbone_trace.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/backbone_trace.cc.o -MF CMakeFiles/ost_gfx.dir/impl/backbone_trace.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/backbone_trace.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/impl/backbone_trace.cc +[ 38%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/accessibility.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/accessibility.cc.o -MF CMakeFiles/ost_mol_alg.dir/accessibility.cc.o.d -o CMakeFiles/ost_mol_alg.dir/accessibility.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/src/accessibility.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, - from /build/openstructure-2.3.1/modules/mol/alg/src/contact_overlap.cc:2: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, + from /build/openstructure-2.3.1/modules/mol/alg/src/similarity_matrix.hh:7, + from /build/openstructure-2.3.1/modules/mol/alg/src/similarity_matrix.cc:1: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -13615,9 +13516,9 @@ from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/ostream:38, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, - from /build/openstructure-2.3.1/modules/mol/alg/src/contact_overlap.cc:1: + from /usr/include/c++/12/istream:38, + from /usr/include/c++/12/fstream:38, + from /build/openstructure-2.3.1/modules/mol/alg/src/similarity_matrix.hh:5: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -13627,28 +13528,26 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, - from /build/openstructure-2.3.1/modules/mol/alg/src/contact_overlap.cc:3: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 32 | : public std::iterator{ - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ +[ 38%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/sec_struct.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/sec_struct.cc.o -MF CMakeFiles/ost_mol_alg.dir/sec_struct.cc.o.d -o CMakeFiles/ost_mol_alg.dir/sec_struct.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/src/sec_struct.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color.hh:31, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/scene.hh:37, - from /build/openstructure-2.3.1/modules/gfx/src/impl/fast_spheres.cc:28: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/backbone_trace.hh:26, + from /build/openstructure-2.3.1/modules/gfx/src/impl/line_trace_renderer.hh:29, + from /build/openstructure-2.3.1/modules/gfx/src/impl/line_trace_renderer.cc:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/stl_tree.h:63, - from /usr/include/c++/12/map:60, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/scene.hh:26: + from /usr/include/c++/12/bits/specfun.h:45, + from /usr/include/c++/12/cmath:1935, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -13658,30 +13557,30 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 39%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/cpk_render_options.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/cpk_render_options.cc.o -MF CMakeFiles/ost_gfx.dir/render_options/cpk_render_options.cc.o.d -o CMakeFiles/ost_gfx.dir/render_options/cpk_render_options.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/render_options/cpk_render_options.cc -[ 39%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/simple_render_options.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/simple_render_options.cc.o -MF CMakeFiles/ost_gfx.dir/render_options/simple_render_options.cc.o.d -o CMakeFiles/ost_gfx.dir/render_options/simple_render_options.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/render_options/simple_render_options.cc -[ 39%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/sline_render_options.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/sline_render_options.cc.o -MF CMakeFiles/ost_gfx.dir/render_options/sline_render_options.cc.o.d -o CMakeFiles/ost_gfx.dir/render_options/sline_render_options.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/render_options/sline_render_options.cc +[ 38%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/connect_renderer_base.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/connect_renderer_base.cc.o -MF CMakeFiles/ost_gfx.dir/impl/connect_renderer_base.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/connect_renderer_base.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/impl/connect_renderer_base.cc +[ 38%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/nonstandard.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/nonstandard.cc.o -MF CMakeFiles/ost_mol_alg.dir/nonstandard.cc.o.d -o CMakeFiles/ost_mol_alg.dir/nonstandard.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/src/nonstandard.cc +[ 38%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/trace_renderer_base.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/trace_renderer_base.cc.o -MF CMakeFiles/ost_gfx.dir/impl/trace_renderer_base.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/trace_renderer_base.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/impl/trace_renderer_base.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, - from /build/openstructure-2.3.1/modules/mol/alg/src/similarity_matrix.hh:7, - from /build/openstructure-2.3.1/modules/mol/alg/src/similarity_matrix.cc:1: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/extent.hh:34, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_factory.hh:32, + from /build/openstructure-2.3.1/modules/mol/alg/src/domain_find.cc:3: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/istream:38, - from /usr/include/c++/12/fstream:38, - from /build/openstructure-2.3.1/modules/mol/alg/src/similarity_matrix.hh:5: + from /usr/include/boost/thread/exceptions.hpp:20, + from /usr/include/boost/thread/pthread/thread_data.hpp:10, + from /usr/include/boost/thread/thread_only.hpp:17, + from /usr/include/boost/thread/thread.hpp:12, + from /usr/include/boost/thread.hpp:13, + from /build/openstructure-2.3.1/modules/mol/alg/src/domain_find.cc:1: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -13691,19 +13590,30 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 39%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/line_trace_render_options.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/line_trace_render_options.cc.o -MF CMakeFiles/ost_gfx.dir/render_options/line_trace_render_options.cc.o.d -o CMakeFiles/ost_gfx.dir/render_options/line_trace_render_options.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/render_options/line_trace_render_options.cc +[ 38%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/mapped_property.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/mapped_property.cc.o -MF CMakeFiles/ost_gfx.dir/impl/mapped_property.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/mapped_property.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/impl/mapped_property.cc +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, + from /build/openstructure-2.3.1/modules/mol/alg/src/domain_find.cc:9: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 32 | : public std::iterator{ + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 39%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/tabulated_trig.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/tabulated_trig.cc.o -MF CMakeFiles/ost_gfx.dir/impl/tabulated_trig.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/tabulated_trig.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/impl/tabulated_trig.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:29, - from /build/openstructure-2.3.1/modules/gfx/src/impl/trace_renderer.cc:24: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/sec_struct.hh:25, + from /build/openstructure-2.3.1/modules/mol/alg/src/sec_struct.cc:1: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:25: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/sec_struct.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -13730,16 +13640,14 @@ /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 39%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/cartoon_render_options.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/cartoon_render_options.cc.o -MF CMakeFiles/ost_gfx.dir/render_options/cartoon_render_options.cc.o.d -o CMakeFiles/ost_gfx.dir/render_options/cartoon_render_options.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/render_options/cartoon_render_options.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:29, - from /build/openstructure-2.3.1/modules/gfx/src/render_options/render_options.cc:23: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/accessibility.hh:23, + from /build/openstructure-2.3.1/modules/mol/alg/src/accessibility.cc:1: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -13747,9 +13655,8 @@ from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/module_config.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/input.hh:30, - from /build/openstructure-2.3.1/modules/gfx/src/render_options/render_options.cc:22: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -13759,36 +13666,28 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 41%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/trace_render_options.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/trace_render_options.cc.o -MF CMakeFiles/ost_gfx.dir/render_options/trace_render_options.cc.o.d -o CMakeFiles/ost_gfx.dir/render_options/trace_render_options.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/render_options/trace_render_options.cc -[ 41%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/map_handle_color_op.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/map_handle_color_op.cc.o -MF CMakeFiles/ost_gfx.dir/color_ops/map_handle_color_op.cc.o.d -o CMakeFiles/ost_gfx.dir/color_ops/map_handle_color_op.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/color_ops/map_handle_color_op.cc -[ 41%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/map_iso.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/map_iso.cc.o -MF CMakeFiles/ost_gfx.dir/map_iso.cc.o.d -o CMakeFiles/ost_gfx.dir/map_iso.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/map_iso.cc -[ 41%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/accessibility.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/accessibility.cc.o -MF CMakeFiles/ost_mol_alg.dir/accessibility.cc.o.d -o CMakeFiles/ost_mol_alg.dir/accessibility.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/src/accessibility.cc -[ 41%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/sec_struct.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/sec_struct.cc.o -MF CMakeFiles/ost_mol_alg.dir/sec_struct.cc.o.d -o CMakeFiles/ost_mol_alg.dir/sec_struct.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/src/sec_struct.cc -[ 41%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/map_slab.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/map_slab.cc.o -MF CMakeFiles/ost_gfx.dir/map_slab.cc.o.d -o CMakeFiles/ost_gfx.dir/map_slab.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/map_slab.cc +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 39%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/trace_renderer.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/trace_renderer.cc.o -MF CMakeFiles/ost_gfx.dir/impl/trace_renderer.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/trace_renderer.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/impl/trace_renderer.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/info_group.hh:33, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/info.hh:32, - from /build/openstructure-2.3.1/modules/seq/base/pymod/export_sequence.cc:30: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, + from /build/openstructure-2.3.1/modules/gfx/src/impl/backbone_trace.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, - from /usr/include/c++/12/math.h:36, - from /usr/include/python3.11/pyport.h:218, - from /usr/include/python3.11/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -13798,51 +13697,24 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, - from /build/openstructure-2.3.1/modules/seq/base/pymod/export_sequence.cc:34: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 32 | : public std::iterator{ - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_region.hh:27, - from /build/openstructure-2.3.1/modules/seq/base/pymod/export_sequence.cc:37: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_column_iterator.hh:29:43: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 29 | class AlignedColumnIterator : public std::iterator struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/12/string:45, - from /usr/include/boost/thread/exceptions.hpp:20, - from /usr/include/boost/thread/pthread/thread_data.hpp:10, - from /usr/include/boost/thread/thread_only.hpp:17, - from /usr/include/boost/thread/thread.hpp:12, - from /usr/include/boost/thread.hpp:13, - from /build/openstructure-2.3.1/modules/mol/alg/src/domain_find.cc:1: +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/bits/specfun.h:45, + from /usr/include/c++/12/cmath:1935, + from /usr/include/c++/12/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -13852,17 +13724,6 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 41%] Building CXX object modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/export_profile_handle.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_seq_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/export_profile_handle.cc.o -MF CMakeFiles/_ost_seq.dir/export_profile_handle.cc.o.d -o CMakeFiles/_ost_seq.dir/export_profile_handle.cc.o -c /build/openstructure-2.3.1/modules/seq/base/pymod/export_profile_handle.cc -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, - from /build/openstructure-2.3.1/modules/mol/alg/src/domain_find.cc:9: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 32 | : public std::iterator{ - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ In file included from /usr/include/c++/12/string:53: In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:866:17, @@ -13952,20 +13813,64 @@ /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, + from /build/openstructure-2.3.1/modules/seq/base/pymod/export_sequence.cc:34: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 32 | : public std::iterator{ + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_region.hh:27, + from /build/openstructure-2.3.1/modules/seq/base/pymod/export_sequence.cc:37: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_column_iterator.hh:29:43: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 29 | class AlignedColumnIterator : public std::iterator struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color.hh:31, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/scene.hh:37, + from /build/openstructure-2.3.1/modules/gfx/src/impl/connect_renderer_base.cc:23: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/bits/stl_tree.h:63, + from /usr/include/c++/12/map:60, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/scene.hh:26: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/ostream:38, - from /usr/include/c++/12/iostream:39, - from /build/openstructure-2.3.1/modules/gfx/src/impl/map_iso_gen.cc:23: + from /usr/include/c++/12/stdexcept:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, + from /build/openstructure-2.3.1/modules/mol/alg/src/nonstandard.cc:24: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -14235,18 +14140,40 @@ from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/accessibility.hh:23, - from /build/openstructure-2.3.1/modules/mol/alg/src/accessibility.cc:1: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_property_mapper.hh:29, + from /build/openstructure-2.3.1/modules/gfx/src/impl/mapped_property.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/specfun.h:45, - from /usr/include/c++/12/cmath:1935, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:24: + from /usr/include/c++/12/vector:60, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_property_mapper.hh:28: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 39%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/line_render_options.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/line_render_options.cc.o -MF CMakeFiles/ost_gfx.dir/render_options/line_render_options.cc.o.d -o CMakeFiles/ost_gfx.dir/render_options/line_render_options.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/render_options/line_render_options.cc +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color.hh:31, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/scene.hh:37, + from /build/openstructure-2.3.1/modules/gfx/src/impl/trace_renderer_base.cc:24: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/bits/stl_tree.h:63, + from /usr/include/c++/12/map:60, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/scene.hh:26: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -14260,7 +14187,7 @@ from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:29, - from /build/openstructure-2.3.1/modules/gfx/src/color_ops/map_handle_color_op.cc:20: + from /build/openstructure-2.3.1/modules/gfx/src/impl/trace_renderer.cc:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -14276,20 +14203,29 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 41%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/molck.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/molck.cc.o -MF CMakeFiles/ost_mol_alg.dir/molck.cc.o.d -o CMakeFiles/ost_mol_alg.dir/molck.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/src/molck.cc +[ 41%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/custom_render_options.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/custom_render_options.cc.o -MF CMakeFiles/ost_gfx.dir/render_options/custom_render_options.cc.o.d -o CMakeFiles/ost_gfx.dir/render_options/custom_render_options.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/render_options/custom_render_options.cc +[ 41%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/cpk_render_options.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/cpk_render_options.cc.o -MF CMakeFiles/ost_gfx.dir/render_options/cpk_render_options.cc.o.d -o CMakeFiles/ost_gfx.dir/render_options/cpk_render_options.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/render_options/cpk_render_options.cc +[ 41%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/find_membrane.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/find_membrane.cc.o -MF CMakeFiles/ost_mol_alg.dir/find_membrane.cc.o.d -o CMakeFiles/ost_mol_alg.dir/find_membrane.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/src/find_membrane.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/vertex_array.hh:34, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/map_iso_prop.hh:26, - from /build/openstructure-2.3.1/modules/gfx/src/impl/map_iso_gen_o.cc:24: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:29, + from /build/openstructure-2.3.1/modules/gfx/src/render_options/render_options.cc:23: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/memory:63, - from /usr/include/boost/smart_ptr/shared_array.hpp:19, - from /usr/include/boost/shared_array.hpp:17, - from /build/openstructure-2.3.1/modules/gfx/src/impl/map_iso_gen_o.cc:21: + from /usr/include/c++/12/bits/specfun.h:45, + from /usr/include/c++/12/cmath:1935, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/module_config.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/input.hh:30, + from /build/openstructure-2.3.1/modules/gfx/src/render_options/render_options.cc:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -14299,17 +14235,21 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 41%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/entity_to_density.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/entity_to_density.cc.o -MF CMakeFiles/ost_mol_alg.dir/entity_to_density.cc.o.d -o CMakeFiles/ost_mol_alg.dir/entity_to_density.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/src/entity_to_density.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/sec_struct.hh:25, - from /build/openstructure-2.3.1/modules/mol/alg/src/sec_struct.cc:1: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color.hh:31, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/scene.hh:37, + from /build/openstructure-2.3.1/modules/gfx/src/impl/fast_spheres.cc:28: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/vector:60, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/sec_struct.hh:22: + from /usr/include/c++/12/bits/stl_tree.h:63, + from /usr/include/c++/12/map:60, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/scene.hh:26: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -14319,24 +14259,160 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 41%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/simple_render_options.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/simple_render_options.cc.o -MF CMakeFiles/ost_gfx.dir/render_options/simple_render_options.cc.o.d -o CMakeFiles/ost_gfx.dir/render_options/simple_render_options.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/render_options/simple_render_options.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/discrete_shrink.hh:24, - from /build/openstructure-2.3.1/modules/gfx/src/map_iso.cc:27: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/xcs_editor.hh:26, + from /build/openstructure-2.3.1/modules/mol/alg/src/molck.cc:1: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/12/string:45, +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/bits/specfun.h:45, + from /usr/include/c++/12/cmath:1935, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/xcs_editor.hh:25: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 41%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/sline_render_options.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/sline_render_options.cc.o -MF CMakeFiles/ost_gfx.dir/render_options/sline_render_options.cc.o.d -o CMakeFiles/ost_gfx.dir/render_options/sline_render_options.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/render_options/sline_render_options.cc +[ 41%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/line_trace_render_options.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/line_trace_render_options.cc.o -MF CMakeFiles/ost_gfx.dir/render_options/line_trace_render_options.cc.o.d -o CMakeFiles/ost_gfx.dir/render_options/line_trace_render_options.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/render_options/line_trace_render_options.cc +[ 41%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/cartoon_render_options.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/cartoon_render_options.cc.o -MF CMakeFiles/ost_gfx.dir/render_options/cartoon_render_options.cc.o.d -o CMakeFiles/ost_gfx.dir/render_options/cartoon_render_options.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/render_options/cartoon_render_options.cc +In file included from /usr/include/c++/12/string:53, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/ostream:38, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, - from /build/openstructure-2.3.1/modules/gfx/src/map_iso.cc:23: + from /usr/include/c++/12/istream:38, + from /usr/include/c++/12/sstream:38, + from /usr/include/c++/12/complex:45, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:24: +In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', + inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:866:17, + inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, + inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, + inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, + inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, + inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, + inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, + inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, + inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, + inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, + inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, + inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38: +/usr/include/c++/12/bits/basic_string.h:1064:16: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] + 1064 | { return _M_string_length; } + | ^~~~~~~~~~~~~~~~ +In file included from /usr/include/boost/variant.hpp:17, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:34, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_base.hh:25, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:27: +/usr/include/boost/variant/variant.hpp: In member function 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]': +/usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here + 2107 | variant temp(rhs); + | ^~~~ +In file included from /usr/include/c++/12/ios:40: +In static member function 'static constexpr void std::char_traits::assign(char_type&, const char_type&)', + inlined from 'static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:421:23, + inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:867:18, + inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, + inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, + inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, + inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, + inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, + inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, + inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, + inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, + inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, + inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, + inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38: +/usr/include/c++/12/bits/char_traits.h:354:16: warning: '((const std::char_traits::char_type*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]' may be used uninitialized [-Wmaybe-uninitialized] + 354 | __c1 = __c2; + | ^~~~ +/usr/include/boost/variant/variant.hpp: In member function 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]': +/usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here + 2107 | variant temp(rhs); + | ^~~~ +In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', + inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, + inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, + inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, + inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, + inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, + inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, + inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, + inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, + inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, + inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, + inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, + inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38: +/usr/include/c++/12/bits/basic_string.h:1071:16: warning: '*(const __vector(2) long unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' may be used uninitialized [-Wmaybe-uninitialized] + 1071 | { return _M_string_length; } + | ^~~~~~~~~~~~~~~~ +/usr/include/boost/variant/variant.hpp: In member function 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]': +/usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here + 2107 | variant temp(rhs); + | ^~~~ +In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', + inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, + inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, + inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, + inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, + inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, + inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, + inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, + inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, + inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, + inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, + inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, + inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38: +/usr/include/c++/12/bits/basic_string.h:1071:16: warning: '*(const __vector(2) long unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' may be used uninitialized [-Wmaybe-uninitialized] + 1071 | { return _M_string_length; } + | ^~~~~~~~~~~~~~~~ +/usr/include/boost/variant/variant.hpp: In member function 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]': +/usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here + 2107 | variant temp(rhs); + | ^~~~ +In file included from /build/openstructure-2.3.1/modules/mol/alg/src/molck.cc:4: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/amino_acids.hh:61:42: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 61 | class AminoAcidSetIterator : public std::iterator struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/bits/specfun.h:45, + from /usr/include/c++/12/cmath:1935, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -14346,6 +14422,27 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 42%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/map_iso.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/map_iso.cc.o -MF CMakeFiles/ost_gfx.dir/map_iso.cc.o.d -o CMakeFiles/ost_gfx.dir/map_iso.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/map_iso.cc +[ 42%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/map_slab.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/map_slab.cc.o -MF CMakeFiles/ost_gfx.dir/map_slab.cc.o.d -o CMakeFiles/ost_gfx.dir/map_slab.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/map_slab.cc +[ 42%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/map_iso_gen.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/map_iso_gen.cc.o -MF CMakeFiles/ost_gfx.dir/impl/map_iso_gen.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/map_iso_gen.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/impl/map_iso_gen.cc +[ 42%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/map_iso_gen_s.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/map_iso_gen_s.cc.o -MF CMakeFiles/ost_gfx.dir/impl/map_iso_gen_s.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/map_iso_gen_s.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/impl/map_iso_gen_s.cc +In file included from /build/openstructure-2.3.1/modules/mol/alg/src/domain_find.cc:11: +In member function 'void ost::mol::alg::AdjacencyBitmap::set(size_t, size_t, bool, bool)', + inlined from 'ost::mol::alg::AdjacencyBitmap::AdjacencyBitmap(const ost::mol::alg::DistanceMatrix&, const ost::mol::alg::DistanceMatrix&, Real, Real, int, int)' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/adjacency_bitmap.hh:49:16, + inlined from 'static ost::mol::alg::DomainsPtr ost::mol::alg::Domains::FromDistMats(const ost::mol::alg::DistanceMatrix&, const ost::mol::alg::DistanceMatrix&, Real, Real, Real, int, bool, bool)' at /build/openstructure-2.3.1/modules/mol/alg/src/domain_find.cc:363:37: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/adjacency_bitmap.hh:109:23: warning: 'malloc' may be used uninitialized [-Wmaybe-uninitialized] + 109 | data_[byte_index] &= ~(one << bit_index); + | ~~~~~~~~~~~~~~~~^ +[ 42%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/map_iso_gen_o.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/map_iso_gen_o.cc.o -MF CMakeFiles/ost_gfx.dir/impl/map_iso_gen_o.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/map_iso_gen_o.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/impl/map_iso_gen_o.cc +[ 42%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/map_octree.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/map_octree.cc.o -MF CMakeFiles/ost_gfx.dir/impl/map_octree.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/map_octree.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/impl/map_octree.cc +[ 42%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/octree_isocont.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/octree_isocont.cc.o -MF CMakeFiles/ost_gfx.dir/impl/octree_isocont.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/octree_isocont.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/impl/octree_isocont.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -14353,14 +14450,18 @@ from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/stat.hh:30, - from /build/openstructure-2.3.1/modules/gfx/src/map_slab.cc:26: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/dft.hh:24, + from /build/openstructure-2.3.1/modules/mol/alg/src/entity_to_density.cc:10: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/vector:60, - from /build/openstructure-2.3.1/modules/gfx/src/map_slab.cc:22: +In file included from /usr/include/c++/12/string:45, + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/istream:38, + from /usr/include/c++/12/sstream:38, + from /build/openstructure-2.3.1/modules/mol/alg/src/entity_to_density.cc:1: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -14370,25 +14471,26 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 42%] Building CXX object modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/export_profile_handle.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_seq_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/export_profile_handle.cc.o -MF CMakeFiles/_ost_seq.dir/export_profile_handle.cc.o.d -o CMakeFiles/_ost_seq.dir/export_profile_handle.cc.o -c /build/openstructure-2.3.1/modules/seq/base/pymod/export_profile_handle.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_handle.hh:38, - from /build/openstructure-2.3.1/modules/gfx/src/impl/map_octree.hh:22, - from /build/openstructure-2.3.1/modules/gfx/src/impl/map_octree.cc:24: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/discrete_shrink.hh:24, + from /build/openstructure-2.3.1/modules/gfx/src/map_iso.cc:27: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/memory:63, - from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, - from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, - from /usr/include/boost/shared_ptr.hpp:17, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_handle.hh:32: +In file included from /usr/include/c++/12/string:45, + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/ostream:38, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, + from /build/openstructure-2.3.1/modules/gfx/src/map_iso.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -14401,20 +14503,14 @@ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, - from /build/openstructure-2.3.1/modules/gfx/src/impl/map_iso_gen_s.cc:25: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:29, + from /build/openstructure-2.3.1/modules/gfx/src/color_ops/map_handle_color_op.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/memory:63, - from /usr/include/boost/smart_ptr/shared_array.hpp:19, - from /usr/include/boost/shared_array.hpp:17, - from /build/openstructure-2.3.1/modules/gfx/src/impl/map_iso_gen_s.cc:21: + from /usr/include/c++/12/vector:60, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -14424,34 +14520,20 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 41%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/nonstandard.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/nonstandard.cc.o -MF CMakeFiles/ost_mol_alg.dir/nonstandard.cc.o.d -o CMakeFiles/ost_mol_alg.dir/nonstandard.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/src/nonstandard.cc -[ 41%] Building CXX object modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/wrap_seq.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_seq_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/wrap_seq.cc.o -MF CMakeFiles/_ost_seq.dir/wrap_seq.cc.o.d -o CMakeFiles/_ost_seq.dir/wrap_seq.cc.o -c /build/openstructure-2.3.1/modules/seq/base/pymod/wrap_seq.cc -[ 42%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/molck.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/molck.cc.o -MF CMakeFiles/ost_mol_alg.dir/molck.cc.o.d -o CMakeFiles/ost_mol_alg.dir/molck.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/src/molck.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_handle.hh:38, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/octree_isocont.hh:27, - from /build/openstructure-2.3.1/modules/gfx/src/impl/octree_isocont.cc:24: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/vertex_array.hh:34, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/map_iso_prop.hh:26, + from /build/openstructure-2.3.1/modules/gfx/src/impl/map_iso_gen_o.cc:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_construct.h:61, - from /usr/include/c++/12/bits/alloc_traits.h:33, - from /usr/include/c++/12/ext/alloc_traits.h:34, - from /usr/include/c++/12/unordered_map:41, - from /usr/include/c++/12/functional:61, - from /usr/include/boost/container_hash/hash.hpp:20, - from /usr/include/boost/functional/hash.hpp:6, - from /usr/include/boost/unordered/unordered_map.hpp:18, - from /usr/include/boost/unordered_map.hpp:17, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/octree_isocont.hh:25: +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/memory:63, + from /usr/include/boost/smart_ptr/shared_array.hpp:19, + from /usr/include/boost/shared_array.hpp:17, + from /build/openstructure-2.3.1/modules/gfx/src/impl/map_iso_gen_o.cc:21: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -14464,18 +14546,18 @@ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/conop.hh:24, - from /build/openstructure-2.3.1/modules/mol/alg/src/nonstandard.cc:27: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/stat.hh:30, + from /build/openstructure-2.3.1/modules/gfx/src/map_slab.cc:26: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/12/string:45, - from /usr/include/c++/12/stdexcept:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, - from /build/openstructure-2.3.1/modules/mol/alg/src/nonstandard.cc:24: +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/vector:60, + from /build/openstructure-2.3.1/modules/gfx/src/map_slab.cc:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -14485,24 +14567,25 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 42%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/find_membrane.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/find_membrane.cc.o -MF CMakeFiles/ost_mol_alg.dir/find_membrane.cc.o.d -o CMakeFiles/ost_mol_alg.dir/find_membrane.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/src/find_membrane.cc -[ 42%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/entity_to_density.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/entity_to_density.cc.o -MF CMakeFiles/ost_mol_alg.dir/entity_to_density.cc.o.d -o CMakeFiles/ost_mol_alg.dir/entity_to_density.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/src/entity_to_density.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/xcs_editor.hh:26, - from /build/openstructure-2.3.1/modules/mol/alg/src/molck.cc:1: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_handle.hh:38, + from /build/openstructure-2.3.1/modules/gfx/src/impl/map_octree.hh:22, + from /build/openstructure-2.3.1/modules/gfx/src/impl/map_octree.cc:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/specfun.h:45, - from /usr/include/c++/12/cmath:1935, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/xcs_editor.hh:25: + from /usr/include/c++/12/memory:63, + from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, + from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, + from /usr/include/boost/shared_ptr.hpp:17, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_handle.hh:32: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -14515,21 +14598,17 @@ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/find_membrane.hh:22, - from /build/openstructure-2.3.1/modules/mol/alg/src/find_membrane.cc:1: + from /build/openstructure-2.3.1/modules/gfx/src/impl/map_iso_gen.cc:28: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/specfun.h:45, - from /usr/include/c++/12/cmath:1935, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: +In file included from /usr/include/c++/12/string:45, + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/ostream:38, + from /usr/include/c++/12/iostream:39, + from /build/openstructure-2.3.1/modules/gfx/src/impl/map_iso_gen.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -14539,13 +14618,6 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/openstructure-2.3.1/modules/mol/alg/src/molck.cc:4: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/amino_acids.hh:61:42: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 61 | class AminoAcidSetIterator : public std::iterator::run(Index, Index, const LhsScalar*, Index, const RhsScalar*, Index, ResScalar*, Index, const ResScalar&) [with Index = long int; int Mode = 6; LhsScalar = float; bool ConjLhs = false; RhsScalar = float; bool ConjRhs = false; int Version = 0]' declared here 105 | EIGEN_DONT_INLINE void triangular_matrix_vector_product | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, + from /build/openstructure-2.3.1/modules/gfx/src/impl/map_iso_gen_s.cc:25: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/memory:63, + from /usr/include/boost/smart_ptr/shared_array.hpp:19, + from /usr/include/boost/shared_array.hpp:17, + from /build/openstructure-2.3.1/modules/gfx/src/impl/map_iso_gen_s.cc:21: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_handle.hh:38, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/octree_isocont.hh:27, + from /build/openstructure-2.3.1/modules/gfx/src/impl/octree_isocont.cc:24: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/12/bits/stl_construct.h:61, + from /usr/include/c++/12/bits/alloc_traits.h:33, + from /usr/include/c++/12/ext/alloc_traits.h:34, + from /usr/include/c++/12/unordered_map:41, + from /usr/include/c++/12/functional:61, + from /usr/include/boost/container_hash/hash.hpp:20, + from /usr/include/boost/functional/hash.hpp:6, + from /usr/include/boost/unordered/unordered_map.hpp:18, + from /usr/include/boost/unordered_map.hpp:17, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/octree_isocont.hh:25: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 42%] Building CXX object modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/wrap_seq.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_seq_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/wrap_seq.cc.o -MF CMakeFiles/_ost_seq.dir/wrap_seq.cc.o.d -o CMakeFiles/_ost_seq.dir/wrap_seq.cc.o -c /build/openstructure-2.3.1/modules/seq/base/pymod/wrap_seq.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -14597,107 +14728,6 @@ /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/string:53, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/istream:38, - from /usr/include/c++/12/sstream:38, - from /usr/include/c++/12/complex:45, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:24: -In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', - inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:866:17, - inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, - inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, - inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, - inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, - inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, - inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, - inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, - inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, - inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, - inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, - inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38: -/usr/include/c++/12/bits/basic_string.h:1064:16: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] - 1064 | { return _M_string_length; } - | ^~~~~~~~~~~~~~~~ -In file included from /usr/include/boost/variant.hpp:17, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:34, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_base.hh:25, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:27: -/usr/include/boost/variant/variant.hpp: In member function 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]': -/usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here - 2107 | variant temp(rhs); - | ^~~~ -In file included from /usr/include/c++/12/ios:40: -In static member function 'static constexpr void std::char_traits::assign(char_type&, const char_type&)', - inlined from 'static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:421:23, - inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:867:18, - inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, - inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, - inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, - inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, - inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, - inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, - inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, - inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, - inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, - inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, - inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38: -/usr/include/c++/12/bits/char_traits.h:354:16: warning: '((const std::char_traits::char_type*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]' may be used uninitialized [-Wmaybe-uninitialized] - 354 | __c1 = __c2; - | ^~~~ -/usr/include/boost/variant/variant.hpp: In member function 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]': -/usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here - 2107 | variant temp(rhs); - | ^~~~ -In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', - inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, - inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, - inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, - inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, - inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, - inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, - inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, - inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, - inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, - inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, - inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, - inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38: -/usr/include/c++/12/bits/basic_string.h:1071:16: warning: '*(const __vector(2) long unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' may be used uninitialized [-Wmaybe-uninitialized] - 1071 | { return _M_string_length; } - | ^~~~~~~~~~~~~~~~ -/usr/include/boost/variant/variant.hpp: In member function 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]': -/usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here - 2107 | variant temp(rhs); - | ^~~~ -In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', - inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, - inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, - inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, - inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, - inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, - inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, - inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, - inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, - inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, - inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, - inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, - inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38: -/usr/include/c++/12/bits/basic_string.h:1071:16: warning: '*(const __vector(2) long unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' may be used uninitialized [-Wmaybe-uninitialized] - 1071 | { return _M_string_length; } - | ^~~~~~~~~~~~~~~~ -/usr/include/boost/variant/variant.hpp: In member function 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]': -/usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here - 2107 | variant temp(rhs); - | ^~~~ -In file included from /build/openstructure-2.3.1/modules/mol/alg/src/domain_find.cc:11: -In member function 'void ost::mol::alg::AdjacencyBitmap::set(size_t, size_t, bool, bool)', - inlined from 'ost::mol::alg::AdjacencyBitmap::AdjacencyBitmap(const ost::mol::alg::DistanceMatrix&, const ost::mol::alg::DistanceMatrix&, Real, Real, int, int)' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/adjacency_bitmap.hh:49:16, - inlined from 'static ost::mol::alg::DomainsPtr ost::mol::alg::Domains::FromDistMats(const ost::mol::alg::DistanceMatrix&, const ost::mol::alg::DistanceMatrix&, Real, Real, Real, int, bool, bool)' at /build/openstructure-2.3.1/modules/mol/alg/src/domain_find.cc:363:37: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/adjacency_bitmap.hh:109:23: warning: 'malloc' may be used uninitialized [-Wmaybe-uninitialized] - 109 | data_[byte_index] &= ~(one << bit_index); - | ~~~~~~~~~~~~~~~~^ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -14718,34 +14748,6 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/dft.hh:24, - from /build/openstructure-2.3.1/modules/mol/alg/src/entity_to_density.cc:10: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/12/string:45, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/istream:38, - from /usr/include/c++/12/sstream:38, - from /build/openstructure-2.3.1/modules/mol/alg/src/entity_to_density.cc:1: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:866:17, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, @@ -15267,19 +15269,11 @@ /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ -[ 42%] Linking CXX shared library ../../../stage/lib/libost_gfx.so -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/test_texture.png /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/share/openstructure/textures/test_texture.png -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/glyph_texture.png /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/share/openstructure/textures/glyph_texture.png -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_gfx.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libost_gfx.so.2.3 -o ../../../stage/lib/libost_gfx.so.2.3.1 CMakeFiles/ost_gfx.dir/bitmap_io.cc.o CMakeFiles/ost_gfx.dir/exporter.cc.o CMakeFiles/ost_gfx.dir/collada_exporter.cc.o CMakeFiles/ost_gfx.dir/color.cc.o CMakeFiles/ost_gfx.dir/primitives.cc.o CMakeFiles/ost_gfx.dir/entity.cc.o CMakeFiles/ost_gfx.dir/symmetry_node.cc.o CMakeFiles/ost_gfx.dir/gfx_node.cc.o CMakeFiles/ost_gfx.dir/gfx_object.cc.o CMakeFiles/ost_gfx.dir/gfx_prim.cc.o CMakeFiles/ost_gfx.dir/gfx_test_object.cc.o CMakeFiles/ost_gfx.dir/input.cc.o CMakeFiles/ost_gfx.dir/prim_list.cc.o CMakeFiles/ost_gfx.dir/scene.cc.o CMakeFiles/ost_gfx.dir/selection.cc.o CMakeFiles/ost_gfx.dir/surface.cc.o CMakeFiles/ost_gfx.dir/gradient.cc.o CMakeFiles/ost_gfx.dir/gradient_manager.cc.o CMakeFiles/ost_gfx.dir/vertex_array.cc.o CMakeFiles/ost_gfx.dir/vertex_array_helper.cc.o CMakeFiles/ost_gfx.dir/material.cc.o CMakeFiles/ost_gfx.dir/povray.cc.o CMakeFiles/ost_gfx.dir/gost_exporter.cc.o CMakeFiles/ost_gfx.dir/texture.cc.o CMakeFiles/ost_gfx.dir/color_ops/color_op.cc.o CMakeFiles/ost_gfx.dir/color_ops/by_element_color_op.cc.o CMakeFiles/ost_gfx.dir/color_ops/by_chain_color_op.cc.o CMakeFiles/ost_gfx.dir/color_ops/uniform_color_op.cc.o CMakeFiles/ost_gfx.dir/color_ops/gradient_color_op.cc.o CMakeFiles/ost_gfx.dir/color_ops/entity_view_color_op.cc.o CMakeFiles/ost_gfx.dir/color_ops/basic_gradient_color_op.cc.o CMakeFiles/ost_gfx.dir/color_ops/gradient_level_color_op.cc.o CMakeFiles/ost_gfx.dir/impl/entity_renderer.cc.o CMakeFiles/ost_gfx.dir/impl/entity_detail.cc.o CMakeFiles/ost_gfx.dir/impl/cartoon_renderer.cc.o CMakeFiles/ost_gfx.dir/impl/custom_renderer.cc.o CMakeFiles/ost_gfx.dir/impl/cpk_renderer.cc.o CMakeFiles/ost_gfx.dir/impl/debug_renderer.cc.o CMakeFiles/ost_gfx.dir/impl/simple_renderer.cc.o CMakeFiles/ost_gfx.dir/impl/sline_renderer.cc.o CMakeFiles/ost_gfx.dir/impl/line_trace_renderer.cc.o CMakeFiles/ost_gfx.dir/impl/backbone_trace.cc.o CMakeFiles/ost_gfx.dir/impl/connect_renderer_base.cc.o CMakeFiles/ost_gfx.dir/impl/trace_renderer_base.cc.o CMakeFiles/ost_gfx.dir/impl/mapped_property.cc.o CMakeFiles/ost_gfx.dir/impl/tabulated_trig.cc.o CMakeFiles/ost_gfx.dir/impl/trace_renderer.cc.o CMakeFiles/ost_gfx.dir/impl/fast_spheres.cc.o CMakeFiles/ost_gfx.dir/render_options/render_options.cc.o CMakeFiles/ost_gfx.dir/render_options/line_render_options.cc.o CMakeFiles/ost_gfx.dir/render_options/custom_render_options.cc.o CMakeFiles/ost_gfx.dir/render_options/cpk_render_options.cc.o CMakeFiles/ost_gfx.dir/render_options/simple_render_options.cc.o CMakeFiles/ost_gfx.dir/render_options/sline_render_options.cc.o CMakeFiles/ost_gfx.dir/render_options/line_trace_render_options.cc.o CMakeFiles/ost_gfx.dir/render_options/cartoon_render_options.cc.o CMakeFiles/ost_gfx.dir/render_options/trace_render_options.cc.o CMakeFiles/ost_gfx.dir/color_ops/map_handle_color_op.cc.o CMakeFiles/ost_gfx.dir/map_iso.cc.o CMakeFiles/ost_gfx.dir/map_slab.cc.o CMakeFiles/ost_gfx.dir/impl/map_iso_gen.cc.o CMakeFiles/ost_gfx.dir/impl/map_iso_gen_s.cc.o CMakeFiles/ost_gfx.dir/impl/map_iso_gen_o.cc.o CMakeFiles/ost_gfx.dir/impl/map_octree.cc.o CMakeFiles/ost_gfx.dir/impl/octree_isocont.cc.o -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib: ../../../stage/lib/libost_conop.so.2.3.1 ../../../stage/lib/libost_img_alg.so.2.3.1 /usr/lib/x86_64-linux-gnu/libOpenGL.so /usr/lib/x86_64-linux-gnu/libGLX.so /usr/lib/x86_64-linux-gnu/libGLU.so /usr/lib/x86_64-linux-gnu/libpng.so /usr/lib/x86_64-linux-gnu/libz.so ../../../stage/lib/libost_db.so.2.3.1 ../../../stage/lib/libost_seq.so.2.3.1 ../../../stage/lib/libost_mol.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libsqlite3.so ../../../stage/lib/libost_img.so.2.3.1 ../../../stage/lib/libost_info.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 ../../../stage/lib/libost_base.so.2.3.1 ../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libfftw3f_threads.so [ 42%] Linking CXX shared library ../../../../stage/lib/libost_mol_alg.so cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/atom_scattering_properties.txt /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/share/openstructure/atom_scattering_properties.txt cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/stereo_chemical_props.txt /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/share/openstructure/stereo_chemical_props.txt cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_mol_alg.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libost_mol_alg.so.2.3 -o ../../../../stage/lib/libost_mol_alg.so.2.3.1 CMakeFiles/ost_mol_alg.dir/svd_superpose.cc.o CMakeFiles/ost_mol_alg.dir/clash_score.cc.o CMakeFiles/ost_mol_alg.dir/sec_structure_segments.cc.o CMakeFiles/ost_mol_alg.dir/local_dist_diff_test.cc.o CMakeFiles/ost_mol_alg.dir/distance_test_common.cc.o CMakeFiles/ost_mol_alg.dir/distance_rmsd_test.cc.o CMakeFiles/ost_mol_alg.dir/superpose_frames.cc.o CMakeFiles/ost_mol_alg.dir/filter_clashes.cc.o CMakeFiles/ost_mol_alg.dir/construct_cbeta.cc.o CMakeFiles/ost_mol_alg.dir/trajectory_analysis.cc.o CMakeFiles/ost_mol_alg.dir/structure_analysis.cc.o CMakeFiles/ost_mol_alg.dir/consistency_checks.cc.o CMakeFiles/ost_mol_alg.dir/pdbize.cc.o CMakeFiles/ost_mol_alg.dir/adjacency_bitmap.cc.o CMakeFiles/ost_mol_alg.dir/contact_overlap.cc.o CMakeFiles/ost_mol_alg.dir/domain_find.cc.o CMakeFiles/ost_mol_alg.dir/similarity_matrix.cc.o CMakeFiles/ost_mol_alg.dir/accessibility.cc.o CMakeFiles/ost_mol_alg.dir/sec_struct.cc.o CMakeFiles/ost_mol_alg.dir/nonstandard.cc.o CMakeFiles/ost_mol_alg.dir/molck.cc.o CMakeFiles/ost_mol_alg.dir/find_membrane.cc.o CMakeFiles/ost_mol_alg.dir/entity_to_density.cc.o -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib: /usr/lib/x86_64-linux-gnu/libboost_program_options.so /usr/lib/x86_64-linux-gnu/libboost_thread.so /usr/lib/x86_64-linux-gnu/libboost_chrono.so /usr/lib/x86_64-linux-gnu/libboost_date_time.so /usr/lib/x86_64-linux-gnu/libboost_atomic.so ../../../../stage/lib/libost_img_alg.so.2.3.1 ../../../../stage/lib/libost_seq_alg.so.2.3.1 ../../../../stage/lib/libost_conop.so.2.3.1 ../../../../stage/lib/libost_img.so.2.3.1 /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libfftw3f_threads.so ../../../../stage/lib/libost_db.so.2.3.1 ../../../../stage/lib/libost_seq.so.2.3.1 ../../../../stage/lib/libost_mol.so.2.3.1 ../../../../stage/lib/libost_info.so.2.3.1 /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../../stage/lib/libost_base.so.2.3.1 ../../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libsqlite3.so -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E cmake_symlink_library ../../../stage/lib/libost_gfx.so.2.3.1 ../../../stage/lib/libost_gfx.so.2.3 ../../../stage/lib/libost_gfx.so -make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 42%] Built target ost_gfx cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E cmake_symlink_library ../../../../stage/lib/libost_mol_alg.so.2.3.1 ../../../../stage/lib/libost_mol_alg.so.2.3 ../../../../stage/lib/libost_mol_alg.so make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 42%] Built target ost_mol_alg @@ -15291,36 +15285,37 @@ make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 42%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/io_manager.cc.o [ 42%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/convert.cc.o +[ 42%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/io_utils.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/io_manager.cc.o -MF CMakeFiles/ost_io.dir/io_manager.cc.o.d -o CMakeFiles/ost_io.dir/io_manager.cc.o -c /build/openstructure-2.3.1/modules/io/src/io_manager.cc -[ 42%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/entity_io_pqr_handler.cc.o [ 42%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/entity_io_crd_handler.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/convert.cc.o -MF CMakeFiles/ost_io.dir/convert.cc.o.d -o CMakeFiles/ost_io.dir/convert.cc.o -c /build/openstructure-2.3.1/modules/io/src/convert.cc -[ 42%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/io_utils.cc.o +[ 42%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/entity_io_pqr_handler.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/io_utils.cc.o -MF CMakeFiles/ost_io.dir/io_utils.cc.o.d -o CMakeFiles/ost_io.dir/io_utils.cc.o -c /build/openstructure-2.3.1/modules/io/src/io_utils.cc -[ 43%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/entity_io_pdb_handler.cc.o -[ 43%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/pdb_reader.cc.o -[ 43%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/entity_io_mae_handler.cc.o +[ 42%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/entity_io_mae_handler.cc.o +[ 42%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/pdb_reader.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/entity_io_crd_handler.cc.o -MF CMakeFiles/ost_io.dir/mol/entity_io_crd_handler.cc.o.d -o CMakeFiles/ost_io.dir/mol/entity_io_crd_handler.cc.o -c /build/openstructure-2.3.1/modules/io/src/mol/entity_io_crd_handler.cc cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/entity_io_pqr_handler.cc.o -MF CMakeFiles/ost_io.dir/mol/entity_io_pqr_handler.cc.o.d -o CMakeFiles/ost_io.dir/mol/entity_io_pqr_handler.cc.o -c /build/openstructure-2.3.1/modules/io/src/mol/entity_io_pqr_handler.cc -[ 43%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/pdb_writer.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/entity_io_mae_handler.cc.o -MF CMakeFiles/ost_io.dir/mol/entity_io_mae_handler.cc.o.d -o CMakeFiles/ost_io.dir/mol/entity_io_mae_handler.cc.o -c /build/openstructure-2.3.1/modules/io/src/mol/entity_io_mae_handler.cc cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/pdb_reader.cc.o -MF CMakeFiles/ost_io.dir/mol/pdb_reader.cc.o.d -o CMakeFiles/ost_io.dir/mol/pdb_reader.cc.o -c /build/openstructure-2.3.1/modules/io/src/mol/pdb_reader.cc +[ 43%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/entity_io_pdb_handler.cc.o +[ 43%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/pdb_writer.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/entity_io_pdb_handler.cc.o -MF CMakeFiles/ost_io.dir/mol/entity_io_pdb_handler.cc.o.d -o CMakeFiles/ost_io.dir/mol/entity_io_pdb_handler.cc.o -c /build/openstructure-2.3.1/modules/io/src/mol/entity_io_pdb_handler.cc cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/pdb_writer.cc.o -MF CMakeFiles/ost_io.dir/mol/pdb_writer.cc.o.d -o CMakeFiles/ost_io.dir/mol/pdb_writer.cc.o -c /build/openstructure-2.3.1/modules/io/src/mol/pdb_writer.cc [ 43%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/entity_io_mmcif_handler.cc.o -[ 43%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/entity_io_sdf_handler.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/entity_io_mmcif_handler.cc.o -MF CMakeFiles/ost_io.dir/mol/entity_io_mmcif_handler.cc.o.d -o CMakeFiles/ost_io.dir/mol/entity_io_mmcif_handler.cc.o -c /build/openstructure-2.3.1/modules/io/src/mol/entity_io_mmcif_handler.cc -[ 43%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/sdf_reader.cc.o +[ 43%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/entity_io_sdf_handler.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/entity_io_sdf_handler.cc.o -MF CMakeFiles/ost_io.dir/mol/entity_io_sdf_handler.cc.o.d -o CMakeFiles/ost_io.dir/mol/entity_io_sdf_handler.cc.o -c /build/openstructure-2.3.1/modules/io/src/mol/entity_io_sdf_handler.cc -[ 43%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/sdf_writer.cc.o +[ 43%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/sdf_reader.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/sdf_reader.cc.o -MF CMakeFiles/ost_io.dir/mol/sdf_reader.cc.o.d -o CMakeFiles/ost_io.dir/mol/sdf_reader.cc.o -c /build/openstructure-2.3.1/modules/io/src/mol/sdf_reader.cc +[ 43%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/sdf_writer.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/sdf_writer.cc.o -MF CMakeFiles/ost_io.dir/mol/sdf_writer.cc.o.d -o CMakeFiles/ost_io.dir/mol/sdf_writer.cc.o -c /build/openstructure-2.3.1/modules/io/src/mol/sdf_writer.cc +[ 43%] Linking CXX shared library ../../../stage/lib/libost_gfx.so +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/test_texture.png /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/share/openstructure/textures/test_texture.png +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/glyph_texture.png /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/share/openstructure/textures/glyph_texture.png +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_gfx.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libost_gfx.so.2.3 -o ../../../stage/lib/libost_gfx.so.2.3.1 CMakeFiles/ost_gfx.dir/bitmap_io.cc.o CMakeFiles/ost_gfx.dir/exporter.cc.o CMakeFiles/ost_gfx.dir/collada_exporter.cc.o CMakeFiles/ost_gfx.dir/color.cc.o CMakeFiles/ost_gfx.dir/primitives.cc.o CMakeFiles/ost_gfx.dir/entity.cc.o CMakeFiles/ost_gfx.dir/symmetry_node.cc.o CMakeFiles/ost_gfx.dir/gfx_node.cc.o CMakeFiles/ost_gfx.dir/gfx_object.cc.o CMakeFiles/ost_gfx.dir/gfx_prim.cc.o CMakeFiles/ost_gfx.dir/gfx_test_object.cc.o CMakeFiles/ost_gfx.dir/input.cc.o CMakeFiles/ost_gfx.dir/prim_list.cc.o CMakeFiles/ost_gfx.dir/scene.cc.o CMakeFiles/ost_gfx.dir/selection.cc.o CMakeFiles/ost_gfx.dir/surface.cc.o CMakeFiles/ost_gfx.dir/gradient.cc.o CMakeFiles/ost_gfx.dir/gradient_manager.cc.o CMakeFiles/ost_gfx.dir/vertex_array.cc.o CMakeFiles/ost_gfx.dir/vertex_array_helper.cc.o CMakeFiles/ost_gfx.dir/material.cc.o CMakeFiles/ost_gfx.dir/povray.cc.o CMakeFiles/ost_gfx.dir/gost_exporter.cc.o CMakeFiles/ost_gfx.dir/texture.cc.o CMakeFiles/ost_gfx.dir/color_ops/color_op.cc.o CMakeFiles/ost_gfx.dir/color_ops/by_element_color_op.cc.o CMakeFiles/ost_gfx.dir/color_ops/by_chain_color_op.cc.o CMakeFiles/ost_gfx.dir/color_ops/uniform_color_op.cc.o CMakeFiles/ost_gfx.dir/color_ops/gradient_color_op.cc.o CMakeFiles/ost_gfx.dir/color_ops/entity_view_color_op.cc.o CMakeFiles/ost_gfx.dir/color_ops/basic_gradient_color_op.cc.o CMakeFiles/ost_gfx.dir/color_ops/gradient_level_color_op.cc.o CMakeFiles/ost_gfx.dir/impl/entity_renderer.cc.o CMakeFiles/ost_gfx.dir/impl/entity_detail.cc.o CMakeFiles/ost_gfx.dir/impl/cartoon_renderer.cc.o CMakeFiles/ost_gfx.dir/impl/custom_renderer.cc.o CMakeFiles/ost_gfx.dir/impl/cpk_renderer.cc.o CMakeFiles/ost_gfx.dir/impl/debug_renderer.cc.o CMakeFiles/ost_gfx.dir/impl/simple_renderer.cc.o CMakeFiles/ost_gfx.dir/impl/sline_renderer.cc.o CMakeFiles/ost_gfx.dir/impl/line_trace_renderer.cc.o CMakeFiles/ost_gfx.dir/impl/backbone_trace.cc.o CMakeFiles/ost_gfx.dir/impl/connect_renderer_base.cc.o CMakeFiles/ost_gfx.dir/impl/trace_renderer_base.cc.o CMakeFiles/ost_gfx.dir/impl/mapped_property.cc.o CMakeFiles/ost_gfx.dir/impl/tabulated_trig.cc.o CMakeFiles/ost_gfx.dir/impl/trace_renderer.cc.o CMakeFiles/ost_gfx.dir/impl/fast_spheres.cc.o CMakeFiles/ost_gfx.dir/render_options/render_options.cc.o CMakeFiles/ost_gfx.dir/render_options/line_render_options.cc.o CMakeFiles/ost_gfx.dir/render_options/custom_render_options.cc.o CMakeFiles/ost_gfx.dir/render_options/cpk_render_options.cc.o CMakeFiles/ost_gfx.dir/render_options/simple_render_options.cc.o CMakeFiles/ost_gfx.dir/render_options/sline_render_options.cc.o CMakeFiles/ost_gfx.dir/render_options/line_trace_render_options.cc.o CMakeFiles/ost_gfx.dir/render_options/cartoon_render_options.cc.o CMakeFiles/ost_gfx.dir/render_options/trace_render_options.cc.o CMakeFiles/ost_gfx.dir/color_ops/map_handle_color_op.cc.o CMakeFiles/ost_gfx.dir/map_iso.cc.o CMakeFiles/ost_gfx.dir/map_slab.cc.o CMakeFiles/ost_gfx.dir/impl/map_iso_gen.cc.o CMakeFiles/ost_gfx.dir/impl/map_iso_gen_s.cc.o CMakeFiles/ost_gfx.dir/impl/map_iso_gen_o.cc.o CMakeFiles/ost_gfx.dir/impl/map_octree.cc.o CMakeFiles/ost_gfx.dir/impl/octree_isocont.cc.o -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib: ../../../stage/lib/libost_conop.so.2.3.1 ../../../stage/lib/libost_img_alg.so.2.3.1 /usr/lib/x86_64-linux-gnu/libOpenGL.so /usr/lib/x86_64-linux-gnu/libGLX.so /usr/lib/x86_64-linux-gnu/libGLU.so /usr/lib/x86_64-linux-gnu/libpng.so /usr/lib/x86_64-linux-gnu/libz.so ../../../stage/lib/libost_db.so.2.3.1 ../../../stage/lib/libost_seq.so.2.3.1 ../../../stage/lib/libost_mol.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libsqlite3.so ../../../stage/lib/libost_img.so.2.3.1 ../../../stage/lib/libost_info.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 ../../../stage/lib/libost_base.so.2.3.1 ../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libfftw3f_threads.so [ 43%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/save_entity.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/save_entity.cc.o -MF CMakeFiles/ost_io.dir/mol/save_entity.cc.o.d -o CMakeFiles/ost_io.dir/mol/save_entity.cc.o -c /build/openstructure-2.3.1/modules/io/src/mol/save_entity.cc -[ 43%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/load_entity.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/load_entity.cc.o -MF CMakeFiles/ost_io.dir/mol/load_entity.cc.o.d -o CMakeFiles/ost_io.dir/mol/load_entity.cc.o -c /build/openstructure-2.3.1/modules/io/src/mol/load_entity.cc -[ 43%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/surface_io_msms_handler.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/surface_io_msms_handler.cc.o -MF CMakeFiles/ost_io.dir/mol/surface_io_msms_handler.cc.o.d -o CMakeFiles/ost_io.dir/mol/surface_io_msms_handler.cc.o -c /build/openstructure-2.3.1/modules/io/src/mol/surface_io_msms_handler.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/io_manager.hh:28, @@ -15334,8 +15329,6 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 43%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/load_surface.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/load_surface.cc.o -MF CMakeFiles/ost_io.dir/mol/load_surface.cc.o.d -o CMakeFiles/ost_io.dir/mol/load_surface.cc.o -c /build/openstructure-2.3.1/modules/io/src/mol/load_surface.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -15356,6 +15349,13 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 43%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/load_entity.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/load_entity.cc.o -MF CMakeFiles/ost_io.dir/mol/load_entity.cc.o.d -o CMakeFiles/ost_io.dir/mol/load_entity.cc.o -c /build/openstructure-2.3.1/modules/io/src/mol/load_entity.cc +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E cmake_symlink_library ../../../stage/lib/libost_gfx.so.2.3.1 ../../../stage/lib/libost_gfx.so.2.3 ../../../stage/lib/libost_gfx.so +make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[ 43%] Built target ost_gfx +[ 43%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/surface_io_msms_handler.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/surface_io_msms_handler.cc.o -MF CMakeFiles/ost_io.dir/mol/surface_io_msms_handler.cc.o.d -o CMakeFiles/ost_io.dir/mol/surface_io_msms_handler.cc.o -c /build/openstructure-2.3.1/modules/io/src/mol/surface_io_msms_handler.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -15363,7 +15363,8 @@ from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/conop.hh:24, - from /build/openstructure-2.3.1/modules/io/src/mol/load_entity.cc:20: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/sdf_writer.hh:35, + from /build/openstructure-2.3.1/modules/io/src/mol/entity_io_sdf_handler.cc:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -15373,79 +15374,7 @@ from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, - from /build/openstructure-2.3.1/modules/io/src/mol/load_entity.cc:19: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/io_manager.hh:28, - from /build/openstructure-2.3.1/modules/io/src/mol/save_entity.cc:20: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 32 | : public std::iterator{ - | ^~~~~~~~ -In file included from /usr/include/c++/12/string:45, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/ostream:38, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, - from /build/openstructure-2.3.1/modules/io/src/mol/save_entity.cc:19: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/io_manager.hh:28, - from /build/openstructure-2.3.1/modules/io/src/mol/load_entity.cc:24: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 32 | : public std::iterator{ - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/surface_prop.hh:25, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/surface_handle.hh:24, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/surface.hh:22, - from /build/openstructure-2.3.1/modules/io/src/mol/surface_io_handler.hh:25, - from /build/openstructure-2.3.1/modules/io/src/mol/surface_io_msms_handler.hh:22, - from /build/openstructure-2.3.1/modules/io/src/mol/surface_io_msms_handler.cc:26: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/stl_tree.h:63, - from /usr/include/c++/12/map:60, - from /build/openstructure-2.3.1/modules/io/src/mol/surface_io_msms_handler.cc:20: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ + from /build/openstructure-2.3.1/modules/io/src/mol/entity_io_sdf_handler.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -15478,38 +15407,6 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/mmcif_reader.hh:24, - from /build/openstructure-2.3.1/modules/io/src/mol/entity_io_mmcif_handler.cc:35: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/12/string:45, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/ostream:38, - from /usr/include/c++/12/iostream:39, - from /build/openstructure-2.3.1/modules/io/src/mol/entity_io_mmcif_handler.cc:22: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/mmcif_reader.hh:25: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 32 | : public std::iterator{ - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, from /build/openstructure-2.3.1/modules/io/src/mol/entity_io_pdb_handler.cc:35: @@ -15533,8 +15430,7 @@ from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/conop.hh:24, - from /build/openstructure-2.3.1/modules/io/src/mol/sdf_writer.hh:35, - from /build/openstructure-2.3.1/modules/io/src/mol/sdf_writer.cc:23: + from /build/openstructure-2.3.1/modules/io/src/mol/entity_io_crd_handler.cc:33: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -15544,7 +15440,7 @@ from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, - from /build/openstructure-2.3.1/modules/io/src/mol/sdf_writer.hh:25: + from /build/openstructure-2.3.1/modules/io/src/mol/entity_io_crd_handler.cc:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -15557,12 +15453,8 @@ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/conop.hh:24, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/sdf_writer.hh:35, - from /build/openstructure-2.3.1/modules/io/src/mol/entity_io_sdf_handler.cc:24: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/mmcif_reader.hh:24, + from /build/openstructure-2.3.1/modules/io/src/mol/entity_io_mmcif_handler.cc:35: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -15571,8 +15463,8 @@ from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, - from /build/openstructure-2.3.1/modules/io/src/mol/entity_io_sdf_handler.cc:23: + from /usr/include/c++/12/iostream:39, + from /build/openstructure-2.3.1/modules/io/src/mol/entity_io_mmcif_handler.cc:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -15582,6 +15474,14 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/mmcif_reader.hh:25: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 32 | : public std::iterator{ + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -15609,14 +15509,15 @@ from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/conop.hh:24, - from /build/openstructure-2.3.1/modules/io/src/mol/pdb_reader.cc:31: + from /build/openstructure-2.3.1/modules/io/src/mol/sdf_reader.cc:27: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/algorithm:60, - from /usr/include/boost/iostreams/filter/gzip.hpp:21, - from /build/openstructure-2.3.1/modules/io/src/mol/pdb_reader.cc:19: +In file included from /usr/include/c++/12/string:45, + from /usr/include/boost/algorithm/string/std/string_traits.hpp:15, + from /usr/include/boost/algorithm/string/std_containers_traits.hpp:19, + from /usr/include/boost/algorithm/string.hpp:18, + from /build/openstructure-2.3.1/modules/io/src/mol/sdf_reader.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -15626,8 +15527,6 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 43%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/chemdict_parser.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/chemdict_parser.cc.o -MF CMakeFiles/ost_io.dir/mol/chemdict_parser.cc.o.d -o CMakeFiles/ost_io.dir/mol/chemdict_parser.cc.o -c /build/openstructure-2.3.1/modules/io/src/mol/chemdict_parser.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -15635,17 +15534,14 @@ from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/conop.hh:24, - from /build/openstructure-2.3.1/modules/io/src/mol/entity_io_crd_handler.cc:33: + from /build/openstructure-2.3.1/modules/io/src/mol/pdb_reader.cc:31: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/12/string:45, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/ostream:38, - from /usr/include/c++/12/iostream:39, - from /build/openstructure-2.3.1/modules/io/src/mol/entity_io_crd_handler.cc:22: +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/algorithm:60, + from /usr/include/boost/iostreams/filter/gzip.hpp:21, + from /build/openstructure-2.3.1/modules/io/src/mol/pdb_reader.cc:19: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -15662,7 +15558,7 @@ from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/conop.hh:24, - from /build/openstructure-2.3.1/modules/io/src/mol/entity_io_mae_handler.cc:38: + from /build/openstructure-2.3.1/modules/io/src/mol/entity_io_pqr_handler.cc:35: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -15672,7 +15568,7 @@ from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, - from /build/openstructure-2.3.1/modules/io/src/mol/entity_io_mae_handler.cc:22: + from /build/openstructure-2.3.1/modules/io/src/mol/entity_io_pqr_handler.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -15682,6 +15578,23 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/io_manager.hh:28, + from /build/openstructure-2.3.1/modules/io/src/mol/save_entity.cc:20: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 32 | : public std::iterator{ + | ^~~~~~~~ +In file included from /usr/include/c++/12/string:45, + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/ostream:38, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, + from /build/openstructure-2.3.1/modules/io/src/mol/save_entity.cc:19: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -15689,7 +15602,7 @@ from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/conop.hh:24, - from /build/openstructure-2.3.1/modules/io/src/mol/entity_io_pqr_handler.cc:35: + from /build/openstructure-2.3.1/modules/io/src/mol/entity_io_mae_handler.cc:38: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -15699,7 +15612,7 @@ from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, - from /build/openstructure-2.3.1/modules/io/src/mol/entity_io_pqr_handler.cc:23: + from /build/openstructure-2.3.1/modules/io/src/mol/entity_io_mae_handler.cc:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -15721,19 +15634,69 @@ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/surface_prop.hh:25, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/surface_handle.hh:24, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/surface.hh:22, + from /build/openstructure-2.3.1/modules/io/src/mol/surface_io_handler.hh:25, + from /build/openstructure-2.3.1/modules/io/src/mol/surface_io_msms_handler.hh:22, + from /build/openstructure-2.3.1/modules/io/src/mol/surface_io_msms_handler.cc:26: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/bits/stl_tree.h:63, + from /usr/include/c++/12/map:60, + from /build/openstructure-2.3.1/modules/io/src/mol/surface_io_msms_handler.cc:20: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 43%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/load_surface.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/load_surface.cc.o -MF CMakeFiles/ost_io.dir/mol/load_surface.cc.o.d -o CMakeFiles/ost_io.dir/mol/load_surface.cc.o -c /build/openstructure-2.3.1/modules/io/src/mol/load_surface.cc +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/conop.hh:24, - from /build/openstructure-2.3.1/modules/io/src/mol/sdf_reader.cc:27: + from /build/openstructure-2.3.1/modules/io/src/mol/sdf_writer.hh:35, + from /build/openstructure-2.3.1/modules/io/src/mol/sdf_writer.cc:23: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, - from /usr/include/boost/algorithm/string/std/string_traits.hpp:15, - from /usr/include/boost/algorithm/string/std_containers_traits.hpp:19, - from /usr/include/boost/algorithm/string.hpp:18, - from /build/openstructure-2.3.1/modules/io/src/mol/sdf_reader.cc:23: + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/ostream:38, + from /usr/include/c++/12/iostream:39, + from /build/openstructure-2.3.1/modules/io/src/mol/sdf_writer.hh:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -15746,9 +15709,11 @@ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/surface_prop.hh:25, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/surface_handle.hh:24, - from /build/openstructure-2.3.1/modules/io/src/mol/load_surface.cc:20: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/conop.hh:24, + from /build/openstructure-2.3.1/modules/io/src/mol/load_entity.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -15758,7 +15723,7 @@ from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, - from /build/openstructure-2.3.1/modules/io/src/mol/load_surface.cc:19: + from /build/openstructure-2.3.1/modules/io/src/mol/load_entity.cc:19: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -15768,10 +15733,16 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 44%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/io_profile.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/io_profile.cc.o -MF CMakeFiles/ost_io.dir/mol/io_profile.cc.o.d -o CMakeFiles/ost_io.dir/mol/io_profile.cc.o -c /build/openstructure-2.3.1/modules/io/src/mol/io_profile.cc -[ 44%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/dcd_io.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/dcd_io.cc.o -MF CMakeFiles/ost_io.dir/mol/dcd_io.cc.o.d -o CMakeFiles/ost_io.dir/mol/dcd_io.cc.o -c /build/openstructure-2.3.1/modules/io/src/mol/dcd_io.cc +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/io_manager.hh:28, + from /build/openstructure-2.3.1/modules/io/src/mol/load_entity.cc:24: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 32 | : public std::iterator{ + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -15786,6 +15757,37 @@ /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ +[ 43%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/chemdict_parser.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/chemdict_parser.cc.o -MF CMakeFiles/ost_io.dir/mol/chemdict_parser.cc.o.d -o CMakeFiles/ost_io.dir/mol/chemdict_parser.cc.o -c /build/openstructure-2.3.1/modules/io/src/mol/chemdict_parser.cc +[ 44%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/io_profile.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/io_profile.cc.o -MF CMakeFiles/ost_io.dir/mol/io_profile.cc.o.d -o CMakeFiles/ost_io.dir/mol/io_profile.cc.o -c /build/openstructure-2.3.1/modules/io/src/mol/io_profile.cc +[ 44%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/dcd_io.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/dcd_io.cc.o -MF CMakeFiles/ost_io.dir/mol/dcd_io.cc.o.d -o CMakeFiles/ost_io.dir/mol/dcd_io.cc.o -c /build/openstructure-2.3.1/modules/io/src/mol/dcd_io.cc +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/surface_prop.hh:25, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/surface_handle.hh:24, + from /build/openstructure-2.3.1/modules/io/src/mol/load_surface.cc:20: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/12/string:45, + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/ostream:38, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, + from /build/openstructure-2.3.1/modules/io/src/mol/load_surface.cc:19: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/io_manager.hh:28, @@ -15798,26 +15800,26 @@ | ^~~~~~~~ [ 44%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/star_parser.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/star_parser.cc.o -MF CMakeFiles/ost_io.dir/mol/star_parser.cc.o.d -o CMakeFiles/ost_io.dir/mol/star_parser.cc.o -c /build/openstructure-2.3.1/modules/io/src/mol/star_parser.cc +[ 44%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/mmcif_reader.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/mmcif_reader.cc.o -MF CMakeFiles/ost_io.dir/mol/mmcif_reader.cc.o.d -o CMakeFiles/ost_io.dir/mol/mmcif_reader.cc.o -c /build/openstructure-2.3.1/modules/io/src/mol/mmcif_reader.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/compound_lib_base.hh:5, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/compound_lib.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/chemdict_parser.hh:30, - from /build/openstructure-2.3.1/modules/io/src/mol/chemdict_parser.cc:1: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, + from /build/openstructure-2.3.1/modules/io/src/mol/io_profile.hh:24, + from /build/openstructure-2.3.1/modules/io/src/mol/io_profile.cc:1: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/specfun.h:45, - from /usr/include/c++/12/cmath:1935, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/chem_class.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/chemdict_parser.hh:27: +In file included from /usr/include/c++/12/string:45, + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/ostream:38, + from /usr/include/c++/12/iostream:39, + from /build/openstructure-2.3.1/modules/io/src/mol/io_profile.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -15827,26 +15829,26 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 44%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/mmcif_reader.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/mmcif_reader.cc.o -MF CMakeFiles/ost_io.dir/mol/mmcif_reader.cc.o.d -o CMakeFiles/ost_io.dir/mol/mmcif_reader.cc.o -c /build/openstructure-2.3.1/modules/io/src/mol/mmcif_reader.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, - from /build/openstructure-2.3.1/modules/io/src/mol/io_profile.hh:24, - from /build/openstructure-2.3.1/modules/io/src/mol/io_profile.cc:1: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/compound_lib_base.hh:5, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/compound_lib.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/chemdict_parser.hh:30, + from /build/openstructure-2.3.1/modules/io/src/mol/chemdict_parser.cc:1: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/12/string:45, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/ostream:38, - from /usr/include/c++/12/iostream:39, - from /build/openstructure-2.3.1/modules/io/src/mol/io_profile.hh:22: +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/bits/specfun.h:45, + from /usr/include/c++/12/cmath:1935, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/chem_class.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/chemdict_parser.hh:27: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -15856,10 +15858,6 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 44%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/mmcif_info.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/mmcif_info.cc.o -MF CMakeFiles/ost_io.dir/mol/mmcif_info.cc.o.d -o CMakeFiles/ost_io.dir/mol/mmcif_info.cc.o -c /build/openstructure-2.3.1/modules/io/src/mol/mmcif_info.cc -[ 44%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/pdb_str.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/pdb_str.cc.o -MF CMakeFiles/ost_io.dir/mol/pdb_str.cc.o.d -o CMakeFiles/ost_io.dir/mol/pdb_str.cc.o -c /build/openstructure-2.3.1/modules/io/src/mol/pdb_str.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -15887,28 +15885,36 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 44%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/mmcif_info.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/mmcif_info.cc.o -MF CMakeFiles/ost_io.dir/mol/mmcif_info.cc.o.d -o CMakeFiles/ost_io.dir/mol/mmcif_info.cc.o -c /build/openstructure-2.3.1/modules/io/src/mol/mmcif_info.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/mmcif_info.hh:25, - from /build/openstructure-2.3.1/modules/io/src/mol/mmcif_info.cc:21: + from /build/openstructure-2.3.1/modules/io/src/mol/pdb_reader.hh:28, + from /build/openstructure-2.3.1/modules/io/src/mol/dcd_io.cc:40: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ -In file included from /usr/include/c++/12/string:45, - from /usr/include/c++/12/stdexcept:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/io_exception.hh:22, - from /build/openstructure-2.3.1/modules/io/src/mol/mmcif_info.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 44%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/pdb_str.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/pdb_str.cc.o -MF CMakeFiles/ost_io.dir/mol/pdb_str.cc.o.d -o CMakeFiles/ost_io.dir/mol/pdb_str.cc.o -c /build/openstructure-2.3.1/modules/io/src/mol/pdb_str.cc [ 44%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/stereochemical_params_reader.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/stereochemical_params_reader.cc.o -MF CMakeFiles/ost_io.dir/mol/stereochemical_params_reader.cc.o.d -o CMakeFiles/ost_io.dir/mol/stereochemical_params_reader.cc.o -c /build/openstructure-2.3.1/modules/io/src/mol/stereochemical_params_reader.cc +[ 44%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/omf.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/omf.cc.o -MF CMakeFiles/ost_io.dir/mol/omf.cc.o.d -o CMakeFiles/ost_io.dir/mol/omf.cc.o -c /build/openstructure-2.3.1/modules/io/src/mol/omf.cc +[ 44%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/seq/clustal_io_handler.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/seq/clustal_io_handler.cc.o -MF CMakeFiles/ost_io.dir/seq/clustal_io_handler.cc.o.d -o CMakeFiles/ost_io.dir/seq/clustal_io_handler.cc.o -c /build/openstructure-2.3.1/modules/io/src/seq/clustal_io_handler.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, - from /build/openstructure-2.3.1/modules/io/src/mol/pdb_reader.hh:28, - from /build/openstructure-2.3.1/modules/io/src/mol/dcd_io.cc:40: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/mmcif_info.hh:25, + from /build/openstructure-2.3.1/modules/io/src/mol/mmcif_info.cc:21: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ +In file included from /usr/include/c++/12/string:45, + from /usr/include/c++/12/stdexcept:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/io_exception.hh:22, + from /build/openstructure-2.3.1/modules/io/src/mol/mmcif_info.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -15936,6 +15942,8 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 44%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/seq/load.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/seq/load.cc.o -MF CMakeFiles/ost_io.dir/seq/load.cc.o.d -o CMakeFiles/ost_io.dir/seq/load.cc.o -c /build/openstructure-2.3.1/modules/io/src/seq/load.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -15965,8 +15973,6 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 44%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/omf.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/omf.cc.o -MF CMakeFiles/ost_io.dir/mol/omf.cc.o.d -o CMakeFiles/ost_io.dir/mol/omf.cc.o -c /build/openstructure-2.3.1/modules/io/src/mol/omf.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -15994,17 +16000,6 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, - from /build/openstructure-2.3.1/modules/io/src/mol/pdb_str.cc:22: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 32 | : public std::iterator{ - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -[ 44%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/seq/clustal_io_handler.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/seq/clustal_io_handler.cc.o -MF CMakeFiles/ost_io.dir/seq/clustal_io_handler.cc.o.d -o CMakeFiles/ost_io.dir/seq/clustal_io_handler.cc.o -c /build/openstructure-2.3.1/modules/io/src/seq/clustal_io_handler.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -16037,6 +16032,15 @@ 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, + from /build/openstructure-2.3.1/modules/io/src/mol/pdb_str.cc:22: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 32 | : public std::iterator{ + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/local_dist_diff_test.hh:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] @@ -16045,8 +16049,6 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 44%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/seq/load.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/seq/load.cc.o -MF CMakeFiles/ost_io.dir/seq/load.cc.o.d -o CMakeFiles/ost_io.dir/seq/load.cc.o -c /build/openstructure-2.3.1/modules/io/src/seq/load.cc [ 46%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/seq/save.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/seq/save.cc.o -MF CMakeFiles/ost_io.dir/seq/save.cc.o.d -o CMakeFiles/ost_io.dir/seq/save.cc.o -c /build/openstructure-2.3.1/modules/io/src/seq/save.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, @@ -16075,6 +16077,21 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, + from /build/openstructure-2.3.1/modules/io/src/seq/load.hh:27, + from /build/openstructure-2.3.1/modules/io/src/seq/load.cc:19: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 32 | : public std::iterator{ + | ^~~~~~~~ +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/bits/specfun.h:45, + from /usr/include/c++/12/cmath:1935, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/module_config.hh:22, + from /build/openstructure-2.3.1/modules/io/src/seq/load.hh:26: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ [ 46%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/seq/fasta_io_handler.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/seq/fasta_io_handler.cc.o -MF CMakeFiles/ost_io.dir/seq/fasta_io_handler.cc.o.d -o CMakeFiles/ost_io.dir/seq/fasta_io_handler.cc.o -c /build/openstructure-2.3.1/modules/io/src/seq/fasta_io_handler.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, @@ -16089,17 +16106,66 @@ | ^~~~~~~~ [ 46%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/seq/pir_io_handler.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/seq/pir_io_handler.cc.o -MF CMakeFiles/ost_io.dir/seq/pir_io_handler.cc.o.d -o CMakeFiles/ost_io.dir/seq/pir_io_handler.cc.o -c /build/openstructure-2.3.1/modules/io/src/seq/pir_io_handler.cc +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, + from /build/openstructure-2.3.1/modules/io/src/seq/clustal_io_handler.cc:27: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/bits/stl_tree.h:63, + from /usr/include/c++/12/map:60, + from /build/openstructure-2.3.1/modules/io/src/seq/clustal_io_handler.cc:20: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, + from /build/openstructure-2.3.1/modules/io/src/seq/sequence_io_handler.hh:27, + from /build/openstructure-2.3.1/modules/io/src/seq/clustal_io_handler.hh:25, + from /build/openstructure-2.3.1/modules/io/src/seq/clustal_io_handler.cc:29: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 32 | : public std::iterator{ + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ [ 46%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/seq/promod_io_handler.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/seq/promod_io_handler.cc.o -MF CMakeFiles/ost_io.dir/seq/promod_io_handler.cc.o.d -o CMakeFiles/ost_io.dir/seq/promod_io_handler.cc.o -c /build/openstructure-2.3.1/modules/io/src/seq/promod_io_handler.cc [ 46%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/seq/hhm_io_handler.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/seq/hhm_io_handler.cc.o -MF CMakeFiles/ost_io.dir/seq/hhm_io_handler.cc.o.d -o CMakeFiles/ost_io.dir/seq/hhm_io_handler.cc.o -c /build/openstructure-2.3.1/modules/io/src/seq/hhm_io_handler.cc -[ 47%] Linking CXX shared module ../../../../stage/lib/python3.11/dist-packages/ost/seq/_ost_seq.so -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_seq.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -o ../../../../stage/lib/python3.11/dist-packages/ost/seq/_ost_seq.so CMakeFiles/_ost_seq.dir/export_sequence.cc.o CMakeFiles/_ost_seq.dir/export_profile_handle.cc.o CMakeFiles/_ost_seq.dir/wrap_seq.cc.o -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib: ../../../../stage/lib/libost_seq.so.2.3.1 /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so ../../../../stage/lib/libost_mol.so.2.3.1 ../../../../stage/lib/libost_info.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../../stage/lib/libost_base.so.2.3.1 ../../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 -[ 47%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/seq/pssm_io_handler.cc.o +[ 46%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/seq/pssm_io_handler.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/seq/pssm_io_handler.cc.o -MF CMakeFiles/ost_io.dir/seq/pssm_io_handler.cc.o.d -o CMakeFiles/ost_io.dir/seq/pssm_io_handler.cc.o -c /build/openstructure-2.3.1/modules/io/src/seq/pssm_io_handler.cc -[ 47%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/load_map.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/load_map.cc.o -MF CMakeFiles/ost_io.dir/img/load_map.cc.o.d -o CMakeFiles/ost_io.dir/img/load_map.cc.o -c /build/openstructure-2.3.1/modules/io/src/img/load_map.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/io_manager.hh:28, @@ -16117,25 +16183,6 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, - from /build/openstructure-2.3.1/modules/io/src/seq/load.hh:27, - from /build/openstructure-2.3.1/modules/io/src/seq/load.cc:19: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 32 | : public std::iterator{ - | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/specfun.h:45, - from /usr/include/c++/12/cmath:1935, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/module_config.hh:22, - from /build/openstructure-2.3.1/modules/io/src/seq/load.hh:26: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -[ 47%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_dx_handler.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/map_io_dx_handler.cc.o -MF CMakeFiles/ost_io.dir/img/map_io_dx_handler.cc.o.d -o CMakeFiles/ost_io.dir/img/map_io_dx_handler.cc.o -c /build/openstructure-2.3.1/modules/io/src/img/map_io_dx_handler.cc -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/seq/base/pymod/__init__.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/seq/./__init__.pyc\",\"__init__.py\",doraise=True)" -make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -16156,6 +16203,29 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 47%] Linking CXX shared module ../../../../stage/lib/python3.11/dist-packages/ost/seq/_ost_seq.so +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_seq.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -o ../../../../stage/lib/python3.11/dist-packages/ost/seq/_ost_seq.so CMakeFiles/_ost_seq.dir/export_sequence.cc.o CMakeFiles/_ost_seq.dir/export_profile_handle.cc.o CMakeFiles/_ost_seq.dir/wrap_seq.cc.o -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib: ../../../../stage/lib/libost_seq.so.2.3.1 /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so ../../../../stage/lib/libost_mol.so.2.3.1 ../../../../stage/lib/libost_info.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../../stage/lib/libost_base.so.2.3.1 ../../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, + from /build/openstructure-2.3.1/modules/io/src/seq/sequence_io_handler.hh:27, + from /build/openstructure-2.3.1/modules/io/src/seq/pir_io_handler.hh:25, + from /build/openstructure-2.3.1/modules/io/src/seq/pir_io_handler.cc:19: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 32 | : public std::iterator{ + | ^~~~~~~~ +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/bits/specfun.h:45, + from /usr/include/c++/12/cmath:1935, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/module_config.hh:22, + from /build/openstructure-2.3.1/modules/io/src/seq/pir_io_handler.hh:24: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 47%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/load_map.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/load_map.cc.o -MF CMakeFiles/ost_io.dir/img/load_map.cc.o.d -o CMakeFiles/ost_io.dir/img/load_map.cc.o -c /build/openstructure-2.3.1/modules/io/src/img/load_map.cc +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/seq/base/pymod/__init__.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/seq/./__init__.pyc\",\"__init__.py\",doraise=True)" +make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 47%] Built target _ost_seq make -f modules/bindings/pymod/CMakeFiles/_ost_bindings.dir/build.make modules/bindings/pymod/CMakeFiles/_ost_bindings.dir/depend In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, @@ -16165,14 +16235,10 @@ from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, - from /build/openstructure-2.3.1/modules/io/src/seq/clustal_io_handler.cc:27: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/stl_tree.h:63, - from /usr/include/c++/12/map:60, - from /build/openstructure-2.3.1/modules/io/src/seq/clustal_io_handler.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -16184,25 +16250,11 @@ | ^~~~~~~~ make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/bindings/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod/CMakeFiles/_ost_bindings.dir/DependInfo.cmake --color= -[ 47%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_spi_handler.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/map_io_spi_handler.cc.o -MF CMakeFiles/ost_io.dir/img/map_io_spi_handler.cc.o.d -o CMakeFiles/ost_io.dir/img/map_io_spi_handler.cc.o -c /build/openstructure-2.3.1/modules/io/src/img/map_io_spi_handler.cc make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/bindings/pymod/CMakeFiles/_ost_bindings.dir/build.make modules/bindings/pymod/CMakeFiles/_ost_bindings.dir/build make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 47%] Building CXX object modules/bindings/pymod/CMakeFiles/_ost_bindings.dir/export_tmalign.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_bindings_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/bindings/pymod/CMakeFiles/_ost_bindings.dir/export_tmalign.cc.o -MF CMakeFiles/_ost_bindings.dir/export_tmalign.cc.o.d -o CMakeFiles/_ost_bindings.dir/export_tmalign.cc.o -c /build/openstructure-2.3.1/modules/bindings/pymod/export_tmalign.cc -[ 47%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_situs_handler.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/map_io_situs_handler.cc.o -MF CMakeFiles/ost_io.dir/img/map_io_situs_handler.cc.o.d -o CMakeFiles/ost_io.dir/img/map_io_situs_handler.cc.o -c /build/openstructure-2.3.1/modules/io/src/img/map_io_situs_handler.cc -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, - from /build/openstructure-2.3.1/modules/io/src/seq/sequence_io_handler.hh:27, - from /build/openstructure-2.3.1/modules/io/src/seq/clustal_io_handler.hh:25, - from /build/openstructure-2.3.1/modules/io/src/seq/clustal_io_handler.cc:29: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 32 | : public std::iterator{ - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/modules/io/src/seq/sequence_io_handler.hh:27, from /build/openstructure-2.3.1/modules/io/src/seq/fasta_io_handler.hh:25, @@ -16219,6 +16271,10 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 47%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_dx_handler.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/map_io_dx_handler.cc.o -MF CMakeFiles/ost_io.dir/img/map_io_dx_handler.cc.o.d -o CMakeFiles/ost_io.dir/img/map_io_dx_handler.cc.o -c /build/openstructure-2.3.1/modules/io/src/img/map_io_dx_handler.cc +[ 47%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_spi_handler.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/map_io_spi_handler.cc.o -MF CMakeFiles/ost_io.dir/img/map_io_spi_handler.cc.o.d -o CMakeFiles/ost_io.dir/img/map_io_spi_handler.cc.o -c /build/openstructure-2.3.1/modules/io/src/img/map_io_spi_handler.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -16239,26 +16295,8 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ +[ 47%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_situs_handler.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/map_io_situs_handler.cc.o -MF CMakeFiles/ost_io.dir/img/map_io_situs_handler.cc.o.d -o CMakeFiles/ost_io.dir/img/map_io_situs_handler.cc.o -c /build/openstructure-2.3.1/modules/io/src/img/map_io_situs_handler.cc [ 47%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_mrc_handler.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/map_io_mrc_handler.cc.o -MF CMakeFiles/ost_io.dir/img/map_io_mrc_handler.cc.o.d -o CMakeFiles/ost_io.dir/img/map_io_mrc_handler.cc.o -c /build/openstructure-2.3.1/modules/io/src/img/map_io_mrc_handler.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, @@ -16278,42 +16316,6 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, - from /build/openstructure-2.3.1/modules/io/src/seq/sequence_io_handler.hh:27, - from /build/openstructure-2.3.1/modules/io/src/seq/pir_io_handler.hh:25, - from /build/openstructure-2.3.1/modules/io/src/seq/pir_io_handler.cc:19: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 32 | : public std::iterator{ - | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/specfun.h:45, - from /usr/include/c++/12/cmath:1935, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/module_config.hh:22, - from /build/openstructure-2.3.1/modules/io/src/seq/pir_io_handler.hh:24: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ [ 48%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_dm3_handler.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/map_io_dm3_handler.cc.o -MF CMakeFiles/ost_io.dir/img/map_io_dm3_handler.cc.o.d -o CMakeFiles/ost_io.dir/img/map_io_dm3_handler.cc.o -c /build/openstructure-2.3.1/modules/io/src/img/map_io_dm3_handler.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, @@ -16336,6 +16338,8 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 48%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_tiff_handler.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/map_io_tiff_handler.cc.o -MF CMakeFiles/ost_io.dir/img/map_io_tiff_handler.cc.o.d -o CMakeFiles/ost_io.dir/img/map_io_tiff_handler.cc.o -c /build/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -16373,33 +16377,6 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 48%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_tiff_handler.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/map_io_tiff_handler.cc.o -MF CMakeFiles/ost_io.dir/img/map_io_tiff_handler.cc.o.d -o CMakeFiles/ost_io.dir/img/map_io_tiff_handler.cc.o -c /build/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/normalizer_factory.hh:27, - from /build/openstructure-2.3.1/modules/io/src/img/map_io_situs_handler.cc:34: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/12/string:45, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/iomanip:40, - from /build/openstructure-2.3.1/modules/io/src/img/map_io_situs_handler.cc:26: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -16427,10 +16404,11 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 48%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_dat_handler.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/map_io_dat_handler.cc.o -MF CMakeFiles/ost_io.dir/img/map_io_dat_handler.cc.o.d -o CMakeFiles/ost_io.dir/img/map_io_dat_handler.cc.o -c /build/openstructure-2.3.1/modules/io/src/img/map_io_dat_handler.cc -[ 48%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_ipl_handler.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/map_io_ipl_handler.cc.o -MF CMakeFiles/ost_io.dir/img/map_io_ipl_handler.cc.o.d -o CMakeFiles/ost_io.dir/img/map_io_ipl_handler.cc.o -c /build/openstructure-2.3.1/modules/io/src/img/map_io_ipl_handler.cc +In file included from /usr/include/boost/bind.hpp:30, + from /build/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc:32: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -16455,34 +16433,22 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 48%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_jpk_handler.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/map_io_jpk_handler.cc.o -MF CMakeFiles/ost_io.dir/img/map_io_jpk_handler.cc.o.d -o CMakeFiles/ost_io.dir/img/map_io_jpk_handler.cc.o -c /build/openstructure-2.3.1/modules/io/src/img/map_io_jpk_handler.cc -[ 48%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_nanoscope_handler.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/map_io_nanoscope_handler.cc.o -MF CMakeFiles/ost_io.dir/img/map_io_nanoscope_handler.cc.o.d -o CMakeFiles/ost_io.dir/img/map_io_nanoscope_handler.cc.o -c /build/openstructure-2.3.1/modules/io/src/img/map_io_nanoscope_handler.cc -[ 48%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_png_handler.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/map_io_png_handler.cc.o -MF CMakeFiles/ost_io.dir/img/map_io_png_handler.cc.o.d -o CMakeFiles/ost_io.dir/img/map_io_png_handler.cc.o -c /build/openstructure-2.3.1/modules/io/src/img/map_io_png_handler.cc -In file included from /usr/include/boost/bind.hpp:30, - from /build/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc:32: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, - from /build/openstructure-2.3.1/modules/io/src/img/map_io_dm3_handler.cc:37: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/normalizer_factory.hh:27, + from /build/openstructure-2.3.1/modules/io/src/img/map_io_situs_handler.cc:34: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/ostream:38, - from /usr/include/c++/12/iostream:39, - from /build/openstructure-2.3.1/modules/io/src/img/map_io_dm3_handler.cc:27: + from /usr/include/c++/12/iomanip:40, + from /build/openstructure-2.3.1/modules/io/src/img/map_io_situs_handler.cc:26: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -16492,26 +16458,6 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/bindings/pymod/export_tmalign.cc:20: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -16546,33 +16492,7 @@ from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, - from /build/openstructure-2.3.1/modules/io/src/img/map_io_ipl_handler.cc:31: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/12/string:45, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/iomanip:40, - from /build/openstructure-2.3.1/modules/io/src/img/map_io_ipl_handler.cc:22: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, - from /build/openstructure-2.3.1/modules/io/src/img/map_io_mrc_handler.cc:76: + from /build/openstructure-2.3.1/modules/io/src/img/map_io_dm3_handler.cc:37: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -16582,31 +16502,7 @@ from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, - from /build/openstructure-2.3.1/modules/io/src/img/map_io_mrc_handler.cc:58: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, - from /build/openstructure-2.3.1/modules/io/src/img/map_io_dat_handler.cc:24: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/memory:63, - from /usr/include/boost/smart_ptr/shared_array.hpp:19, - from /usr/include/boost/shared_array.hpp:17, - from /build/openstructure-2.3.1/modules/io/src/img/map_io_dat_handler.cc:21: + from /build/openstructure-2.3.1/modules/io/src/img/map_io_dm3_handler.cc:27: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -16616,6 +16512,23 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/openstructure-2.3.1/modules/bindings/pymod/export_tmalign.cc:20: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc:43: /build/openstructure-2.3.1/modules/io/src/img/tiff_util.hh:51:40: warning: 'int32' is deprecated [-Wdeprecated-declarations] 51 | class complexint32:public std::complex{ @@ -16642,6 +16555,9 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ /build/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc: In member function 'virtual void ost::io::MapIOTiffHandler::do_export(const ost::img::MapHandle&, TIFF*, ost::io::TIF&) const': /build/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc:310:10: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 310 | uint16 spp=1; @@ -16709,8 +16625,6 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 48%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_df3_handler.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/map_io_df3_handler.cc.o -MF CMakeFiles/ost_io.dir/img/map_io_df3_handler.cc.o.d -o CMakeFiles/ost_io.dir/img/map_io_df3_handler.cc.o -c /build/openstructure-2.3.1/modules/io/src/img/map_io_df3_handler.cc /build/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc:406:54: warning: 'int8' is deprecated [-Wdeprecated-declarations] 406 | fsc=detail::do_tiff_write,img::image_state::ComplexSpatialImageState>; | ^~~~ @@ -16865,6 +16779,40 @@ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, + from /build/openstructure-2.3.1/modules/io/src/img/map_io_mrc_handler.cc:76: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/12/string:45, + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/ostream:38, + from /usr/include/c++/12/iostream:39, + from /build/openstructure-2.3.1/modules/io/src/img/map_io_mrc_handler.cc:58: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 48%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_dat_handler.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/map_io_dat_handler.cc.o -MF CMakeFiles/ost_io.dir/img/map_io_dat_handler.cc.o.d -o CMakeFiles/ost_io.dir/img/map_io_dat_handler.cc.o -c /build/openstructure-2.3.1/modules/io/src/img/map_io_dat_handler.cc +[ 48%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_ipl_handler.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/map_io_ipl_handler.cc.o -MF CMakeFiles/ost_io.dir/img/map_io_ipl_handler.cc.o.d -o CMakeFiles/ost_io.dir/img/map_io_ipl_handler.cc.o -c /build/openstructure-2.3.1/modules/io/src/img/map_io_ipl_handler.cc +[ 48%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_jpk_handler.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/map_io_jpk_handler.cc.o -MF CMakeFiles/ost_io.dir/img/map_io_jpk_handler.cc.o.d -o CMakeFiles/ost_io.dir/img/map_io_jpk_handler.cc.o -c /build/openstructure-2.3.1/modules/io/src/img/map_io_jpk_handler.cc +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, @@ -16893,6 +16841,8 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 48%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_nanoscope_handler.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/map_io_nanoscope_handler.cc.o -MF CMakeFiles/ost_io.dir/img/map_io_nanoscope_handler.cc.o.d -o CMakeFiles/ost_io.dir/img/map_io_nanoscope_handler.cc.o -c /build/openstructure-2.3.1/modules/io/src/img/map_io_nanoscope_handler.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] @@ -16901,26 +16851,49 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 48%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_png_handler.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/map_io_png_handler.cc.o -MF CMakeFiles/ost_io.dir/img/map_io_png_handler.cc.o.d -o CMakeFiles/ost_io.dir/img/map_io_png_handler.cc.o -c /build/openstructure-2.3.1/modules/io/src/img/map_io_png_handler.cc +[ 48%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_df3_handler.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/map_io_df3_handler.cc.o -MF CMakeFiles/ost_io.dir/img/map_io_df3_handler.cc.o.d -o CMakeFiles/ost_io.dir/img/map_io_df3_handler.cc.o -c /build/openstructure-2.3.1/modules/io/src/img/map_io_df3_handler.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/normalizer_impl.hh:32, - from /build/openstructure-2.3.1/modules/io/src/img/map_io_png_handler.cc:34: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, + from /build/openstructure-2.3.1/modules/io/src/img/map_io_dat_handler.cc:24: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/memory:63, + from /usr/include/boost/smart_ptr/shared_array.hpp:19, + from /usr/include/boost/shared_array.hpp:17, + from /build/openstructure-2.3.1/modules/io/src/img/map_io_dat_handler.cc:21: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, + from /build/openstructure-2.3.1/modules/io/src/img/map_io_ipl_handler.cc:31: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/ostream:38, - from /usr/include/c++/12/iostream:39, - from /build/openstructure-2.3.1/modules/io/src/img/map_io_png_handler.cc:27: + from /usr/include/c++/12/iomanip:40, + from /build/openstructure-2.3.1/modules/io/src/img/map_io_ipl_handler.cc:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -16955,6 +16928,37 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 48%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/image_format.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/image_format.cc.o -MF CMakeFiles/ost_io.dir/img/image_format.cc.o.d -o CMakeFiles/ost_io.dir/img/image_format.cc.o -c /build/openstructure-2.3.1/modules/io/src/img/image_format.cc +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/normalizer_impl.hh:32, + from /build/openstructure-2.3.1/modules/io/src/img/map_io_png_handler.cc:34: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/12/string:45, + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/ostream:38, + from /usr/include/c++/12/iostream:39, + from /build/openstructure-2.3.1/modules/io/src/img/map_io_png_handler.cc:27: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -17018,8 +17022,6 @@ /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 48%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/image_format.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/image_format.cc.o -MF CMakeFiles/ost_io.dir/img/image_format.cc.o.d -o CMakeFiles/ost_io.dir/img/image_format.cc.o -c /build/openstructure-2.3.1/modules/io/src/img/image_format.cc [ 48%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/tiff_util.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/tiff_util.cc.o -MF CMakeFiles/ost_io.dir/img/tiff_util.cc.o.d -o CMakeFiles/ost_io.dir/img/tiff_util.cc.o -c /build/openstructure-2.3.1/modules/io/src/img/tiff_util.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, @@ -17056,11 +17058,21 @@ make -f modules/db/pymod/CMakeFiles/_ost_db.dir/build.make modules/db/pymod/CMakeFiles/_ost_db.dir/depend make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/db/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/pymod/CMakeFiles/_ost_db.dir/DependInfo.cmake --color= +make -f modules/seq/alg/pymod/CMakeFiles/_ost_seq_alg.dir/build.make modules/seq/alg/pymod/CMakeFiles/_ost_seq_alg.dir/depend +make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/seq/alg/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/pymod/CMakeFiles/_ost_seq_alg.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/db/pymod/CMakeFiles/_ost_db.dir/build.make modules/db/pymod/CMakeFiles/_ost_db.dir/build make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +make -f modules/seq/alg/pymod/CMakeFiles/_ost_seq_alg.dir/build.make modules/seq/alg/pymod/CMakeFiles/_ost_seq_alg.dir/build +make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 48%] Building CXX object modules/db/pymod/CMakeFiles/_ost_db.dir/export_linear_db.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_db_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/db/pymod/CMakeFiles/_ost_db.dir/export_linear_db.cc.o -MF CMakeFiles/_ost_db.dir/export_linear_db.cc.o.d -o CMakeFiles/_ost_db.dir/export_linear_db.cc.o -c /build/openstructure-2.3.1/modules/db/pymod/export_linear_db.cc +[ 48%] Building CXX object modules/seq/alg/pymod/CMakeFiles/_ost_seq_alg.dir/wrap_seq_alg.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_seq_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/pymod/CMakeFiles/_ost_seq_alg.dir/wrap_seq_alg.cc.o -MF CMakeFiles/_ost_seq_alg.dir/wrap_seq_alg.cc.o.d -o CMakeFiles/_ost_seq_alg.dir/wrap_seq_alg.cc.o -c /build/openstructure-2.3.1/modules/seq/alg/pymod/wrap_seq_alg.cc +[ 48%] Building CXX object modules/db/pymod/CMakeFiles/_ost_db.dir/wrap_db.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_db_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/db/pymod/CMakeFiles/_ost_db.dir/wrap_db.cc.o -MF CMakeFiles/_ost_db.dir/wrap_db.cc.o.d -o CMakeFiles/_ost_db.dir/wrap_db.cc.o -c /build/openstructure-2.3.1/modules/db/pymod/wrap_db.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -17086,16 +17098,6 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -make -f modules/seq/alg/pymod/CMakeFiles/_ost_seq_alg.dir/build.make modules/seq/alg/pymod/CMakeFiles/_ost_seq_alg.dir/depend -make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/seq/alg/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/pymod/CMakeFiles/_ost_seq_alg.dir/DependInfo.cmake --color= -make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/seq/alg/pymod/CMakeFiles/_ost_seq_alg.dir/build.make modules/seq/alg/pymod/CMakeFiles/_ost_seq_alg.dir/build -make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 48%] Building CXX object modules/seq/alg/pymod/CMakeFiles/_ost_seq_alg.dir/wrap_seq_alg.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_seq_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/pymod/CMakeFiles/_ost_seq_alg.dir/wrap_seq_alg.cc.o -MF CMakeFiles/_ost_seq_alg.dir/wrap_seq_alg.cc.o.d -o CMakeFiles/_ost_seq_alg.dir/wrap_seq_alg.cc.o -c /build/openstructure-2.3.1/modules/seq/alg/pymod/wrap_seq_alg.cc -[ 48%] Building CXX object modules/db/pymod/CMakeFiles/_ost_db.dir/wrap_db.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_db_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/db/pymod/CMakeFiles/_ost_db.dir/wrap_db.cc.o -MF CMakeFiles/_ost_db.dir/wrap_db.cc.o.d -o CMakeFiles/_ost_db.dir/wrap_db.cc.o -c /build/openstructure-2.3.1/modules/db/pymod/wrap_db.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -17195,16 +17197,52 @@ cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/bindings/pymod/hbplus.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./hbplus.pyc\",\"hbplus.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/bindings/pymod/msms.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./msms.pyc\",\"msms.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/bindings/pymod/tmtools.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./tmtools.pyc\",\"tmtools.py\",doraise=True)" +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/openstructure-2.3.1/modules/seq/alg/pymod/wrap_seq_alg.cc:19: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/bindings/pymod/dssp.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./dssp.pyc\",\"dssp.py\",doraise=True)" +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/bindings/pymod/clustalw.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./clustalw.pyc\",\"clustalw.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/bindings/pymod/utils.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./utils.pyc\",\"utils.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/bindings/pymod/naccess.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./naccess.pyc\",\"naccess.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/bindings/pymod/hhblits.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./hhblits.pyc\",\"hhblits.py\",doraise=True)" +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/openstructure-2.3.1/modules/db/pymod/wrap_db.cc:21: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/bindings/pymod/hhblits2.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./hhblits2.pyc\",\"hhblits2.py\",doraise=True)" -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/bindings/pymod/hhblits3.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./hhblits3.pyc\",\"hhblits3.py\",doraise=True)" -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/bindings/pymod/blast.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./blast.pyc\",\"blast.py\",doraise=True)" -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/bindings/pymod/cadscore.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./cadscore.pyc\",\"cadscore.py\",doraise=True)" -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/bindings/pymod/kclust.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./kclust.pyc\",\"kclust.py\",doraise=True)" In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -17235,8 +17273,7 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/bindings/pymod/ialign.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./ialign.pyc\",\"ialign.py\",doraise=True)" -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/bindings/pymod/mmseqs2.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./mmseqs2.pyc\",\"mmseqs2.py\",doraise=True)" +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/bindings/pymod/hhblits3.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./hhblits3.pyc\",\"hhblits3.py\",doraise=True)" In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/db/extract_data_helper.hh:27: @@ -17246,48 +17283,13 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/bindings/pymod/blast.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./blast.pyc\",\"blast.py\",doraise=True)" +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/bindings/pymod/cadscore.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./cadscore.pyc\",\"cadscore.py\",doraise=True)" +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/bindings/pymod/kclust.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./kclust.pyc\",\"kclust.py\",doraise=True)" +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/bindings/pymod/ialign.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./ialign.pyc\",\"ialign.py\",doraise=True)" +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/bindings/pymod/mmseqs2.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./mmseqs2.pyc\",\"mmseqs2.py\",doraise=True)" make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 48%] Built target _ost_bindings -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/db/pymod/wrap_db.cc:21: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/seq/alg/pymod/wrap_seq_alg.cc:19: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -17339,305 +17341,205 @@ [ 48%] Linking CXX shared library ../../../stage/lib/libost_io.so cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_io.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libost_io.so.2.3 -o ../../../stage/lib/libost_io.so.2.3.1 CMakeFiles/ost_io.dir/io_manager.cc.o CMakeFiles/ost_io.dir/convert.cc.o CMakeFiles/ost_io.dir/io_utils.cc.o CMakeFiles/ost_io.dir/mol/entity_io_crd_handler.cc.o CMakeFiles/ost_io.dir/mol/entity_io_pqr_handler.cc.o CMakeFiles/ost_io.dir/mol/entity_io_mae_handler.cc.o CMakeFiles/ost_io.dir/mol/pdb_reader.cc.o CMakeFiles/ost_io.dir/mol/entity_io_pdb_handler.cc.o CMakeFiles/ost_io.dir/mol/pdb_writer.cc.o CMakeFiles/ost_io.dir/mol/entity_io_sdf_handler.cc.o CMakeFiles/ost_io.dir/mol/entity_io_mmcif_handler.cc.o CMakeFiles/ost_io.dir/mol/sdf_reader.cc.o CMakeFiles/ost_io.dir/mol/sdf_writer.cc.o CMakeFiles/ost_io.dir/mol/save_entity.cc.o CMakeFiles/ost_io.dir/mol/load_entity.cc.o CMakeFiles/ost_io.dir/mol/surface_io_msms_handler.cc.o CMakeFiles/ost_io.dir/mol/load_surface.cc.o CMakeFiles/ost_io.dir/mol/chemdict_parser.cc.o CMakeFiles/ost_io.dir/mol/io_profile.cc.o CMakeFiles/ost_io.dir/mol/dcd_io.cc.o CMakeFiles/ost_io.dir/mol/star_parser.cc.o CMakeFiles/ost_io.dir/mol/mmcif_reader.cc.o CMakeFiles/ost_io.dir/mol/mmcif_info.cc.o CMakeFiles/ost_io.dir/mol/pdb_str.cc.o CMakeFiles/ost_io.dir/mol/stereochemical_params_reader.cc.o CMakeFiles/ost_io.dir/mol/omf.cc.o CMakeFiles/ost_io.dir/seq/clustal_io_handler.cc.o CMakeFiles/ost_io.dir/seq/load.cc.o CMakeFiles/ost_io.dir/seq/save.cc.o CMakeFiles/ost_io.dir/seq/fasta_io_handler.cc.o CMakeFiles/ost_io.dir/seq/pir_io_handler.cc.o CMakeFiles/ost_io.dir/seq/promod_io_handler.cc.o CMakeFiles/ost_io.dir/seq/hhm_io_handler.cc.o CMakeFiles/ost_io.dir/seq/pssm_io_handler.cc.o CMakeFiles/ost_io.dir/img/load_map.cc.o CMakeFiles/ost_io.dir/img/map_io_dx_handler.cc.o CMakeFiles/ost_io.dir/img/map_io_spi_handler.cc.o CMakeFiles/ost_io.dir/img/map_io_situs_handler.cc.o CMakeFiles/ost_io.dir/img/map_io_mrc_handler.cc.o CMakeFiles/ost_io.dir/img/map_io_dm3_handler.cc.o CMakeFiles/ost_io.dir/img/map_io_tiff_handler.cc.o CMakeFiles/ost_io.dir/img/map_io_dat_handler.cc.o CMakeFiles/ost_io.dir/img/map_io_ipl_handler.cc.o CMakeFiles/ost_io.dir/img/map_io_jpk_handler.cc.o CMakeFiles/ost_io.dir/img/map_io_nanoscope_handler.cc.o CMakeFiles/ost_io.dir/img/map_io_png_handler.cc.o CMakeFiles/ost_io.dir/img/map_io_df3_handler.cc.o CMakeFiles/ost_io.dir/img/image_format.cc.o CMakeFiles/ost_io.dir/img/tiff_util.cc.o -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib: ../../../stage/lib/libost_mol_alg.so.2.3.1 ../../../stage/lib/libost_img_alg.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libtiff.so /usr/lib/x86_64-linux-gnu/libpng.so /usr/lib/x86_64-linux-gnu/libz.so ../../../stage/lib/libost_conop.so.2.3.1 ../../../stage/lib/libost_db.so.2.3.1 /usr/lib/x86_64-linux-gnu/libsqlite3.so ../../../stage/lib/libost_img.so.2.3.1 /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libfftw3f_threads.so /usr/lib/x86_64-linux-gnu/libboost_program_options.so /usr/lib/x86_64-linux-gnu/libboost_thread.so /usr/lib/x86_64-linux-gnu/libboost_chrono.so /usr/lib/x86_64-linux-gnu/libboost_date_time.so /usr/lib/x86_64-linux-gnu/libboost_atomic.so ../../../stage/lib/libost_seq_alg.so.2.3.1 ../../../stage/lib/libost_seq.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so ../../../stage/lib/libost_mol.so.2.3.1 ../../../stage/lib/libost_info.so.2.3.1 ../../../stage/lib/libost_base.so.2.3.1 ../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 -[ 48%] Linking CXX shared module ../../../stage/lib/python3.11/dist-packages/ost/db/_ost_db.so -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_db.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -o ../../../stage/lib/python3.11/dist-packages/ost/db/_ost_db.so CMakeFiles/_ost_db.dir/export_linear_db.cc.o CMakeFiles/_ost_db.dir/wrap_db.cc.o -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib: ../../../stage/lib/libost_db.so.2.3.1 /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so /usr/lib/x86_64-linux-gnu/libsqlite3.so ../../../stage/lib/libost_seq.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so ../../../stage/lib/libost_mol.so.2.3.1 ../../../stage/lib/libost_info.so.2.3.1 ../../../stage/lib/libost_base.so.2.3.1 ../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/db/pymod/__init__.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/db/./__init__.pyc\",\"__init__.py\",doraise=True)" -make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 48%] Built target _ost_db -make -f modules/conop/pymod/CMakeFiles/_ost_conop.dir/build.make modules/conop/pymod/CMakeFiles/_ost_conop.dir/depend -make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/conop/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/pymod/CMakeFiles/_ost_conop.dir/DependInfo.cmake --color= -make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/conop/pymod/CMakeFiles/_ost_conop.dir/build.make modules/conop/pymod/CMakeFiles/_ost_conop.dir/build -make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 48%] Building CXX object modules/conop/pymod/CMakeFiles/_ost_conop.dir/wrap_conop.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_conop_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/pymod/CMakeFiles/_ost_conop.dir/wrap_conop.cc.o -MF CMakeFiles/_ost_conop.dir/wrap_conop.cc.o.d -o CMakeFiles/_ost_conop.dir/wrap_conop.cc.o -c /build/openstructure-2.3.1/modules/conop/pymod/wrap_conop.cc -[ 48%] Building CXX object modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_compound.cc.o -[ 48%] Building CXX object modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_heuristic.cc.o -[ 50%] Building CXX object modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_processor.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_conop_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_processor.cc.o -MF CMakeFiles/_ost_conop.dir/export_processor.cc.o.d -o CMakeFiles/_ost_conop.dir/export_processor.cc.o -c /build/openstructure-2.3.1/modules/conop/pymod/export_processor.cc -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_conop_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_compound.cc.o -MF CMakeFiles/_ost_conop.dir/export_compound.cc.o.d -o CMakeFiles/_ost_conop.dir/export_compound.cc.o -c /build/openstructure-2.3.1/modules/conop/pymod/export_compound.cc -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_conop_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_heuristic.cc.o -MF CMakeFiles/_ost_conop.dir/export_heuristic.cc.o.d -o CMakeFiles/_ost_conop.dir/export_heuristic.cc.o -c /build/openstructure-2.3.1/modules/conop/pymod/export_heuristic.cc -[ 50%] Building CXX object modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_diag.cc.o -[ 50%] Building CXX object modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_amino_acids.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_conop_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_diag.cc.o -MF CMakeFiles/_ost_conop.dir/export_diag.cc.o.d -o CMakeFiles/_ost_conop.dir/export_diag.cc.o -c /build/openstructure-2.3.1/modules/conop/pymod/export_diag.cc -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_conop_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_amino_acids.cc.o -MF CMakeFiles/_ost_conop.dir/export_amino_acids.cc.o.d -o CMakeFiles/_ost_conop.dir/export_amino_acids.cc.o -c /build/openstructure-2.3.1/modules/conop/pymod/export_amino_acids.cc -[ 50%] Building CXX object modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_conop.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_conop_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_conop.cc.o -MF CMakeFiles/_ost_conop.dir/export_conop.cc.o.d -o CMakeFiles/_ost_conop.dir/export_conop.cc.o -c /build/openstructure-2.3.1/modules/conop/pymod/export_conop.cc -[ 50%] Building CXX object modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_ring_finder.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_conop_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_ring_finder.cc.o -MF CMakeFiles/_ost_conop.dir/export_ring_finder.cc.o.d -o CMakeFiles/_ost_conop.dir/export_ring_finder.cc.o -c /build/openstructure-2.3.1/modules/conop/pymod/export_ring_finder.cc -[ 50%] Building CXX object modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_rule_based.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_conop_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_rule_based.cc.o -MF CMakeFiles/_ost_conop.dir/export_rule_based.cc.o.d -o CMakeFiles/_ost_conop.dir/export_rule_based.cc.o -c /build/openstructure-2.3.1/modules/conop/pymod/export_rule_based.cc cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E cmake_symlink_library ../../../stage/lib/libost_io.so.2.3.1 ../../../stage/lib/libost_io.so.2.3 ../../../stage/lib/libost_io.so make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 50%] Built target ost_io +[ 48%] Built target ost_io make -f modules/conop/src/CMakeFiles/chemdict_tool.dir/build.make modules/conop/src/CMakeFiles/chemdict_tool.dir/depend -make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/conop/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu 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modules/mol/alg/src/CMakeFiles/lddt.dir/depend +make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/io/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/tests/CMakeFiles/test_mae_standalone.dir/DependInfo.cmake --color= make -f modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/build.make modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/depend +make -f tools/molck/CMakeFiles/molck.dir/build.make tools/molck/CMakeFiles/molck.dir/depend make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/alg/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src/CMakeFiles/lddt.dir/DependInfo.cmake --color= -make -f tools/molck/CMakeFiles/molck.dir/build.make tools/molck/CMakeFiles/molck.dir/depend make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/io/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/tests/CMakeFiles/test_mae_standalone.dir/DependInfo.cmake --color= make -f 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/usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/lddt.dir/lddt.cc.o -MF CMakeFiles/lddt.dir/lddt.cc.o.d -o CMakeFiles/lddt.dir/lddt.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/src/lddt.cc +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/tools/molck /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/tools/molck 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/usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/conop/src/CMakeFiles/chemdict_tool.dir/chemdict_tool.cc.o -MF CMakeFiles/chemdict_tool.dir/chemdict_tool.cc.o.d -o CMakeFiles/chemdict_tool.dir/chemdict_tool.cc.o -c /build/openstructure-2.3.1/modules/conop/src/chemdict_tool.cc make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f tools/molck/CMakeFiles/molck.dir/build.make tools/molck/CMakeFiles/molck.dir/build -[ 50%] Building CXX object modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/forcefield.cc.o +make -f modules/mol/alg/src/CMakeFiles/lddt.dir/build.make modules/mol/alg/src/CMakeFiles/lddt.dir/build make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_MM -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_mm_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/forcefield.cc.o -MF CMakeFiles/ost_mol_mm.dir/forcefield.cc.o.d -o CMakeFiles/ost_mol_mm.dir/forcefield.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/src/forcefield.cc -[ 50%] Building CXX object modules/io/tests/CMakeFiles/test_mae_standalone.dir/test_mae_standalone.cc.o +[ 48%] Building CXX object modules/io/tests/CMakeFiles/test_mae_standalone.dir/test_mae_standalone.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat 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+make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/lddt.dir/lddt.cc.o -MF CMakeFiles/lddt.dir/lddt.cc.o.d -o CMakeFiles/lddt.dir/lddt.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/src/lddt.cc +[ 48%] Building CXX object tools/molck/CMakeFiles/molck.dir/main.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/tools/molck && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT tools/molck/CMakeFiles/molck.dir/main.cc.o -MF CMakeFiles/molck.dir/main.cc.o.d -o CMakeFiles/molck.dir/main.cc.o -c 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-fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/forcefield.cc.o -MF CMakeFiles/ost_mol_mm.dir/forcefield.cc.o.d -o CMakeFiles/ost_mol_mm.dir/forcefield.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/src/forcefield.cc +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_MM -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_mm_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/ff_reader.cc.o -MF CMakeFiles/ost_mol_mm.dir/ff_reader.cc.o.d -o CMakeFiles/ost_mol_mm.dir/ff_reader.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/src/ff_reader.cc +[ 48%] Building CXX object modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/heuristic_block_modifiers.cc.o +[ 48%] Building CXX object modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/buildingblock.cc.o make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 50%] Generating tools/moc_tool_options_win.cpp +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_MM -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_mm_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/buildingblock.cc.o -MF CMakeFiles/ost_mol_mm.dir/buildingblock.cc.o.d -o CMakeFiles/ost_mol_mm.dir/buildingblock.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/src/buildingblock.cc +[ 48%] Building CXX object modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/gromacs_block_modifiers.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_MM -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_mm_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/gromacs_block_modifiers.cc.o -MF CMakeFiles/ost_mol_mm.dir/gromacs_block_modifiers.cc.o.d -o CMakeFiles/ost_mol_mm.dir/gromacs_block_modifiers.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/src/gromacs_block_modifiers.cc +[ 48%] Building CXX object modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/interaction.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_MM -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_mm_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/heuristic_block_modifiers.cc.o -MF CMakeFiles/ost_mol_mm.dir/heuristic_block_modifiers.cc.o.d -o CMakeFiles/ost_mol_mm.dir/heuristic_block_modifiers.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/src/heuristic_block_modifiers.cc +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_MM -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_mm_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/interaction.cc.o -MF CMakeFiles/ost_mol_mm.dir/interaction.cc.o.d -o CMakeFiles/ost_mol_mm.dir/interaction.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/src/interaction.cc +[ 48%] Generating tools/moc_tool_options_win.cpp cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/tools && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/tools/moc_tool_options_win.cpp_parameters -[ 50%] Generating data_viewer/moc_argand.cpp +[ 48%] Generating data_viewer/moc_argand.cpp cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_argand.cpp_parameters -[ 50%] Generating data_viewer/moc_data_viewer.cpp +[ 48%] Generating data_viewer/moc_data_viewer.cpp cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_data_viewer.cpp_parameters -[ 50%] Generating data_viewer/moc_data_viewer_panel_base.cpp +[ 48%] Generating data_viewer/moc_data_viewer_panel_base.cpp cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_data_viewer_panel_base.cpp_parameters -[ 51%] Generating data_viewer/moc_fft_panel.cpp +[ 50%] Generating data_viewer/moc_fft_panel.cpp cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_fft_panel.cpp_parameters -[ 51%] Generating data_viewer/moc_info_panel.cpp +[ 48%] Generating data_viewer/moc_info_panel.cpp cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_info_panel.cpp_parameters -[ 51%] Generating data_viewer/moc_null_overlay.cpp +[ 50%] Generating data_viewer/moc_null_overlay.cpp cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_null_overlay.cpp_parameters -[ 51%] Generating data_viewer/moc_overlay_base.cpp +[ 50%] Generating data_viewer/moc_overlay_base.cpp cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_overlay_base.cpp_parameters -[ 51%] Generating data_viewer/moc_overlay_manager_gui.cpp +[ 50%] Generating data_viewer/moc_overlay_manager_gui.cpp cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_overlay_manager_gui.cpp_parameters -[ 51%] Generating data_viewer/moc_pointlist_overlay_base.cpp +[ 50%] Generating data_viewer/moc_pointlist_overlay_base.cpp cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_pointlist_overlay_base.cpp_parameters -[ 51%] Generating messages/moc_log_reader.cpp +[ 50%] Generating messages/moc_log_reader.cpp cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/messages && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/messages/moc_log_reader.cpp_parameters -[ 51%] Generating messages/moc_message_box_widget.cpp +[ 50%] Generating messages/moc_message_box_widget.cpp cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/messages && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/messages/moc_message_box_widget.cpp_parameters -[ 51%] Generating messages/moc_message_widget.cpp +[ 50%] Generating messages/moc_message_widget.cpp cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/messages && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/messages/moc_message_widget.cpp_parameters -[ 51%] Generating moc_dock_widget.cpp +[ 50%] Generating moc_dock_widget.cpp cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_dock_widget.cpp_parameters -[ 51%] Generating moc_file_browser.cpp +[ 50%] Generating moc_file_browser.cpp cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_file_browser.cpp_parameters -[ 51%] Generating moc_file_type_dialog.cpp +[ 50%] Generating moc_file_type_dialog.cpp cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_file_type_dialog.cpp_parameters -[ 51%] Generating moc_file_viewer.cpp -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_file_viewer.cpp_parameters -[ 51%] Generating moc_gl_canvas.cpp +[ 50%] Generating moc_gl_canvas.cpp cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_gl_canvas.cpp_parameters -[ 52%] Generating moc_gl_win.cpp -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_gl_win.cpp_parameters -[ 52%] Generating moc_gosty_app.cpp +[ 50%] Generating moc_file_viewer.cpp +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_file_viewer.cpp_parameters +[ 50%] Generating moc_gosty_app.cpp +[ 51%] Generating moc_gl_win.cpp cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_gosty_app.cpp_parameters -[ 52%] Generating moc_main.cpp +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_gl_win.cpp_parameters +[ 51%] Generating moc_main.cpp cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_main.cpp_parameters -[ 52%] Generating moc_main_area.cpp +[ 51%] Generating moc_main_area.cpp cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_main_area.cpp_parameters -[ 52%] Generating moc_main_window.cpp +[ 51%] Building CXX object modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/simulation.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_MM -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_mm_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/simulation.cc.o -MF CMakeFiles/ost_mol_mm.dir/simulation.cc.o.d -o CMakeFiles/ost_mol_mm.dir/simulation.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/src/simulation.cc +[ 51%] Generating moc_main_window.cpp cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_main_window.cpp_parameters -[ 52%] Generating moc_perspective.cpp +[ 51%] Generating moc_perspective.cpp cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_perspective.cpp_parameters -[ 52%] Generating moc_scene_menu.cpp +[ 51%] Generating moc_scene_menu.cpp cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_scene_menu.cpp_parameters -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/conop/pymod/export_amino_acids.cc:19: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 52%] Generating moc_scene_selection.cpp +[ 51%] Generating moc_scene_selection.cpp cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_scene_selection.cpp_parameters -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/conop/pymod/wrap_conop.cc:19: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/conop/pymod/export_ring_finder.cc:19: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 52%] Generating moc_widget.cpp +[ 51%] Generating moc_widget.cpp cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_widget.cpp_parameters -[ 52%] Generating moc_widget_geom_handler.cpp +[ 51%] Generating moc_widget_geom_handler.cpp cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_widget_geom_handler.cpp_parameters -[ 53%] Generating moc_widget_pool.cpp +[ 52%] Generating moc_widget_pool.cpp cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_widget_pool.cpp_parameters -[ 53%] Generating panels/moc_bottom_bar.cpp +[ 52%] Generating panels/moc_bottom_bar.cpp cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/panels && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_bottom_bar.cpp_parameters -[ 53%] Generating panels/moc_button_bar.cpp +[ 52%] Generating panels/moc_button_bar.cpp cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/panels && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_button_bar.cpp_parameters -[ 53%] Generating panels/moc_button_box.cpp +[ 52%] Generating panels/moc_button_box.cpp cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/panels && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_button_box.cpp_parameters -[ 53%] Generating panels/moc_drop_box.cpp +[ 52%] Generating panels/moc_drop_box.cpp cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/panels && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_drop_box.cpp_parameters -[ 53%] Generating panels/moc_event_button.cpp +[ 52%] Generating panels/moc_event_button.cpp cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/panels && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_event_button.cpp_parameters -[ 53%] Generating panels/moc_panel_bar.cpp +[ 52%] Generating panels/moc_panel_bar.cpp cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/panels && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_panel_bar.cpp_parameters -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/conop/pymod/export_processor.cc:20: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/conop.hh:24, - from /build/openstructure-2.3.1/modules/io/tests/test_mae_standalone.cc:2: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/12/string:45, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/ostream:38, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, - from /build/openstructure-2.3.1/modules/io/tests/test_mae_standalone.cc:1: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 53%] Generating panels/moc_panel_bar_widget_holder.cpp +[ 52%] Generating panels/moc_panel_bar_widget_holder.cpp cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/panels && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_panel_bar_widget_holder.cpp_parameters -[ 55%] Generating panels/moc_panel_manager.cpp +[ 53%] Generating panels/moc_panel_manager.cpp cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/panels && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_panel_manager.cpp_parameters -[ 55%] Generating panels/moc_panel_widget_container.cpp +[ 53%] Generating panels/moc_panel_widget_container.cpp cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/panels && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_panel_widget_container.cpp_parameters -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/conop/pymod/export_diag.cc:20: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 55%] Generating panels/moc_side_bar.cpp +[ 53%] Generating panels/moc_side_bar.cpp +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/panels && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_side_bar.cpp_parameters +[ 53%] Generating panels/moc_splitter_panel_bar.cpp +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/panels && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_splitter_panel_bar.cpp_parameters +[ 53%] Generating python_shell/moc_completer_base.cpp +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_completer_base.cpp_parameters +[ 53%] Generating python_shell/moc_gutter.cpp +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_gutter.cpp_parameters +[ 53%] Generating panels/moc_tabbed_panel_bar.cpp +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/panels && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_tabbed_panel_bar.cpp_parameters +[ 53%] Generating python_shell/moc_main_thread_runner.cpp +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_main_thread_runner.cpp_parameters +[ 53%] Generating python_shell/moc_output_redirector.cpp +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_output_redirector.cpp_parameters +[ 53%] Generating python_shell/moc_path_completer.cpp +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_path_completer.cpp_parameters +[ 53%] Generating python_shell/moc_python_completer.cpp +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_python_completer.cpp_parameters +[ 53%] Generating python_shell/moc_python_interpreter.cpp +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_python_interpreter.cpp_parameters +[ 53%] Generating python_shell/moc_python_interpreter_worker.cpp +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_python_interpreter_worker.cpp_parameters +[ 55%] Generating python_shell/moc_python_namespace_tree_model.cpp +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_python_namespace_tree_model.cpp_parameters +[ 55%] Generating python_shell/moc_python_shell.cpp +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_python_shell.cpp_parameters +[ 55%] Generating python_shell/moc_python_shell_widget.cpp +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_python_shell_widget.cpp_parameters +[ 55%] Generating python_shell/moc_state.cpp +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_state.cpp_parameters +[ 55%] Generating python_shell/moc_state_machine.cpp +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_state_machine.cpp_parameters +[ 55%] Generating python_shell/moc_text_logger.cpp +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_text_logger.cpp_parameters +[ 55%] Generating python_shell/moc_transition.cpp +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_transition.cpp_parameters +[ 55%] Generating python_shell/moc_transition_guard.cpp +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_transition_guard.cpp_parameters +[ 55%] Generating scene_win/moc_context_menu.cpp +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_context_menu.cpp_parameters +[ 55%] Generating scene_win/moc_current_selection_node.cpp +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_current_selection_node.cpp_parameters +[ 56%] Generating scene_win/moc_custom_part_node.cpp +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_custom_part_node.cpp_parameters +[ 56%] Generating scene_win/moc_entity_node.cpp +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_entity_node.cpp_parameters +[ 56%] Generating scene_win/moc_entity_part_node.cpp +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_entity_part_node.cpp_parameters In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/amino_acids.hh:26, - from /build/openstructure-2.3.1/modules/conop/pymod/export_amino_acids.cc:21: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/heuristic_block_modifiers.hh:28, + from /build/openstructure-2.3.1/modules/mol/mm/src/heuristic_block_modifiers.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/specfun.h:45, - from /usr/include/c++/12/cmath:1935, - from /usr/include/c++/12/math.h:36, - from /usr/include/python3.11/pyport.h:218, - from /usr/include/python3.11/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8: + from /usr/include/c++/12/memory:63, + from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, + from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, + from /usr/include/boost/shared_ptr.hpp:17, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/heuristic_block_modifiers.hh:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -17647,39 +17549,20 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/panels && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_side_bar.cpp_parameters -[ 55%] Generating panels/moc_splitter_panel_bar.cpp -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/panels && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_splitter_panel_bar.cpp_parameters -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/conop/pymod/export_heuristic.cc:21: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 56%] Generating scene_win/moc_gfx_scene_node.cpp +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_gfx_scene_node.cpp_parameters +[ 56%] Generating scene_win/moc_label_node.cpp +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_label_node.cpp_parameters +[ 56%] Generating scene_win/moc_render_mode_node.cpp +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_render_mode_node.cpp_parameters In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/compound_lib_base.hh:5, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/compound_lib.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/chemdict_parser.hh:30, - from /build/openstructure-2.3.1/modules/conop/src/chemdict_tool.cc:32: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/conop.hh:24, + from /build/openstructure-2.3.1/modules/io/tests/test_mae_standalone.cc:2: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -17688,8 +17571,8 @@ from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, - from /usr/include/c++/12/iostream:39, - from /build/openstructure-2.3.1/modules/conop/src/chemdict_tool.cc:24: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, + from /build/openstructure-2.3.1/modules/io/tests/test_mae_standalone.cc:1: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -17699,62 +17582,23 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/conop/pymod/export_rule_based.cc:20: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 55%] Generating panels/moc_tabbed_panel_bar.cpp -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/panels && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_tabbed_panel_bar.cpp_parameters -[ 55%] Generating python_shell/moc_completer_base.cpp -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_completer_base.cpp_parameters -[ 55%] Building CXX object modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/ff_reader.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_MM -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_mm_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/ff_reader.cc.o -MF CMakeFiles/ost_mol_mm.dir/ff_reader.cc.o.d -o CMakeFiles/ost_mol_mm.dir/ff_reader.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/src/ff_reader.cc -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/amino_acids.hh:61:42: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 61 | class AminoAcidSetIterator : public std::iterator struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/specfun.h:45, - from /usr/include/c++/12/cmath:1935, - from /usr/include/c++/12/math.h:36, - from /usr/include/python3.11/pyport.h:218, - from /usr/include/python3.11/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8: + from /usr/include/c++/12/vector:60, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/buildingblock.hh:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -17764,32 +17608,22 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 55%] Generating python_shell/moc_output_redirector.cpp -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_output_redirector.cpp_parameters -[ 55%] Generating python_shell/moc_path_completer.cpp -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_path_completer.cpp_parameters -[ 55%] Generating python_shell/moc_python_completer.cpp -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_python_completer.cpp_parameters In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/diag.hh:23, - from /build/openstructure-2.3.1/modules/conop/pymod/export_diag.cc:21: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/interaction.hh:34, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/buildingblock.hh:29, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/forcefield.hh:31, + from /build/openstructure-2.3.1/modules/mol/mm/src/forcefield.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/specfun.h:45, - from /usr/include/c++/12/cmath:1935, - from /usr/include/c++/12/math.h:36, - from /usr/include/python3.11/pyport.h:218, - from /usr/include/python3.11/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8: + from /usr/include/c++/12/vector:60, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/forcefield.hh:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -17799,46 +17633,24 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 55%] Generating python_shell/moc_python_interpreter.cpp -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_python_interpreter.cpp_parameters -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/conop/pymod/export_conop.cc:19: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 55%] Generating python_shell/moc_python_interpreter_worker.cpp -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_python_interpreter_worker.cpp_parameters In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/interaction.hh:34, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/buildingblock.hh:29, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/forcefield.hh:31, - from /build/openstructure-2.3.1/modules/mol/mm/src/forcefield.cc:20: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/gromacs_block_modifiers.hh:28, + from /build/openstructure-2.3.1/modules/mol/mm/src/gromacs_block_modifiers.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/vector:60, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/forcefield.hh:23: + from /usr/include/c++/12/memory:63, + from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, + from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, + from /usr/include/boost/shared_ptr.hpp:17, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/gromacs_block_modifiers.hh:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -17848,30 +17660,20 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 56%] Generating python_shell/moc_python_namespace_tree_model.cpp -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_python_namespace_tree_model.cpp_parameters -[ 56%] Generating python_shell/moc_python_shell.cpp -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_python_shell.cpp_parameters In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/heuristic.hh:22, - from /build/openstructure-2.3.1/modules/conop/pymod/export_heuristic.cc:23: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/interaction.hh:34, + from /build/openstructure-2.3.1/modules/mol/mm/src/interaction.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/specfun.h:45, - from /usr/include/c++/12/cmath:1935, - from /usr/include/c++/12/math.h:36, - from /usr/include/python3.11/pyport.h:218, - from /usr/include/python3.11/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8: + from /usr/include/c++/12/vector:60, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/interaction.hh:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -17881,26 +17683,29 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 56%] Generating scene_win/moc_root_node.cpp +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_root_node.cpp_parameters +[ 56%] Generating scene_win/moc_scene_node.cpp +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_scene_node.cpp_parameters +[ 56%] Generating scene_win/moc_scene_win.cpp +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_scene_win.cpp_parameters +[ 56%] Generating scene_win/moc_scene_win_model.cpp +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_scene_win_model.cpp_parameters In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/processor.hh:22, - from /build/openstructure-2.3.1/modules/conop/pymod/export_processor.cc:21: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/simulation.hh:26, + from /build/openstructure-2.3.1/modules/mol/mm/src/simulation.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/specfun.h:45, - from /usr/include/c++/12/cmath:1935, - from /usr/include/c++/12/math.h:36, - from /usr/include/python3.11/pyport.h:218, - from /usr/include/python3.11/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8: + from /usr/include/c++/12/vector:60, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/simulation.hh:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -17913,16 +17718,24 @@ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/chain_view.hh:23, - from /build/openstructure-2.3.1/modules/mol/alg/src/lddt.cc:30: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/interaction.hh:34, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/buildingblock.hh:29, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/forcefield.hh:31, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/ff_reader.hh:32, + from /build/openstructure-2.3.1/modules/mol/mm/src/ff_reader.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/iomanip:40, - from /build/openstructure-2.3.1/modules/mol/alg/src/lddt.cc:19: + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/istream:38, + from /usr/include/c++/12/fstream:38, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/ff_reader.hh:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -17932,32 +17745,26 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 56%] Generating python_shell/moc_python_shell_widget.cpp -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_python_shell_widget.cpp_parameters -[ 56%] Generating python_shell/moc_state.cpp -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_state.cpp_parameters -[ 56%] Generating python_shell/moc_state_machine.cpp -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_state_machine.cpp_parameters -[ 56%] Generating python_shell/moc_text_logger.cpp -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_text_logger.cpp_parameters -[ 56%] Generating python_shell/moc_transition.cpp -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_transition.cpp_parameters In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/conop.hh:24, - from /build/openstructure-2.3.1/tools/molck/main.cc:8: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/compound_lib_base.hh:5, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/compound_lib.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/chemdict_parser.hh:30, + from /build/openstructure-2.3.1/modules/conop/src/chemdict_tool.cc:32: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, - from /usr/include/boost/program_options/errors.hpp:12, - from /usr/include/boost/program_options/options_description.hpp:12, - from /usr/include/boost/program_options.hpp:15, - from /build/openstructure-2.3.1/tools/molck/main.cc:2: + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/ostream:38, + from /usr/include/c++/12/iostream:39, + from /build/openstructure-2.3.1/modules/conop/src/chemdict_tool.cc:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -17967,27 +17774,12 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/local_dist_diff_test.hh:24, - from /build/openstructure-2.3.1/modules/mol/alg/src/lddt.cc:31: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 32 | : public std::iterator{ - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/openstructure-2.3.1/modules/mol/alg/src/lddt.cc:39: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/amino_acids.hh:61:42: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 61 | class AminoAcidSetIterator : public std::iterator struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/specfun.h:45, - from /usr/include/c++/12/cmath:1935, - from /usr/include/c++/12/math.h:36, - from /usr/include/python3.11/pyport.h:218, - from /usr/include/python3.11/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8: +In file included from /usr/include/c++/12/string:45, + from /usr/include/boost/program_options/errors.hpp:12, + from /usr/include/boost/program_options/options_description.hpp:12, + from /usr/include/boost/program_options.hpp:15, + from /build/openstructure-2.3.1/tools/molck/main.cc:2: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -18020,23 +17808,16 @@ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/rule_based.hh:22, - from /build/openstructure-2.3.1/modules/conop/pymod/export_rule_based.cc:22: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/chain_view.hh:23, + from /build/openstructure-2.3.1/modules/mol/alg/src/lddt.cc:30: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/specfun.h:45, - from /usr/include/c++/12/cmath:1935, - from /usr/include/c++/12/math.h:36, - from /usr/include/python3.11/pyport.h:218, - from /usr/include/python3.11/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8: +In file included from /usr/include/c++/12/string:45, + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/iomanip:40, + from /build/openstructure-2.3.1/modules/mol/alg/src/lddt.cc:19: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -18046,279 +17827,160 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/conop/pymod/export_compound.cc:19: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 56%] Generating scene_win/moc_current_selection_node.cpp -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_current_selection_node.cpp_parameters +[ 56%] Generating sequence_viewer/moc_base_row.cpp +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_base_row.cpp_parameters +[ 57%] Generating sequence_viewer/moc_base_view_object.cpp +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_base_view_object.cpp_parameters +[ 57%] Linking CXX executable ../../../stage/bin/test_mae_standalone +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_mae_standalone.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro CMakeFiles/test_mae_standalone.dir/test_mae_standalone.cc.o -o ../../../stage/bin/test_mae_standalone -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib ../../../stage/lib/libost_io.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../stage/lib/libost_mol_alg.so.2.3.1 ../../../stage/lib/libost_conop.so.2.3.1 ../../../stage/lib/libost_db.so.2.3.1 /usr/lib/x86_64-linux-gnu/libsqlite3.so /usr/lib/x86_64-linux-gnu/libboost_program_options.so /usr/lib/x86_64-linux-gnu/libboost_thread.so /usr/lib/x86_64-linux-gnu/libboost_chrono.so /usr/lib/x86_64-linux-gnu/libboost_date_time.so /usr/lib/x86_64-linux-gnu/libboost_atomic.so ../../../stage/lib/libost_seq_alg.so.2.3.1 ../../../stage/lib/libost_seq.so.2.3.1 ../../../stage/lib/libost_mol.so.2.3.1 ../../../stage/lib/libost_img_alg.so.2.3.1 ../../../stage/lib/libost_img.so.2.3.1 ../../../stage/lib/libost_info.so.2.3.1 ../../../stage/lib/libost_base.so.2.3.1 ../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libfftw3f_threads.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libtiff.so /usr/lib/x86_64-linux-gnu/libpng.so /usr/lib/x86_64-linux-gnu/libz.so In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, - from /build/openstructure-2.3.1/tools/molck/main.cc:10: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/modeller.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/system_creator.hh:35, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/simulation.hh:27: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 57%] Generating scene_win/moc_custom_part_node.cpp -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_custom_part_node.cpp_parameters -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/compound_lib_base.hh:5, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/compound_lib.hh:27, - from /build/openstructure-2.3.1/modules/conop/pymod/export_compound.cc:26: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/specfun.h:45, - from /usr/include/c++/12/cmath:1935, - from /usr/include/c++/12/math.h:36, - from /usr/include/python3.11/pyport.h:218, - from /usr/include/python3.11/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8: +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, + from /build/openstructure-2.3.1/tools/molck/main.cc:10: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 32 | : public std::iterator{ + | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/local_dist_diff_test.hh:24, + from /build/openstructure-2.3.1/modules/mol/alg/src/lddt.cc:31: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 32 | : public std::iterator{ + | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 57%] Generating scene_win/moc_entity_node.cpp -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_entity_node.cpp_parameters -[ 57%] Generating scene_win/moc_entity_part_node.cpp -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_entity_part_node.cpp_parameters -[ 57%] Linking CXX executable ../../../stage/bin/test_mae_standalone -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_mae_standalone.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro CMakeFiles/test_mae_standalone.dir/test_mae_standalone.cc.o -o ../../../stage/bin/test_mae_standalone -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib ../../../stage/lib/libost_io.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../stage/lib/libost_mol_alg.so.2.3.1 ../../../stage/lib/libost_conop.so.2.3.1 ../../../stage/lib/libost_db.so.2.3.1 /usr/lib/x86_64-linux-gnu/libsqlite3.so /usr/lib/x86_64-linux-gnu/libboost_program_options.so /usr/lib/x86_64-linux-gnu/libboost_thread.so /usr/lib/x86_64-linux-gnu/libboost_chrono.so /usr/lib/x86_64-linux-gnu/libboost_date_time.so /usr/lib/x86_64-linux-gnu/libboost_atomic.so ../../../stage/lib/libost_seq_alg.so.2.3.1 ../../../stage/lib/libost_seq.so.2.3.1 ../../../stage/lib/libost_mol.so.2.3.1 ../../../stage/lib/libost_img_alg.so.2.3.1 ../../../stage/lib/libost_img.so.2.3.1 ../../../stage/lib/libost_info.so.2.3.1 ../../../stage/lib/libost_base.so.2.3.1 ../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libfftw3f_threads.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libtiff.so /usr/lib/x86_64-linux-gnu/libpng.so /usr/lib/x86_64-linux-gnu/libz.so -[ 57%] Generating scene_win/moc_gfx_scene_node.cpp -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_gfx_scene_node.cpp_parameters -[ 57%] Generating scene_win/moc_label_node.cpp -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_label_node.cpp_parameters -[ 57%] Generating scene_win/moc_render_modes_node.cpp -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_render_modes_node.cpp_parameters -[ 57%] Generating scene_win/moc_render_mode_node.cpp -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_render_mode_node.cpp_parameters make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 57%] Built target test_mae_standalone -[ 57%] Building CXX object modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/buildingblock.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_MM -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_mm_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/buildingblock.cc.o -MF CMakeFiles/ost_mol_mm.dir/buildingblock.cc.o.d -o CMakeFiles/ost_mol_mm.dir/buildingblock.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/src/buildingblock.cc -[ 57%] Generating scene_win/moc_root_node.cpp -[ 57%] Generating scene_win/moc_scene_node.cpp -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_root_node.cpp_parameters -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_scene_node.cpp_parameters -[ 57%] Generating scene_win/moc_scene_win.cpp -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_scene_win.cpp_parameters -[ 57%] Generating scene_win/moc_scene_win_model.cpp -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_scene_win_model.cpp_parameters -[ 57%] Generating sequence_viewer/moc_align_properties_painter.cpp -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_align_properties_painter.cpp_parameters -[ 57%] Generating sequence_viewer/moc_alignment_view_object.cpp -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_alignment_view_object.cpp_parameters -[ 57%] Generating sequence_viewer/moc_background_painter.cpp -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_background_painter.cpp_parameters -[ 57%] Generating sequence_viewer/moc_base_row.cpp -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_base_row.cpp_parameters -[ 57%] Building CXX object modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/gromacs_block_modifiers.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_MM -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_mm_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/gromacs_block_modifiers.cc.o -MF CMakeFiles/ost_mol_mm.dir/gromacs_block_modifiers.cc.o.d -o CMakeFiles/ost_mol_mm.dir/gromacs_block_modifiers.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/src/gromacs_block_modifiers.cc -[ 58%] Generating sequence_viewer/moc_base_view_object.cpp -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_base_view_object.cpp_parameters -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/interaction.hh:34, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/buildingblock.hh:29, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/forcefield.hh:31, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/ff_reader.hh:32, - from /build/openstructure-2.3.1/modules/mol/mm/src/ff_reader.cc:20: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/12/string:45, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/istream:38, - from /usr/include/c++/12/fstream:38, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/ff_reader.hh:23: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -[ 58%] Generating sequence_viewer/moc_conservation_painter.cpp +[ 57%] Generating sequence_viewer/moc_conservation_painter.cpp cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_conservation_painter.cpp_parameters -[ 58%] Generating sequence_viewer/moc_painter.cpp +[ 57%] Generating sequence_viewer/moc_painter.cpp cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_painter.cpp_parameters -[ 58%] Generating sequence_viewer/moc_secstr_row.cpp +[ 57%] Generating sequence_viewer/moc_secstr_row.cpp cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_secstr_row.cpp_parameters -[ 58%] Building CXX object modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/heuristic_block_modifiers.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_MM -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_mm_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/heuristic_block_modifiers.cc.o -MF CMakeFiles/ost_mol_mm.dir/heuristic_block_modifiers.cc.o.d -o CMakeFiles/ost_mol_mm.dir/heuristic_block_modifiers.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/src/heuristic_block_modifiers.cc -[ 58%] Generating sequence_viewer/moc_seq_secstr_painter.cpp +In file included from /build/openstructure-2.3.1/modules/mol/alg/src/lddt.cc:39: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/amino_acids.hh:61:42: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 61 | class AminoAcidSetIterator : public std::iterator struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/memory:63, - from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, - from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, - from /usr/include/boost/shared_ptr.hpp:17, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/gromacs_block_modifiers.hh:24: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -[ 61%] Building CXX object modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/observer.cc.o +[ 60%] Building CXX object modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/observer.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_MM -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_mm_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/observer.cc.o -MF CMakeFiles/ost_mol_mm.dir/observer.cc.o.d -o CMakeFiles/ost_mol_mm.dir/observer.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/src/observer.cc +[ 61%] Building CXX object modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/system_creator.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_MM -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_mm_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/system_creator.cc.o -MF CMakeFiles/ost_mol_mm.dir/system_creator.cc.o.d -o CMakeFiles/ost_mol_mm.dir/system_creator.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/src/system_creator.cc cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/gui/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/CMakeFiles/ost_gui.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/gui/src/CMakeFiles/ost_gui.dir/build.make modules/gui/src/CMakeFiles/ost_gui.dir/build -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/heuristic_block_modifiers.hh:28, - from /build/openstructure-2.3.1/modules/mol/mm/src/heuristic_block_modifiers.cc:20: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ +make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[ 61%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_file_browser.cpp.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_file_browser.cpp.o -MF CMakeFiles/ost_gui.dir/moc_file_browser.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_file_browser.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_file_browser.cpp +[ 61%] Linking CXX executable ../../../stage/bin/chemdict_tool +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/chemdict_tool.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro CMakeFiles/chemdict_tool.dir/chemdict_tool.cc.o -o ../../../stage/bin/chemdict_tool -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib: ../../../stage/lib/libost_io.so.2.3.1 ../../../stage/lib/libost_mol_alg.so.2.3.1 ../../../stage/lib/libost_conop.so.2.3.1 ../../../stage/lib/libost_db.so.2.3.1 /usr/lib/x86_64-linux-gnu/libsqlite3.so /usr/lib/x86_64-linux-gnu/libboost_program_options.so /usr/lib/x86_64-linux-gnu/libboost_thread.so /usr/lib/x86_64-linux-gnu/libboost_chrono.so /usr/lib/x86_64-linux-gnu/libboost_date_time.so /usr/lib/x86_64-linux-gnu/libboost_atomic.so ../../../stage/lib/libost_seq_alg.so.2.3.1 ../../../stage/lib/libost_seq.so.2.3.1 ../../../stage/lib/libost_mol.so.2.3.1 ../../../stage/lib/libost_img_alg.so.2.3.1 ../../../stage/lib/libost_img.so.2.3.1 ../../../stage/lib/libost_info.so.2.3.1 ../../../stage/lib/libost_base.so.2.3.1 ../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libfftw3f_threads.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libtiff.so /usr/lib/x86_64-linux-gnu/libpng.so /usr/lib/x86_64-linux-gnu/libz.so +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/modeller.hh:28, + from /build/openstructure-2.3.1/modules/mol/mm/src/modeller.cc:20: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 32 | : public std::iterator{ + | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/memory:63, - from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, - from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, - from /usr/include/boost/shared_ptr.hpp:17, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/heuristic_block_modifiers.hh:24: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ + from /usr/include/c++/12/vector:60, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/modeller.hh:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 61%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_file_browser.cpp.o +make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[ 61%] Built target chemdict_tool +[ 61%] Building CXX object modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/topology_creator.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_MM -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_mm_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/topology_creator.cc.o -MF CMakeFiles/ost_mol_mm.dir/topology_creator.cc.o.d -o CMakeFiles/ost_mol_mm.dir/topology_creator.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/src/topology_creator.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/interaction.hh:34, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/buildingblock.hh:29, - from /build/openstructure-2.3.1/modules/mol/mm/src/buildingblock.cc:20: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/vector:60, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/buildingblock.hh:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_file_browser.cpp.o -MF CMakeFiles/ost_gui.dir/moc_file_browser.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_file_browser.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_file_browser.cpp /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ @@ -18328,17 +17990,16 @@ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/interaction.hh:34, - from /build/openstructure-2.3.1/modules/mol/mm/src/interaction.cc:20: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/../../../../modules/gui/src/file_browser.hh:23, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_file_browser.cpp:10: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/vector:60, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/interaction.hh:23: + from /usr/include/c++/12/memory:63, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_file_browser.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -18376,94 +18037,20 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 61%] Linking CXX executable ../../../../stage/bin/lddt -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/lddt.dir/link.txt --verbose=1 In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/simulation.hh:26, - from /build/openstructure-2.3.1/modules/mol/mm/src/simulation.cc:20: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/system_creator.hh:28, + from /build/openstructure-2.3.1/modules/mol/mm/src/system_creator.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/simulation.hh:23: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro CMakeFiles/lddt.dir/lddt.cc.o -o ../../../../stage/bin/lddt -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib: ../../../../stage/lib/libost_io.so.2.3.1 ../../../../stage/lib/libost_mol_alg.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_program_options.so /usr/lib/x86_64-linux-gnu/libboost_thread.so /usr/lib/x86_64-linux-gnu/libboost_chrono.so /usr/lib/x86_64-linux-gnu/libboost_date_time.so /usr/lib/x86_64-linux-gnu/libboost_atomic.so ../../../../stage/lib/libost_seq_alg.so.2.3.1 ../../../../stage/lib/libost_img_alg.so.2.3.1 ../../../../stage/lib/libost_img.so.2.3.1 /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libfftw3f_threads.so ../../../../stage/lib/libost_conop.so.2.3.1 ../../../../stage/lib/libost_db.so.2.3.1 ../../../../stage/lib/libost_seq.so.2.3.1 ../../../../stage/lib/libost_mol.so.2.3.1 ../../../../stage/lib/libost_info.so.2.3.1 ../../../../stage/lib/libost_base.so.2.3.1 ../../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/x86_64-linux-gnu/libsqlite3.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libtiff.so /usr/lib/x86_64-linux-gnu/libpng.so /usr/lib/x86_64-linux-gnu/libz.so -[ 62%] Building CXX object modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/system_creator.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_MM -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_mm_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/system_creator.cc.o -MF CMakeFiles/ost_mol_mm.dir/system_creator.cc.o.d -o CMakeFiles/ost_mol_mm.dir/system_creator.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/src/system_creator.cc -[ 62%] Building CXX object modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/topology_creator.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_MM -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_mm_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/topology_creator.cc.o -MF CMakeFiles/ost_mol_mm.dir/topology_creator.cc.o.d -o CMakeFiles/ost_mol_mm.dir/topology_creator.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/src/topology_creator.cc -make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 62%] Linking CXX executable ../../stage/bin/molck -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/tools/molck && /usr/bin/cmake -E cmake_link_script CMakeFiles/molck.dir/link.txt --verbose=1 -[ 62%] Built target lddt -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro CMakeFiles/molck.dir/main.cc.o -o ../../stage/bin/molck -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib: ../../stage/lib/libost_io.so.2.3.1 ../../stage/lib/libost_mol_alg.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_program_options.so /usr/lib/x86_64-linux-gnu/libboost_thread.so /usr/lib/x86_64-linux-gnu/libboost_chrono.so /usr/lib/x86_64-linux-gnu/libboost_date_time.so /usr/lib/x86_64-linux-gnu/libboost_atomic.so ../../stage/lib/libost_seq_alg.so.2.3.1 ../../stage/lib/libost_conop.so.2.3.1 ../../stage/lib/libost_db.so.2.3.1 /usr/lib/x86_64-linux-gnu/libsqlite3.so ../../stage/lib/libost_seq.so.2.3.1 ../../stage/lib/libost_mol.so.2.3.1 ../../stage/lib/libost_img_alg.so.2.3.1 ../../stage/lib/libost_img.so.2.3.1 ../../stage/lib/libost_info.so.2.3.1 ../../stage/lib/libost_base.so.2.3.1 ../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libfftw3f_threads.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libtiff.so /usr/lib/x86_64-linux-gnu/libpng.so /usr/lib/x86_64-linux-gnu/libz.so -[ 62%] Building CXX object modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/topology.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_MM -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_mm_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/topology.cc.o -MF CMakeFiles/ost_mol_mm.dir/topology.cc.o.d -o CMakeFiles/ost_mol_mm.dir/topology.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/src/topology.cc -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/modeller.hh:28, - from /build/openstructure-2.3.1/modules/mol/mm/src/modeller.cc:20: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 32 | : public std::iterator{ - | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/vector:60, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/modeller.hh:24: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 62%] Built target molck -[ 62%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_file_type_dialog.cpp.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_file_type_dialog.cpp.o -MF CMakeFiles/ost_gui.dir/moc_file_type_dialog.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_file_type_dialog.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_file_type_dialog.cpp -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/../../../../modules/gui/src/file_browser.hh:23, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_file_browser.cpp:10: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/memory:63, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_file_browser.cpp:9: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/system_creator.hh:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -18476,65 +18063,63 @@ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/modeller.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/system_creator.hh:35, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/simulation.hh:27: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/observer.hh:33: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 62%] Building CXX object modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/steep.cc.o +[ 61%] Building CXX object modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/topology.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_MM -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_mm_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/topology.cc.o -MF CMakeFiles/ost_mol_mm.dir/topology.cc.o.d -o CMakeFiles/ost_mol_mm.dir/topology.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/src/topology.cc +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/openstructure-2.3.1/modules/conop/pymod/wrap_conop.cc:19: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 61%] Building CXX object modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/steep.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_MM -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_mm_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/steep.cc.o -MF CMakeFiles/ost_mol_mm.dir/steep.cc.o.d -o CMakeFiles/ost_mol_mm.dir/steep.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/src/steep.cc +[ 61%] Building CXX object modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_compound.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_conop_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_compound.cc.o -MF CMakeFiles/_ost_conop.dir/export_compound.cc.o.d -o CMakeFiles/_ost_conop.dir/export_compound.cc.o -c /build/openstructure-2.3.1/modules/conop/pymod/export_compound.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/modeller.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/observer.hh:33: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/system_creator.hh:35: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 62%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_file_viewer.cpp.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_file_viewer.cpp.o -MF CMakeFiles/ost_gui.dir/moc_file_viewer.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_file_viewer.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_file_viewer.cpp -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/topology.hh:31, - from /build/openstructure-2.3.1/modules/mol/mm/src/topology.cc:20: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/vector:60, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/topology.hh:23: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/system_creator.hh:28, - from /build/openstructure-2.3.1/modules/mol/mm/src/system_creator.cc:20: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/topology_creator.hh:29, + from /build/openstructure-2.3.1/modules/mol/mm/src/topology_creator.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/system_creator.hh:23: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/topology_creator.hh:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -18544,20 +18129,32 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 61%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_file_type_dialog.cpp.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_file_type_dialog.cpp.o -MF CMakeFiles/ost_gui.dir/moc_file_type_dialog.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_file_type_dialog.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_file_type_dialog.cpp +[ 61%] Linking CXX executable ../../../../stage/bin/lddt +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/lddt.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro CMakeFiles/lddt.dir/lddt.cc.o -o ../../../../stage/bin/lddt -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib: ../../../../stage/lib/libost_io.so.2.3.1 ../../../../stage/lib/libost_mol_alg.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_program_options.so /usr/lib/x86_64-linux-gnu/libboost_thread.so /usr/lib/x86_64-linux-gnu/libboost_chrono.so /usr/lib/x86_64-linux-gnu/libboost_date_time.so /usr/lib/x86_64-linux-gnu/libboost_atomic.so ../../../../stage/lib/libost_seq_alg.so.2.3.1 ../../../../stage/lib/libost_img_alg.so.2.3.1 ../../../../stage/lib/libost_img.so.2.3.1 /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libfftw3f_threads.so ../../../../stage/lib/libost_conop.so.2.3.1 ../../../../stage/lib/libost_db.so.2.3.1 ../../../../stage/lib/libost_seq.so.2.3.1 ../../../../stage/lib/libost_mol.so.2.3.1 ../../../../stage/lib/libost_info.so.2.3.1 ../../../../stage/lib/libost_base.so.2.3.1 ../../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/x86_64-linux-gnu/libsqlite3.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libtiff.so /usr/lib/x86_64-linux-gnu/libpng.so /usr/lib/x86_64-linux-gnu/libz.so +[ 61%] Linking CXX executable ../../stage/bin/molck +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/tools/molck && /usr/bin/cmake -E cmake_link_script CMakeFiles/molck.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro CMakeFiles/molck.dir/main.cc.o -o ../../stage/bin/molck -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib: ../../stage/lib/libost_io.so.2.3.1 ../../stage/lib/libost_mol_alg.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_program_options.so /usr/lib/x86_64-linux-gnu/libboost_thread.so /usr/lib/x86_64-linux-gnu/libboost_chrono.so /usr/lib/x86_64-linux-gnu/libboost_date_time.so /usr/lib/x86_64-linux-gnu/libboost_atomic.so ../../stage/lib/libost_seq_alg.so.2.3.1 ../../stage/lib/libost_conop.so.2.3.1 ../../stage/lib/libost_db.so.2.3.1 /usr/lib/x86_64-linux-gnu/libsqlite3.so ../../stage/lib/libost_seq.so.2.3.1 ../../stage/lib/libost_mol.so.2.3.1 ../../stage/lib/libost_img_alg.so.2.3.1 ../../stage/lib/libost_img.so.2.3.1 ../../stage/lib/libost_info.so.2.3.1 ../../stage/lib/libost_base.so.2.3.1 ../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libfftw3f_threads.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libtiff.so /usr/lib/x86_64-linux-gnu/libpng.so /usr/lib/x86_64-linux-gnu/libz.so +make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[ 61%] Built target lddt +[ 62%] Building CXX object modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_processor.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_conop_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_processor.cc.o -MF CMakeFiles/_ost_conop.dir/export_processor.cc.o.d -o CMakeFiles/_ost_conop.dir/export_processor.cc.o -c /build/openstructure-2.3.1/modules/conop/pymod/export_processor.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/topology_creator.hh:29, - from /build/openstructure-2.3.1/modules/mol/mm/src/topology_creator.cc:20: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/topology.hh:31, + from /build/openstructure-2.3.1/modules/mol/mm/src/topology.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/topology_creator.hh:23: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/topology.hh:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -18567,16 +18164,26 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[ 62%] Built target molck +[ 62%] Building CXX object modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_heuristic.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_conop_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_heuristic.cc.o -MF CMakeFiles/_ost_conop.dir/export_heuristic.cc.o.d -o CMakeFiles/_ost_conop.dir/export_heuristic.cc.o -c /build/openstructure-2.3.1/modules/conop/pymod/export_heuristic.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/modeller.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/system_creator.hh:35: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/topology_creator.hh:37: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 62%] Building CXX object modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_amino_acids.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_conop_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_amino_acids.cc.o -MF CMakeFiles/_ost_conop.dir/export_amino_acids.cc.o.d -o CMakeFiles/_ost_conop.dir/export_amino_acids.cc.o -c /build/openstructure-2.3.1/modules/conop/pymod/export_amino_acids.cc +[ 62%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_file_viewer.cpp.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_file_viewer.cpp.o -MF CMakeFiles/ost_gui.dir/moc_file_viewer.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_file_viewer.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_file_viewer.cpp +[ 64%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_gl_canvas.cpp.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_gl_canvas.cpp.o -MF CMakeFiles/ost_gui.dir/moc_gl_canvas.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_gl_canvas.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_gl_canvas.cpp In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/../../../../modules/gui/src/file_type_dialog.hh:31, @@ -18590,8 +18197,6 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 64%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_gl_canvas.cpp.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_gl_canvas.cpp.o -MF CMakeFiles/ost_gui.dir/moc_gl_canvas.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_gl_canvas.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_gl_canvas.cpp In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -18614,32 +18219,30 @@ | ^~~~~~~~ [ 64%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_gl_win.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_gl_win.cpp.o -MF CMakeFiles/ost_gui.dir/moc_gl_win.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_gl_win.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_gl_win.cpp -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/modeller.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/topology_creator.hh:37: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 32 | : public std::iterator{ - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ [ 64%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_scene_menu.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_scene_menu.cpp.o -MF CMakeFiles/ost_gui.dir/moc_scene_menu.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_scene_menu.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_scene_menu.cpp [ 64%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_gosty_app.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_gosty_app.cpp.o -MF CMakeFiles/ost_gui.dir/moc_gosty_app.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_gosty_app.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_gosty_app.cpp -[ 64%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_main.cpp.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_main.cpp.o -MF CMakeFiles/ost_gui.dir/moc_main.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_main.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_main.cpp -[ 64%] Linking CXX shared module ../../../../stage/lib/python3.11/dist-packages/ost/seq/alg/_ost_seq_alg.so -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_seq_alg.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -o ../../../../stage/lib/python3.11/dist-packages/ost/seq/alg/_ost_seq_alg.so CMakeFiles/_ost_seq_alg.dir/wrap_seq_alg.cc.o -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib: ../../../../stage/lib/libost_seq_alg.so.2.3.1 /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so ../../../../stage/lib/libost_seq.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so ../../../../stage/lib/libost_mol.so.2.3.1 ../../../../stage/lib/libost_info.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../../stage/lib/libost_base.so.2.3.1 ../../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 -[ 64%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_main_area.cpp.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_main_area.cpp.o -MF CMakeFiles/ost_gui.dir/moc_main_area.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_main_area.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_main_area.cpp -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/seq/alg/pymod/__init__.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/seq/alg/./__init__.pyc\",\"__init__.py\",doraise=True)" -[ 64%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_perspective.cpp.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_perspective.cpp.o -MF CMakeFiles/ost_gui.dir/moc_perspective.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_perspective.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_perspective.cpp -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/seq/alg/pymod/mat.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/seq/alg/./mat.pyc\",\"mat.py\",doraise=True)" -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/seq/alg/pymod/renumber.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/seq/alg/./renumber.pyc\",\"renumber.py\",doraise=True)" +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/openstructure-2.3.1/modules/conop/pymod/export_compound.cc:19: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool.hh:30, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/../../../../modules/gui/src/gl_canvas.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_gl_canvas.cpp:10: @@ -18652,19 +18255,8 @@ /usr/include/x86_64-linux-gnu/qt5/QtCore/qnamespace.h:132:9: note: declared here 132 | MidButton Q_DECL_ENUMERATOR_DEPRECATED_X("MidButton is deprecated. Use MiddleButton instead") = MiddleButton, | ^~~~~~~~~ -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/seq/alg/pymod/aaindex.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/seq/alg/./aaindex.pyc\",\"aaindex.py\",doraise=True)" -make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 64%] Built target _ost_seq_alg -[ 64%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_dock_widget.cpp.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_dock_widget.cpp.o -MF CMakeFiles/ost_gui.dir/moc_dock_widget.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_dock_widget.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_dock_widget.cpp -[ 64%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_main_window.cpp.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_main_window.cpp.o -MF CMakeFiles/ost_gui.dir/moc_main_window.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_main_window.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_main_window.cpp -[ 64%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_scene_selection.cpp.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_scene_selection.cpp.o -MF CMakeFiles/ost_gui.dir/moc_scene_selection.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_scene_selection.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_scene_selection.cpp -[ 65%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_widget_geom_handler.cpp.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_widget_geom_handler.cpp.o -MF CMakeFiles/ost_gui.dir/moc_widget_geom_handler.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_widget_geom_handler.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_widget_geom_handler.cpp -[ 65%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_widget.cpp.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_widget.cpp.o -MF CMakeFiles/ost_gui.dir/moc_widget.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_widget.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_widget.cpp +[ 64%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_main.cpp.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_main.cpp.o -MF CMakeFiles/ost_gui.dir/moc_main.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_main.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_main.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -18678,22 +18270,13 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main.hh:23, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/../../../../modules/gui/src/gosty_app.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_gosty_app.cpp:10: + from /build/openstructure-2.3.1/modules/conop/pymod/export_heuristic.cc:21: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 65%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/messages/moc_message_widget.cpp.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/messages/moc_message_widget.cpp.o -MF CMakeFiles/ost_gui.dir/messages/moc_message_widget.cpp.o.d -o CMakeFiles/ost_gui.dir/messages/moc_message_widget.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/messages/moc_message_widget.cpp -[ 65%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_widget_pool.cpp.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_widget_pool.cpp.o -MF CMakeFiles/ost_gui.dir/moc_widget_pool.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_widget_pool.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_widget_pool.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -18707,79 +18290,34 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/../../../../modules/gui/src/main.hh:23, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_main.cpp:10: + from /build/openstructure-2.3.1/modules/conop/pymod/export_processor.cc:20: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 65%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/messages/moc_message_box_widget.cpp.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/messages/moc_message_box_widget.cpp.o -MF CMakeFiles/ost_gui.dir/messages/moc_message_box_widget.cpp.o.d -o CMakeFiles/ost_gui.dir/messages/moc_message_box_widget.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/messages/moc_message_box_widget.cpp -[ 65%] Linking CXX shared module ../../../stage/lib/python3.11/dist-packages/ost/conop/_ost_conop.so -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_conop.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -o ../../../stage/lib/python3.11/dist-packages/ost/conop/_ost_conop.so CMakeFiles/_ost_conop.dir/wrap_conop.cc.o CMakeFiles/_ost_conop.dir/export_compound.cc.o CMakeFiles/_ost_conop.dir/export_processor.cc.o CMakeFiles/_ost_conop.dir/export_heuristic.cc.o CMakeFiles/_ost_conop.dir/export_amino_acids.cc.o CMakeFiles/_ost_conop.dir/export_conop.cc.o CMakeFiles/_ost_conop.dir/export_diag.cc.o CMakeFiles/_ost_conop.dir/export_rule_based.cc.o CMakeFiles/_ost_conop.dir/export_ring_finder.cc.o -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib: ../../../stage/lib/libost_conop.so.2.3.1 /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so ../../../stage/lib/libost_db.so.2.3.1 /usr/lib/x86_64-linux-gnu/libsqlite3.so ../../../stage/lib/libost_seq.so.2.3.1 ../../../stage/lib/libost_mol.so.2.3.1 ../../../stage/lib/libost_info.so.2.3.1 ../../../stage/lib/libost_base.so.2.3.1 ../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_dock_widget.cpp:10: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/../../../../modules/gui/src/dock_widget.hh:38:77: warning: 'constexpr QFlags::QFlags(Zero) [with Enum = Qt::WindowType; Zero = int QFlags::Private::*]' is deprecated: Use default constructor instead [-Wdeprecated-declarations] - 38 | DockWidget(const QString& title, QWidget* parent=0, Qt::WindowFlags flags=0); - | ^ -In file included from /usr/include/x86_64-linux-gnu/qt5/QtCore/qglobal.h:1305, - from /usr/include/x86_64-linux-gnu/qt5/QtGui/qtguiglobal.h:43, - from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/qtwidgetsglobal.h:43, - from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/qdockwidget.h:43, - from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/QDockWidget:1, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/../../../../modules/gui/src/dock_widget.hh:31: -/usr/include/x86_64-linux-gnu/qt5/QtCore/qflags.h:123:80: note: declared here - 123 | QT_DEPRECATED_X("Use default constructor instead") Q_DECL_CONSTEXPR inline QFlags(Zero) noexcept : i(0) {} - | ^~~~~~ -[ 65%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/messages/moc_log_reader.cpp.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/messages/moc_log_reader.cpp.o -MF CMakeFiles/ost_gui.dir/messages/moc_log_reader.cpp.o.d -o CMakeFiles/ost_gui.dir/messages/moc_log_reader.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/messages/moc_log_reader.cpp -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/conop/pymod/__init__.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/conop/./__init__.pyc\",\"__init__.py\",doraise=True)" -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/conop/pymod/cleanup.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/conop/./cleanup.pyc\",\"cleanup.py\",doraise=True)" -make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 65%] Built target _ost_conop -make -f modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/build.make modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/depend -make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/gfx/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/DependInfo.cmake --color= -[ 65%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_align_properties_painter.cpp.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_align_properties_painter.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_align_properties_painter.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_align_properties_painter.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_align_properties_painter.cpp -make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/build.make modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/build -make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_main_window.cpp:10: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/../../../../modules/gui/src/main_window.hh:46:55: warning: 'constexpr QFlags::QFlags(Zero) [with Enum = Qt::WindowType; Zero = int QFlags::Private::*]' is deprecated: Use default constructor instead [-Wdeprecated-declarations] - 46 | MainWindow(QWidget* parent=0, Qt::WindowFlags flags=0); - | ^ -In file included from /usr/include/x86_64-linux-gnu/qt5/QtCore/qglobal.h:1305, - from /usr/include/x86_64-linux-gnu/qt5/QtGui/qtguiglobal.h:43, - from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/qtwidgetsglobal.h:43, - from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/qmainwindow.h:43, - from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/QMainWindow:1, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/../../../../modules/gui/src/main_window.hh:35: -/usr/include/x86_64-linux-gnu/qt5/QtCore/qflags.h:123:80: note: declared here - 123 | QT_DEPRECATED_X("Use default constructor instead") Q_DECL_CONSTEXPR inline QFlags(Zero) noexcept : i(0) {} - | ^~~~~~ -[ 65%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/wrap_gfx.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/wrap_gfx.cc.o -MF CMakeFiles/_ost_gfx.dir/wrap_gfx.cc.o.d -o CMakeFiles/_ost_gfx.dir/wrap_gfx.cc.o -c /build/openstructure-2.3.1/modules/gfx/pymod/wrap_gfx.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/../../../../modules/gui/src/scene_selection.hh:23, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_scene_selection.cpp:10: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/compound_lib_base.hh:5, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/compound_lib.hh:27, + from /build/openstructure-2.3.1/modules/conop/pymod/export_compound.cc:26: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/memory:63, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_scene_selection.cpp:9: + from /usr/include/c++/12/bits/specfun.h:45, + from /usr/include/c++/12/cmath:1935, + from /usr/include/c++/12/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -18789,31 +18327,140 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 65%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_background_painter.cpp.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_background_painter.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_background_painter.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_background_painter.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_background_painter.cpp -[ 65%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_base_row.cpp.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_base_row.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_base_row.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_base_row.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_base_row.cpp -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/../../../../modules/gui/src/main.hh:28: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/../../../../modules/gui/src/widget_state_saver.hh: In instantiation of 'ost::gui::WidgetStateSaver::~WidgetStateSaver() [with BASE = QMainWindow]': -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/../../../../modules/gui/src/main.hh:40:25: required from here -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/../../../../modules/gui/src/widget_state_saver.hh:323:8: warning: the address of 'ost::gui::WidgetStateSaver::' will never be NULL [-Waddress] - 323 | if(dynamic_cast(this)){ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/../../../../modules/gui/src/widget_state_saver.hh:263:7: note: 'ost::gui::WidgetStateSaver::' declared here - 263 | class WidgetStateSaver: public BASE - | ^~~~~~~~~~~~~~~~~~~~~~ -[ 65%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_conservation_painter.cpp.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_conservation_painter.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_conservation_painter.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_conservation_painter.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_conservation_painter.cpp -[ 65%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_painter.cpp.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_painter.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_painter.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_painter.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_painter.cpp -[ 65%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_secstr_row.cpp.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_secstr_row.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_secstr_row.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_secstr_row.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_secstr_row.cpp -[ 65%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_seq_selection_painter.cpp.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_seq_selection_painter.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_seq_selection_painter.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_seq_selection_painter.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_seq_selection_painter.cpp -[ 66%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_seq_secstr_painter.cpp.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_seq_secstr_painter.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_seq_secstr_painter.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_seq_secstr_painter.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_seq_secstr_painter.cpp -[ 66%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_seq_text_painter.cpp.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_seq_text_painter.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_seq_text_painter.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_seq_text_painter.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_seq_text_painter.cpp +[ 64%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_main_area.cpp.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_main_area.cpp.o -MF CMakeFiles/ost_gui.dir/moc_main_area.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_main_area.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_main_area.cpp +[ 64%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_perspective.cpp.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_perspective.cpp.o -MF CMakeFiles/ost_gui.dir/moc_perspective.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_perspective.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_perspective.cpp +[ 64%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_dock_widget.cpp.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_dock_widget.cpp.o -MF CMakeFiles/ost_gui.dir/moc_dock_widget.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_dock_widget.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_dock_widget.cpp +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/heuristic.hh:22, + from /build/openstructure-2.3.1/modules/conop/pymod/export_heuristic.cc:23: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/bits/specfun.h:45, + from /usr/include/c++/12/cmath:1935, + from /usr/include/c++/12/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/processor.hh:22, + from /build/openstructure-2.3.1/modules/conop/pymod/export_processor.cc:21: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/bits/specfun.h:45, + from /usr/include/c++/12/cmath:1935, + from /usr/include/c++/12/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 64%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_main_window.cpp.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_main_window.cpp.o -MF CMakeFiles/ost_gui.dir/moc_main_window.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_main_window.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_main_window.cpp +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/openstructure-2.3.1/modules/conop/pymod/export_amino_acids.cc:19: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/amino_acids.hh:26, + from /build/openstructure-2.3.1/modules/conop/pymod/export_amino_acids.cc:21: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/bits/specfun.h:45, + from /usr/include/c++/12/cmath:1935, + from /usr/include/c++/12/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/amino_acids.hh:61:42: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 61 | class AminoAcidSetIterator : public std::iterator::QFlags(Zero) [with Enum = Qt::WindowType; Zero = int QFlags::Private::*]' is deprecated: Use default constructor instead [-Wdeprecated-declarations] + 38 | DockWidget(const QString& title, QWidget* parent=0, Qt::WindowFlags flags=0); + | ^ +In file included from /usr/include/x86_64-linux-gnu/qt5/QtCore/qglobal.h:1305, + from /usr/include/x86_64-linux-gnu/qt5/QtGui/qtguiglobal.h:43, + from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/qtwidgetsglobal.h:43, + from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/qdockwidget.h:43, + from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/QDockWidget:1, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/../../../../modules/gui/src/dock_widget.hh:31: +/usr/include/x86_64-linux-gnu/qt5/QtCore/qflags.h:123:80: note: declared here + 123 | QT_DEPRECATED_X("Use default constructor instead") Q_DECL_CONSTEXPR inline QFlags(Zero) noexcept : i(0) {} + | ^~~~~~ In file included from /usr/include/c++/12/string:53, from /usr/include/c++/12/stdexcept:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, @@ -18991,8 +18638,222 @@ /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ -[ 66%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_delegate.cpp.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_delegate.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_delegate.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_delegate.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_delegate.cpp +[ 64%] Building CXX object modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_conop.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_conop_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_conop.cc.o -MF CMakeFiles/_ost_conop.dir/export_conop.cc.o.d -o CMakeFiles/_ost_conop.dir/export_conop.cc.o -c /build/openstructure-2.3.1/modules/conop/pymod/export_conop.cc +[ 64%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_scene_selection.cpp.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_scene_selection.cpp.o -MF CMakeFiles/ost_gui.dir/moc_scene_selection.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_scene_selection.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_scene_selection.cpp +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_main_window.cpp:10: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/../../../../modules/gui/src/main_window.hh:46:55: warning: 'constexpr QFlags::QFlags(Zero) [with Enum = Qt::WindowType; Zero = int QFlags::Private::*]' is deprecated: Use default constructor instead [-Wdeprecated-declarations] + 46 | MainWindow(QWidget* parent=0, Qt::WindowFlags flags=0); + | ^ +In file included from /usr/include/x86_64-linux-gnu/qt5/QtCore/qglobal.h:1305, + from /usr/include/x86_64-linux-gnu/qt5/QtGui/qtguiglobal.h:43, + from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/qtwidgetsglobal.h:43, + from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/qmainwindow.h:43, + from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/QMainWindow:1, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/../../../../modules/gui/src/main_window.hh:35: +/usr/include/x86_64-linux-gnu/qt5/QtCore/qflags.h:123:80: note: declared here + 123 | QT_DEPRECATED_X("Use default constructor instead") Q_DECL_CONSTEXPR inline QFlags(Zero) noexcept : i(0) {} + | ^~~~~~ +[ 64%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_widget.cpp.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_widget.cpp.o -MF CMakeFiles/ost_gui.dir/moc_widget.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_widget.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_widget.cpp +[ 65%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_widget_geom_handler.cpp.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_widget_geom_handler.cpp.o -MF CMakeFiles/ost_gui.dir/moc_widget_geom_handler.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_widget_geom_handler.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_widget_geom_handler.cpp +[ 65%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_widget_pool.cpp.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_widget_pool.cpp.o -MF CMakeFiles/ost_gui.dir/moc_widget_pool.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_widget_pool.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_widget_pool.cpp +[ 65%] Building CXX object modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_diag.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_conop_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_diag.cc.o -MF CMakeFiles/_ost_conop.dir/export_diag.cc.o.d -o CMakeFiles/_ost_conop.dir/export_diag.cc.o -c /build/openstructure-2.3.1/modules/conop/pymod/export_diag.cc +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main.hh:23, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/../../../../modules/gui/src/gosty_app.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_gosty_app.cpp:10: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 65%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/messages/moc_message_widget.cpp.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/messages/moc_message_widget.cpp.o -MF CMakeFiles/ost_gui.dir/messages/moc_message_widget.cpp.o.d -o CMakeFiles/ost_gui.dir/messages/moc_message_widget.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/messages/moc_message_widget.cpp +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/../../../../modules/gui/src/main.hh:23, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_main.cpp:10: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 65%] Linking CXX shared module ../../../../stage/lib/python3.11/dist-packages/ost/seq/alg/_ost_seq_alg.so +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_seq_alg.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -o ../../../../stage/lib/python3.11/dist-packages/ost/seq/alg/_ost_seq_alg.so CMakeFiles/_ost_seq_alg.dir/wrap_seq_alg.cc.o -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib: ../../../../stage/lib/libost_seq_alg.so.2.3.1 /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so ../../../../stage/lib/libost_seq.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so ../../../../stage/lib/libost_mol.so.2.3.1 ../../../../stage/lib/libost_info.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../../stage/lib/libost_base.so.2.3.1 ../../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/seq/alg/pymod/__init__.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/seq/alg/./__init__.pyc\",\"__init__.py\",doraise=True)" +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/seq/alg/pymod/mat.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/seq/alg/./mat.pyc\",\"mat.py\",doraise=True)" +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/seq/alg/pymod/renumber.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/seq/alg/./renumber.pyc\",\"renumber.py\",doraise=True)" +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/seq/alg/pymod/aaindex.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/seq/alg/./aaindex.pyc\",\"aaindex.py\",doraise=True)" +make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[ 65%] Built target _ost_seq_alg +[ 65%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/messages/moc_message_box_widget.cpp.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/messages/moc_message_box_widget.cpp.o -MF CMakeFiles/ost_gui.dir/messages/moc_message_box_widget.cpp.o.d -o CMakeFiles/ost_gui.dir/messages/moc_message_box_widget.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/messages/moc_message_box_widget.cpp +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/../../../../modules/gui/src/scene_selection.hh:23, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_scene_selection.cpp:10: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/memory:63, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_scene_selection.cpp:9: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 65%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/messages/moc_log_reader.cpp.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/messages/moc_log_reader.cpp.o -MF CMakeFiles/ost_gui.dir/messages/moc_log_reader.cpp.o.d -o CMakeFiles/ost_gui.dir/messages/moc_log_reader.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/messages/moc_log_reader.cpp +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/../../../../modules/gui/src/main.hh:28: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/../../../../modules/gui/src/widget_state_saver.hh: In instantiation of 'ost::gui::WidgetStateSaver::~WidgetStateSaver() [with BASE = QMainWindow]': +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/../../../../modules/gui/src/main.hh:40:25: required from here +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/../../../../modules/gui/src/widget_state_saver.hh:323:8: warning: the address of 'ost::gui::WidgetStateSaver::' will never be NULL [-Waddress] + 323 | if(dynamic_cast(this)){ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/../../../../modules/gui/src/widget_state_saver.hh:263:7: note: 'ost::gui::WidgetStateSaver::' declared here + 263 | class WidgetStateSaver: public BASE + | ^~~~~~~~~~~~~~~~~~~~~~ +[ 65%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_align_properties_painter.cpp.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_align_properties_painter.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_align_properties_painter.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_align_properties_painter.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_align_properties_painter.cpp +[ 65%] Building CXX object modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_rule_based.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_conop_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_rule_based.cc.o -MF CMakeFiles/_ost_conop.dir/export_rule_based.cc.o.d -o CMakeFiles/_ost_conop.dir/export_rule_based.cc.o -c /build/openstructure-2.3.1/modules/conop/pymod/export_rule_based.cc +[ 65%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_background_painter.cpp.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_background_painter.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_background_painter.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_background_painter.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_background_painter.cpp +[ 65%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_base_row.cpp.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_base_row.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_base_row.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_base_row.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_base_row.cpp +[ 65%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_conservation_painter.cpp.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_conservation_painter.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_conservation_painter.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_conservation_painter.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_conservation_painter.cpp +[ 65%] Building CXX object modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_ring_finder.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_conop_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_ring_finder.cc.o -MF CMakeFiles/_ost_conop.dir/export_ring_finder.cc.o.d -o CMakeFiles/_ost_conop.dir/export_ring_finder.cc.o -c /build/openstructure-2.3.1/modules/conop/pymod/export_ring_finder.cc +[ 65%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_painter.cpp.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_painter.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_painter.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_painter.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_painter.cpp +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/openstructure-2.3.1/modules/conop/pymod/export_conop.cc:19: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +[ 65%] Linking CXX shared library ../../../../stage/lib/libost_mol_mm.so +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/AMBER03.dat /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/share/openstructure/forcefields/AMBER03.dat +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/CHARMM27.dat /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/share/openstructure/forcefields/CHARMM27.dat +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_mol_mm.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libost_mol_mm.so.2.3 -o ../../../../stage/lib/libost_mol_mm.so.2.3.1 CMakeFiles/ost_mol_mm.dir/forcefield.cc.o CMakeFiles/ost_mol_mm.dir/ff_reader.cc.o CMakeFiles/ost_mol_mm.dir/buildingblock.cc.o CMakeFiles/ost_mol_mm.dir/gromacs_block_modifiers.cc.o CMakeFiles/ost_mol_mm.dir/heuristic_block_modifiers.cc.o CMakeFiles/ost_mol_mm.dir/interaction.cc.o CMakeFiles/ost_mol_mm.dir/simulation.cc.o CMakeFiles/ost_mol_mm.dir/modeller.cc.o CMakeFiles/ost_mol_mm.dir/state_extractor.cc.o CMakeFiles/ost_mol_mm.dir/observer.cc.o CMakeFiles/ost_mol_mm.dir/system_creator.cc.o CMakeFiles/ost_mol_mm.dir/topology_creator.cc.o CMakeFiles/ost_mol_mm.dir/topology.cc.o CMakeFiles/ost_mol_mm.dir/steep.cc.o -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib: /usr/lib/x86_64-linux-gnu/libboost_program_options.so ../../../../stage/lib/libost_io.so.2.3.1 /usr/lib/x86_64-linux-gnu/libOpenMM.so ../../../../stage/lib/libost_mol_alg.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_program_options.so ../../../../stage/lib/libost_conop.so.2.3.1 ../../../../stage/lib/libost_db.so.2.3.1 /usr/lib/x86_64-linux-gnu/libsqlite3.so /usr/lib/x86_64-linux-gnu/libboost_thread.so /usr/lib/x86_64-linux-gnu/libboost_chrono.so /usr/lib/x86_64-linux-gnu/libboost_date_time.so /usr/lib/x86_64-linux-gnu/libboost_atomic.so ../../../../stage/lib/libost_seq_alg.so.2.3.1 ../../../../stage/lib/libost_seq.so.2.3.1 ../../../../stage/lib/libost_mol.so.2.3.1 ../../../../stage/lib/libost_img_alg.so.2.3.1 ../../../../stage/lib/libost_img.so.2.3.1 ../../../../stage/lib/libost_info.so.2.3.1 ../../../../stage/lib/libost_base.so.2.3.1 ../../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libfftw3f_threads.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libtiff.so /usr/lib/x86_64-linux-gnu/libpng.so /usr/lib/x86_64-linux-gnu/libz.so +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E cmake_symlink_library ../../../../stage/lib/libost_mol_mm.so.2.3.1 ../../../../stage/lib/libost_mol_mm.so.2.3 ../../../../stage/lib/libost_mol_mm.so +make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/conop.hh:24, + from /build/openstructure-2.3.1/modules/conop/pymod/export_conop.cc:23: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/bits/specfun.h:45, + from /usr/include/c++/12/cmath:1935, + from /usr/include/c++/12/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 65%] Built target ost_mol_mm +[ 65%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_secstr_row.cpp.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_secstr_row.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_secstr_row.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_secstr_row.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_secstr_row.cpp +[ 66%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_seq_secstr_painter.cpp.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_seq_secstr_painter.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_seq_secstr_painter.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_seq_secstr_painter.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_seq_secstr_painter.cpp +[ 66%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_seq_selection_painter.cpp.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_seq_selection_painter.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_seq_selection_painter.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_seq_selection_painter.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_seq_selection_painter.cpp +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/openstructure-2.3.1/modules/conop/pymod/export_diag.cc:20: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -19018,8 +18879,9 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 66%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_model.cpp.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_model.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_model.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_model.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_model.cpp +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -19028,14 +18890,14 @@ from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/painter.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/background_painter.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_background_painter.cpp:10: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/conservation_painter.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_conservation_painter.cpp:10: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_background_painter.cpp:9: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_conservation_painter.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -19045,6 +18907,8 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 66%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_seq_text_painter.cpp.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_seq_text_painter.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_seq_text_painter.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_seq_text_painter.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_seq_text_painter.cpp In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -19053,14 +18917,14 @@ from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/painter.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/conservation_painter.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_conservation_painter.cpp:10: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/background_painter.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_background_painter.cpp:10: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_conservation_painter.cpp:9: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_background_painter.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -19124,17 +18988,42 @@ from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/painter.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/seq_secstr_painter.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_seq_secstr_painter.cpp:10: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/diag.hh:23, + from /build/openstructure-2.3.1/modules/conop/pymod/export_diag.cc:21: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/bits/specfun.h:45, + from /usr/include/c++/12/cmath:1935, + from /usr/include/c++/12/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/chain_view.hh:23, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/secstr_row.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_secstr_row.cpp:10: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_seq_secstr_painter.cpp:9: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_secstr_row.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -19144,8 +19033,6 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 66%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_row.cpp.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_row.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_row.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_row.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_row.cpp In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -19154,14 +19041,14 @@ from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/painter.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/seq_selection_painter.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_seq_selection_painter.cpp:10: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/seq_secstr_painter.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_seq_secstr_painter.cpp:10: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_seq_selection_painter.cpp:9: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_seq_secstr_painter.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -19171,6 +19058,30 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 66%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_delegate.cpp.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_delegate.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_delegate.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_delegate.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_delegate.cpp +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/openstructure-2.3.1/modules/conop/pymod/export_rule_based.cc:20: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +[ 66%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_model.cpp.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_model.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_model.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_model.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_model.cpp +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -19179,14 +19090,14 @@ from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/painter.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/seq_text_painter.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_seq_text_painter.cpp:10: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/seq_selection_painter.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_seq_selection_painter.cpp:10: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_seq_text_painter.cpp:9: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_seq_selection_painter.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -19199,15 +19110,19 @@ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/chain_view.hh:23, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/secstr_row.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_secstr_row.cpp:10: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/painter.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/seq_text_painter.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_seq_text_painter.cpp:10: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_secstr_row.cpp:9: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_seq_text_painter.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -19220,16 +19135,23 @@ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/chain_view.hh:23, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_model.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_delegate.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_delegate.cpp:10: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/rule_based.hh:22, + from /build/openstructure-2.3.1/modules/conop/pymod/export_rule_based.cc:22: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/memory:63, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_delegate.cpp:9: + from /usr/include/c++/12/bits/specfun.h:45, + from /usr/include/c++/12/cmath:1935, + from /usr/include/c++/12/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -19239,14 +19161,8 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -make -f modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/build.make modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/depend -make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/alg/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/DependInfo.cmake --color= -make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/build.make modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/build -make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 66%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/wrap_mol_alg.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/wrap_mol_alg.cc.o -MF CMakeFiles/_ost_mol_alg.dir/wrap_mol_alg.cc.o.d -o CMakeFiles/_ost_mol_alg.dir/wrap_mol_alg.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/pymod/wrap_mol_alg.cc +[ 66%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_row.cpp.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_row.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_row.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_row.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_row.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -19260,29 +19176,31 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/gfx/pymod/wrap_gfx.cc:19: + from /build/openstructure-2.3.1/modules/conop/pymod/export_ring_finder.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_model.hh:30: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 32 | : public std::iterator{ - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ [ 66%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_search_bar.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_search_bar.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_search_bar.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_search_bar.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_search_bar.cpp +[ 66%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_table_view.cpp.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_table_view.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_table_view.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_table_view.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_table_view.cpp +[ 66%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_viewer.cpp.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_viewer.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_viewer.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_viewer.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_viewer.cpp +[ 66%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_tick_painter.cpp.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_tick_painter.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_tick_painter.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_tick_painter.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_tick_painter.cpp +[ 67%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_title_row.cpp.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_title_row.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_title_row.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_title_row.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_title_row.cpp In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/info_group.hh:33, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/info.hh:32, - from /build/openstructure-2.3.1/modules/gfx/pymod/wrap_gfx.cc:26: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/ring_finder.hh:27, + from /build/openstructure-2.3.1/modules/conop/pymod/export_ring_finder.cc:23: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -19309,13 +19227,14 @@ from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/chain_view.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_model.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_model.cpp:10: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_delegate.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_delegate.cpp:10: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_model.cpp:9: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_delegate.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -19325,33 +19244,18 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 66%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_table_view.cpp.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_table_view.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_table_view.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_table_view.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_table_view.cpp -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_model.hh:30: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 32 | : public std::iterator{ - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -[ 66%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_viewer.cpp.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_viewer.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_viewer.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_viewer.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_viewer.cpp In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_row.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_row.cpp:10: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/chain_view.hh:23, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_model.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_model.cpp:10: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_row.cpp:9: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_model.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -19361,26 +19265,28 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 66%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_tick_painter.cpp.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_tick_painter.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_tick_painter.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_tick_painter.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_tick_painter.cpp -[ 66%] Linking CXX shared library ../../../../stage/lib/libost_mol_mm.so -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/AMBER03.dat /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/share/openstructure/forcefields/AMBER03.dat -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/CHARMM27.dat /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/share/openstructure/forcefields/CHARMM27.dat -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_mol_mm.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libost_mol_mm.so.2.3 -o ../../../../stage/lib/libost_mol_mm.so.2.3.1 CMakeFiles/ost_mol_mm.dir/forcefield.cc.o CMakeFiles/ost_mol_mm.dir/ff_reader.cc.o CMakeFiles/ost_mol_mm.dir/buildingblock.cc.o CMakeFiles/ost_mol_mm.dir/gromacs_block_modifiers.cc.o CMakeFiles/ost_mol_mm.dir/heuristic_block_modifiers.cc.o CMakeFiles/ost_mol_mm.dir/interaction.cc.o CMakeFiles/ost_mol_mm.dir/simulation.cc.o CMakeFiles/ost_mol_mm.dir/modeller.cc.o CMakeFiles/ost_mol_mm.dir/state_extractor.cc.o CMakeFiles/ost_mol_mm.dir/observer.cc.o CMakeFiles/ost_mol_mm.dir/system_creator.cc.o CMakeFiles/ost_mol_mm.dir/topology_creator.cc.o CMakeFiles/ost_mol_mm.dir/topology.cc.o CMakeFiles/ost_mol_mm.dir/steep.cc.o -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib: /usr/lib/x86_64-linux-gnu/libboost_program_options.so ../../../../stage/lib/libost_io.so.2.3.1 /usr/lib/x86_64-linux-gnu/libOpenMM.so ../../../../stage/lib/libost_mol_alg.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_program_options.so ../../../../stage/lib/libost_conop.so.2.3.1 ../../../../stage/lib/libost_db.so.2.3.1 /usr/lib/x86_64-linux-gnu/libsqlite3.so /usr/lib/x86_64-linux-gnu/libboost_thread.so /usr/lib/x86_64-linux-gnu/libboost_chrono.so /usr/lib/x86_64-linux-gnu/libboost_date_time.so /usr/lib/x86_64-linux-gnu/libboost_atomic.so ../../../../stage/lib/libost_seq_alg.so.2.3.1 ../../../../stage/lib/libost_seq.so.2.3.1 ../../../../stage/lib/libost_mol.so.2.3.1 ../../../../stage/lib/libost_img_alg.so.2.3.1 ../../../../stage/lib/libost_img.so.2.3.1 ../../../../stage/lib/libost_info.so.2.3.1 ../../../../stage/lib/libost_base.so.2.3.1 ../../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libfftw3f_threads.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libtiff.so /usr/lib/x86_64-linux-gnu/libpng.so /usr/lib/x86_64-linux-gnu/libz.so -[ 67%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_title_row.cpp.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_title_row.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_title_row.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_title_row.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_title_row.cpp +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_model.hh:30: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 32 | : public std::iterator{ + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ [ 67%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_alignment_view_object.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_alignment_view_object.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_alignment_view_object.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_alignment_view_object.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_alignment_view_object.cpp [ 67%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_base_view_object.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_base_view_object.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_base_view_object.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_base_view_object.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_base_view_object.cpp -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E cmake_symlink_library ../../../../stage/lib/libost_mol_mm.so.2.3.1 ../../../../stage/lib/libost_mol_mm.so.2.3 ../../../../stage/lib/libost_mol_mm.so +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_model.hh:30: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 32 | : public std::iterator{ + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ [ 67%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_view_object.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_view_object.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_view_object.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_view_object.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_view_object.cpp -make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 67%] Built target ost_mol_mm -[ 67%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_main_thread_runner.cpp.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_main_thread_runner.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_main_thread_runner.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_main_thread_runner.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_main_thread_runner.cpp In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -19388,15 +19294,14 @@ from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_search_bar.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_search_bar.cpp:10: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_row.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_row.cpp:10: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_search_bar.cpp:9: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_row.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -19406,32 +19311,24 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 32 | : public std::iterator{ - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -[ 67%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_completer_base.cpp.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_completer_base.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_completer_base.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_completer_base.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_completer_base.cpp -[ 67%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_gutter.cpp.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_gutter.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_gutter.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_gutter.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_gutter.cpp +[ 67%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_main_thread_runner.cpp.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_main_thread_runner.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_main_thread_runner.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_main_thread_runner.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_main_thread_runner.cpp In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/chain_view.hh:23, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_model.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_delegate.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_table_view.hh:29, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_table_view.cpp:10: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/painter.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/tick_painter.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_tick_painter.cpp:10: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_table_view.cpp:9: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_tick_painter.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -19446,18 +19343,17 @@ from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/painter.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/base_row.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/title_row.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_title_row.cpp:10: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_search_bar.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_search_bar.cpp:10: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_title_row.cpp:9: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_search_bar.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -19467,10 +19363,8 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 67%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_scene.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_scene.cc.o -MF CMakeFiles/_ost_gfx.dir/export_scene.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_scene.cc.o -c /build/openstructure-2.3.1/modules/gfx/pymod/export_scene.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_model.hh:30: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ @@ -19485,14 +19379,15 @@ from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/painter.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/tick_painter.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_tick_painter.cpp:10: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/base_row.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/title_row.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_title_row.cpp:10: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_tick_painter.cpp:9: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_title_row.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -19502,25 +19397,20 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 67%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_output_redirector.cpp.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_output_redirector.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_output_redirector.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_output_redirector.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_output_redirector.cpp In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/painter.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/base_row.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/base_view_object.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_base_view_object.cpp:10: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/chain_view.hh:23, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_model.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_delegate.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_table_view.hh:29, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_table_view.cpp:10: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_base_view_object.cpp:9: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_table_view.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -19530,6 +19420,8 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 67%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_completer_base.cpp.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_completer_base.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_completer_base.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_completer_base.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_completer_base.cpp In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -19555,43 +19447,14 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 67%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_path_completer.cpp.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_path_completer.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_path_completer.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_path_completer.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_path_completer.cpp -[ 67%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_python_completer.cpp.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_python_completer.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_python_completer.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_python_completer.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_python_completer.cpp -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/alignment_view_object.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_alignment_view_object.cpp:10: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/memory:63, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_alignment_view_object.cpp:9: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_model.hh:30: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] @@ -19600,46 +19463,25 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/mol/alg/pymod/wrap_mol_alg.cc:20: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 67%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_python_interpreter.cpp.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_python_interpreter.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_python_interpreter.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_python_interpreter.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_python_interpreter.cpp -[ 69%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_python_interpreter_worker.cpp.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_python_interpreter_worker.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_python_interpreter_worker.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_python_interpreter_worker.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_python_interpreter_worker.cpp -[ 69%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_python_namespace_tree_model.cpp.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_python_namespace_tree_model.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_python_namespace_tree_model.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_python_namespace_tree_model.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_python_namespace_tree_model.cpp +[ 67%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_gutter.cpp.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_gutter.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_gutter.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_gutter.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_gutter.cpp In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_view_object.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_view_object.cpp:10: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/painter.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/base_row.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/base_view_object.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_base_view_object.cpp:10: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_view_object.cpp:9: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_base_view_object.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -19649,26 +19491,26 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 67%] Linking CXX shared module ../../../stage/lib/python3.11/dist-packages/ost/conop/_ost_conop.so +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_conop.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -o ../../../stage/lib/python3.11/dist-packages/ost/conop/_ost_conop.so CMakeFiles/_ost_conop.dir/wrap_conop.cc.o CMakeFiles/_ost_conop.dir/export_compound.cc.o CMakeFiles/_ost_conop.dir/export_processor.cc.o CMakeFiles/_ost_conop.dir/export_heuristic.cc.o CMakeFiles/_ost_conop.dir/export_amino_acids.cc.o CMakeFiles/_ost_conop.dir/export_conop.cc.o CMakeFiles/_ost_conop.dir/export_diag.cc.o CMakeFiles/_ost_conop.dir/export_rule_based.cc.o CMakeFiles/_ost_conop.dir/export_ring_finder.cc.o -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib: ../../../stage/lib/libost_conop.so.2.3.1 /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so ../../../stage/lib/libost_db.so.2.3.1 /usr/lib/x86_64-linux-gnu/libsqlite3.so ../../../stage/lib/libost_seq.so.2.3.1 ../../../stage/lib/libost_mol.so.2.3.1 ../../../stage/lib/libost_info.so.2.3.1 ../../../stage/lib/libost_base.so.2.3.1 ../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/conop/pymod/__init__.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/conop/./__init__.pyc\",\"__init__.py\",doraise=True)" In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/local_dist_diff_test.hh:23, - from /build/openstructure-2.3.1/modules/mol/alg/pymod/wrap_mol_alg.cc:25: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/alignment_view_object.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_alignment_view_object.cpp:10: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/specfun.h:45, - from /usr/include/c++/12/cmath:1935, - from /usr/include/c++/12/math.h:36, - from /usr/include/python3.11/pyport.h:218, - from /usr/include/python3.11/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8: + from /usr/include/c++/12/memory:63, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_alignment_view_object.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -19678,19 +19520,66 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/conop/pymod/cleanup.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/conop/./cleanup.pyc\",\"cleanup.py\",doraise=True)" +make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/local_dist_diff_test.hh:24: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 67%] Built target _ost_conop +make -f modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/build.make modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/depend +[ 67%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_output_redirector.cpp.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_output_redirector.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_output_redirector.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_output_redirector.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_output_redirector.cpp +make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/gfx/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/DependInfo.cmake --color= +make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +make -f modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/build.make modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/build +make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[ 67%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/wrap_gfx.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/wrap_gfx.cc.o -MF CMakeFiles/_ost_gfx.dir/wrap_gfx.cc.o.d -o CMakeFiles/_ost_gfx.dir/wrap_gfx.cc.o -c /build/openstructure-2.3.1/modules/gfx/pymod/wrap_gfx.cc +[ 67%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_path_completer.cpp.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_path_completer.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_path_completer.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_path_completer.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_path_completer.cpp +[ 67%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_python_completer.cpp.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_python_completer.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_python_completer.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_python_completer.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_python_completer.cpp +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_view_object.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_view_object.cpp:10: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/memory:63, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_view_object.cpp:9: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 67%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_python_interpreter.cpp.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_python_interpreter.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_python_interpreter.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_python_interpreter.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_python_interpreter.cpp +[ 69%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_python_interpreter_worker.cpp.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_python_interpreter_worker.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_python_interpreter_worker.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_python_interpreter_worker.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_python_interpreter_worker.cpp +[ 69%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_python_namespace_tree_model.cpp.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_python_namespace_tree_model.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_python_namespace_tree_model.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_python_namespace_tree_model.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_python_namespace_tree_model.cpp [ 69%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_python_shell.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_python_shell.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_python_shell.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_python_shell.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_python_shell.cpp [ 69%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_python_shell_widget.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_python_shell_widget.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_python_shell_widget.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_python_shell_widget.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_python_shell_widget.cpp +[ 69%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_text_logger.cpp.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_text_logger.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_text_logger.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_text_logger.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_text_logger.cpp In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_view_object.hh:32: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] @@ -19699,8 +19588,6 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 69%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_text_logger.cpp.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_text_logger.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_text_logger.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_text_logger.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_text_logger.cpp [ 69%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_state_machine.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_state_machine.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_state_machine.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_state_machine.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_state_machine.cpp [ 69%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_state.cpp.o @@ -19711,6 +19598,20 @@ cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_transition_guard.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_transition_guard.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_transition_guard.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_transition_guard.cpp [ 69%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_button_bar.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_button_bar.cpp.o -MF CMakeFiles/ost_gui.dir/panels/moc_button_bar.cpp.o.d -o CMakeFiles/ost_gui.dir/panels/moc_button_bar.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_button_bar.cpp +[ 69%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_drop_box.cpp.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_drop_box.cpp.o -MF CMakeFiles/ost_gui.dir/panels/moc_drop_box.cpp.o.d -o CMakeFiles/ost_gui.dir/panels/moc_drop_box.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_drop_box.cpp +[ 70%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_panel_bar.cpp.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_panel_bar.cpp.o -MF CMakeFiles/ost_gui.dir/panels/moc_panel_bar.cpp.o.d -o CMakeFiles/ost_gui.dir/panels/moc_panel_bar.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_panel_bar.cpp +[ 70%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_panel_manager.cpp.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_panel_manager.cpp.o -MF CMakeFiles/ost_gui.dir/panels/moc_panel_manager.cpp.o.d -o CMakeFiles/ost_gui.dir/panels/moc_panel_manager.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_panel_manager.cpp +[ 70%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_bottom_bar.cpp.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_bottom_bar.cpp.o -MF CMakeFiles/ost_gui.dir/panels/moc_bottom_bar.cpp.o.d -o CMakeFiles/ost_gui.dir/panels/moc_bottom_bar.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_bottom_bar.cpp +[ 70%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_button_box.cpp.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_button_box.cpp.o -MF CMakeFiles/ost_gui.dir/panels/moc_button_box.cpp.o.d -o CMakeFiles/ost_gui.dir/panels/moc_button_box.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_button_box.cpp +[ 70%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_event_button.cpp.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_event_button.cpp.o -MF CMakeFiles/ost_gui.dir/panels/moc_event_button.cpp.o.d -o CMakeFiles/ost_gui.dir/panels/moc_event_button.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_event_button.cpp +[ 70%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_panel_widget_container.cpp.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_panel_widget_container.cpp.o -MF CMakeFiles/ost_gui.dir/panels/moc_panel_widget_container.cpp.o.d -o CMakeFiles/ost_gui.dir/panels/moc_panel_widget_container.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_panel_widget_container.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -19724,52 +19625,15 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/gfx/pymod/export_scene.cc:19: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/../../../../../modules/gui/src/python_shell/python_interpreter_worker.hh:29, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/../../../../../modules/gui/src/python_shell/python_interpreter.hh:31, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_python_interpreter.cpp:10: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 70%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_panel_bar.cpp.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_panel_bar.cpp.o -MF CMakeFiles/ost_gui.dir/panels/moc_panel_bar.cpp.o.d -o CMakeFiles/ost_gui.dir/panels/moc_panel_bar.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_panel_bar.cpp -[ 70%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_drop_box.cpp.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_drop_box.cpp.o -MF CMakeFiles/ost_gui.dir/panels/moc_drop_box.cpp.o.d -o CMakeFiles/ost_gui.dir/panels/moc_drop_box.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_drop_box.cpp -[ 70%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_panel_manager.cpp.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_panel_manager.cpp.o -MF CMakeFiles/ost_gui.dir/panels/moc_panel_manager.cpp.o.d -o CMakeFiles/ost_gui.dir/panels/moc_panel_manager.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_panel_manager.cpp -[ 70%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_bottom_bar.cpp.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_bottom_bar.cpp.o -MF CMakeFiles/ost_gui.dir/panels/moc_bottom_bar.cpp.o.d -o CMakeFiles/ost_gui.dir/panels/moc_bottom_bar.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_bottom_bar.cpp -[ 70%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_button_box.cpp.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_button_box.cpp.o -MF CMakeFiles/ost_gui.dir/panels/moc_button_box.cpp.o.d -o CMakeFiles/ost_gui.dir/panels/moc_button_box.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_button_box.cpp -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, - from /build/openstructure-2.3.1/modules/gfx/pymod/export_scene.cc:22: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/specfun.h:45, - from /usr/include/c++/12/cmath:1935, - from /usr/include/c++/12/math.h:36, - from /usr/include/python3.11/pyport.h:218, - from /usr/include/python3.11/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -[ 70%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_event_button.cpp.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_event_button.cpp.o -MF CMakeFiles/ost_gui.dir/panels/moc_event_button.cpp.o.d -o CMakeFiles/ost_gui.dir/panels/moc_event_button.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_event_button.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -19783,9 +19647,7 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/../../../../../modules/gui/src/python_shell/python_interpreter_worker.hh:29, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/../../../../../modules/gui/src/python_shell/python_interpreter.hh:31, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_python_interpreter.cpp:10: + from /build/openstructure-2.3.1/modules/gfx/pymod/wrap_gfx.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ @@ -19850,18 +19712,43 @@ from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/../../../../../modules/gui/src/python_shell/python_interpreter_worker.hh:29, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/../../../../../modules/gui/src/python_shell/python_interpreter.hh:31, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/../../../../../modules/gui/src/python_shell/python_shell_widget.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_python_shell_widget.cpp:10: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/../../../../../modules/gui/src/python_shell/text_logger.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_text_logger.cpp:10: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 70%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_panel_widget_container.cpp.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_panel_widget_container.cpp.o -MF CMakeFiles/ost_gui.dir/panels/moc_panel_widget_container.cpp.o.d -o CMakeFiles/ost_gui.dir/panels/moc_panel_widget_container.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_panel_widget_container.cpp [ 70%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_panel_bar_widget_holder.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_panel_bar_widget_holder.cpp.o -MF CMakeFiles/ost_gui.dir/panels/moc_panel_bar_widget_holder.cpp.o.d -o CMakeFiles/ost_gui.dir/panels/moc_panel_bar_widget_holder.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_panel_bar_widget_holder.cpp +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/info_group.hh:33, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/info.hh:32, + from /build/openstructure-2.3.1/modules/gfx/pymod/wrap_gfx.cc:26: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/bits/specfun.h:45, + from /usr/include/c++/12/cmath:1935, + from /usr/include/c++/12/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -19877,8 +19764,8 @@ from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/../../../../../modules/gui/src/python_shell/python_interpreter_worker.hh:29, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/../../../../../modules/gui/src/python_shell/python_interpreter.hh:31, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/../../../../../modules/gui/src/python_shell/text_logger.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_text_logger.cpp:10: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/../../../../../modules/gui/src/python_shell/python_shell_widget.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_python_shell_widget.cpp:10: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ @@ -19907,11 +19794,15 @@ /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ +[ 70%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_splitter_panel_bar.cpp.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_splitter_panel_bar.cpp.o -MF CMakeFiles/ost_gui.dir/panels/moc_splitter_panel_bar.cpp.o.d -o CMakeFiles/ost_gui.dir/panels/moc_splitter_panel_bar.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_splitter_panel_bar.cpp /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 70%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_splitter_panel_bar.cpp.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_splitter_panel_bar.cpp.o -MF CMakeFiles/ost_gui.dir/panels/moc_splitter_panel_bar.cpp.o.d -o CMakeFiles/ost_gui.dir/panels/moc_splitter_panel_bar.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_splitter_panel_bar.cpp +[ 70%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_tabbed_panel_bar.cpp.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_tabbed_panel_bar.cpp.o -MF CMakeFiles/ost_gui.dir/panels/moc_tabbed_panel_bar.cpp.o.d -o CMakeFiles/ost_gui.dir/panels/moc_tabbed_panel_bar.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_tabbed_panel_bar.cpp +[ 70%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_context_menu.cpp.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_context_menu.cpp.o -MF CMakeFiles/ost_gui.dir/scene_win/moc_context_menu.cpp.o.d -o CMakeFiles/ost_gui.dir/scene_win/moc_context_menu.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_context_menu.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -19935,10 +19826,6 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 70%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_tabbed_panel_bar.cpp.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_tabbed_panel_bar.cpp.o -MF CMakeFiles/ost_gui.dir/panels/moc_tabbed_panel_bar.cpp.o.d -o CMakeFiles/ost_gui.dir/panels/moc_tabbed_panel_bar.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_tabbed_panel_bar.cpp -[ 70%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_context_menu.cpp.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_context_menu.cpp.o -MF CMakeFiles/ost_gui.dir/scene_win/moc_context_menu.cpp.o.d -o CMakeFiles/ost_gui.dir/scene_win/moc_context_menu.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_context_menu.cpp [ 71%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_current_selection_node.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_current_selection_node.cpp.o -MF CMakeFiles/ost_gui.dir/scene_win/moc_current_selection_node.cpp.o.d -o CMakeFiles/ost_gui.dir/scene_win/moc_current_selection_node.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_current_selection_node.cpp [ 71%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_custom_part_node.cpp.o @@ -19951,24 +19838,28 @@ cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_entity_node.cpp.o -MF CMakeFiles/ost_gui.dir/scene_win/moc_entity_node.cpp.o.d -o CMakeFiles/ost_gui.dir/scene_win/moc_entity_node.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_entity_node.cpp [ 71%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_entity_part_node.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_entity_part_node.cpp.o -MF CMakeFiles/ost_gui.dir/scene_win/moc_entity_part_node.cpp.o.d -o CMakeFiles/ost_gui.dir/scene_win/moc_entity_part_node.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_entity_part_node.cpp -[ 71%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_svd_superpose.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_svd_superpose.cc.o -MF CMakeFiles/_ost_mol_alg.dir/export_svd_superpose.cc.o.d -o CMakeFiles/_ost_mol_alg.dir/export_svd_superpose.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/pymod/export_svd_superpose.cc [ 71%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_render_mode_node.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_render_mode_node.cpp.o -MF CMakeFiles/ost_gui.dir/scene_win/moc_render_mode_node.cpp.o.d -o CMakeFiles/ost_gui.dir/scene_win/moc_render_mode_node.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_render_mode_node.cpp +[ 71%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_render_modes_node.cpp.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_render_modes_node.cpp.o -MF CMakeFiles/ost_gui.dir/scene_win/moc_render_modes_node.cpp.o.d -o CMakeFiles/ost_gui.dir/scene_win/moc_render_modes_node.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_render_modes_node.cpp +[ 71%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_root_node.cpp.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_root_node.cpp.o -MF CMakeFiles/ost_gui.dir/scene_win/moc_root_node.cpp.o.d -o CMakeFiles/ost_gui.dir/scene_win/moc_root_node.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_root_node.cpp In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/../../../../../modules/gui/src/scene_win/current_selection_node.hh:23, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_current_selection_node.cpp:10: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/scene_win_model.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/../../../../../modules/gui/src/scene_win/context_menu.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_context_menu.cpp:10: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_current_selection_node.cpp:9: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_context_menu.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -19978,10 +19869,9 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 71%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_render_modes_node.cpp.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_render_modes_node.cpp.o -MF CMakeFiles/ost_gui.dir/scene_win/moc_render_modes_node.cpp.o.d -o CMakeFiles/ost_gui.dir/scene_win/moc_render_modes_node.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_render_modes_node.cpp -[ 71%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_root_node.cpp.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_root_node.cpp.o -MF CMakeFiles/ost_gui.dir/scene_win/moc_root_node.cpp.o.d -o CMakeFiles/ost_gui.dir/scene_win/moc_root_node.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_root_node.cpp +[ 71%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_scene_node.cpp.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_scene_node.cpp.o -MF CMakeFiles/ost_gui.dir/scene_win/moc_scene_node.cpp.o.d -o CMakeFiles/ost_gui.dir/scene_win/moc_scene_node.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_scene_node.cpp +[ 71%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_scene.cc.o In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -20000,6 +19890,7 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_scene.cc.o -MF CMakeFiles/_ost_gfx.dir/export_scene.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_scene.cc.o -c /build/openstructure-2.3.1/modules/gfx/pymod/export_scene.cc /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ @@ -20012,16 +19903,14 @@ from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/scene_win_model.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/../../../../../modules/gui/src/scene_win/context_menu.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_context_menu.cpp:10: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/../../../../../modules/gui/src/scene_win/current_selection_node.hh:23, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_current_selection_node.cpp:10: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_context_menu.cpp:9: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_current_selection_node.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -20031,26 +19920,31 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 71%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_scene_node.cpp.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_scene_node.cpp.o -MF CMakeFiles/ost_gui.dir/scene_win/moc_scene_node.cpp.o.d -o CMakeFiles/ost_gui.dir/scene_win/moc_scene_node.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_scene_node.cpp [ 73%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_scene_win.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_scene_win.cpp.o -MF CMakeFiles/ost_gui.dir/scene_win/moc_scene_win.cpp.o.d -o CMakeFiles/ost_gui.dir/scene_win/moc_scene_win.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_scene_win.cpp -[ 73%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_clash.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_clash.cc.o -MF CMakeFiles/_ost_mol_alg.dir/export_clash.cc.o.d -o CMakeFiles/_ost_mol_alg.dir/export_clash.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/pymod/export_clash.cc [ 73%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_scene_win_model.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_scene_win_model.cpp.o -MF CMakeFiles/ost_gui.dir/scene_win/moc_scene_win_model.cpp.o.d -o CMakeFiles/ost_gui.dir/scene_win/moc_scene_win_model.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_scene_win_model.cpp +[ 73%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_gfx_node.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_gfx_node.cc.o -MF CMakeFiles/_ost_gfx.dir/export_gfx_node.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_gfx_node.cc.o -c /build/openstructure-2.3.1/modules/gfx/pymod/export_gfx_node.cc +[ 73%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool.cpp.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool.cpp.o -MF CMakeFiles/ost_gui.dir/tools/moc_tool.cpp.o.d -o CMakeFiles/ost_gui.dir/tools/moc_tool.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/tools/moc_tool.cpp +[ 73%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool_option_group.cpp.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool_option_group.cpp.o -MF CMakeFiles/ost_gui.dir/tools/moc_tool_option_group.cpp.o.d -o CMakeFiles/ost_gui.dir/tools/moc_tool_option_group.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/tools/moc_tool_option_group.cpp In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:29, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/../../../../../modules/gui/src/scene_win/entity_node.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_entity_node.cpp:10: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/../../../../../modules/gui/src/scene_win/entity_part_node.hh:23, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_entity_part_node.cpp:10: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_entity_node.cpp:9: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_entity_part_node.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -20060,22 +19954,18 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 73%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool.cpp.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool.cpp.o -MF CMakeFiles/ost_gui.dir/tools/moc_tool.cpp.o.d -o CMakeFiles/ost_gui.dir/tools/moc_tool.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/tools/moc_tool.cpp In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/../../../../../modules/gui/src/scene_win/render_mode_node.hh:23, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_render_mode_node.cpp:10: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:29, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/../../../../../modules/gui/src/scene_win/entity_node.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_entity_node.cpp:10: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_render_mode_node.cpp:9: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_entity_node.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -20085,23 +19975,20 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 73%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool_option_group.cpp.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool_option_group.cpp.o -MF CMakeFiles/ost_gui.dir/tools/moc_tool_option_group.cpp.o.d -o CMakeFiles/ost_gui.dir/tools/moc_tool_option_group.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/tools/moc_tool_option_group.cpp In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/../../../../../modules/gui/src/scene_win/entity_part_node.hh:23, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_entity_part_node.cpp:10: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/../../../../../modules/gui/src/scene_win/render_mode_node.hh:23, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_render_mode_node.cpp:10: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_entity_part_node.cpp:9: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_render_mode_node.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -20191,26 +20078,8 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/mol/alg/pymod/export_svd_superpose.cc:23: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 73%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool_options_widget.cpp.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool_options_widget.cpp.o -MF CMakeFiles/ost_gui.dir/tools/moc_tool_options_widget.cpp.o.d -o CMakeFiles/ost_gui.dir/tools/moc_tool_options_widget.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/tools/moc_tool_options_widget.cpp In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/tools/../../../../../modules/gui/src/tools/tool.hh:30, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/tools/moc_tool.cpp:10: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:37:22: warning: 'Qt::MidButton' is deprecated: MidButton is deprecated. Use MiddleButton instead [-Wdeprecated-declarations] @@ -20222,38 +20091,6 @@ /usr/include/x86_64-linux-gnu/qt5/QtCore/qnamespace.h:132:9: note: declared here 132 | MidButton Q_DECL_ENUMERATOR_DEPRECATED_X("MidButton is deprecated. Use MiddleButton instead") = MiddleButton, | ^~~~~~~~~ -[ 73%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool_options_widget.cpp.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool_options_widget.cpp.o -MF CMakeFiles/ost_gui.dir/tools/moc_tool_options_widget.cpp.o.d -o CMakeFiles/ost_gui.dir/tools/moc_tool_options_widget.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/tools/moc_tool_options_widget.cpp -[ 73%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_gfx_node.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_gfx_node.cc.o -MF CMakeFiles/_ost_gfx.dir/export_gfx_node.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_gfx_node.cc.o -c /build/openstructure-2.3.1/modules/gfx/pymod/export_gfx_node.cc -[ 73%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_symmetry_node.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_symmetry_node.cc.o -MF CMakeFiles/_ost_gfx.dir/export_symmetry_node.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_symmetry_node.cc.o -c /build/openstructure-2.3.1/modules/gfx/pymod/export_symmetry_node.cc -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/svd_superpose.hh:27, - from /build/openstructure-2.3.1/modules/mol/alg/pymod/export_svd_superpose.cc:26: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/specfun.h:45, - from /usr/include/c++/12/cmath:1935, - from /usr/include/c++/12/math.h:36, - from /usr/include/python3.11/pyport.h:218, - from /usr/include/python3.11/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ [ 73%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_measure_tool.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_measure_tool.cpp.o -MF CMakeFiles/ost_gui.dir/tools/moc_measure_tool.cpp.o.d -o CMakeFiles/ost_gui.dir/tools/moc_measure_tool.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/tools/moc_measure_tool.cpp [ 73%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool_options_win.cpp.o @@ -20278,6 +20115,10 @@ /usr/include/x86_64-linux-gnu/qt5/QtCore/qnamespace.h:132:9: note: declared here 132 | MidButton Q_DECL_ENUMERATOR_DEPRECATED_X("MidButton is deprecated. Use MiddleButton instead") = MiddleButton, | ^~~~~~~~~ +[ 74%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_overlay_manager_gui.cpp.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_overlay_manager_gui.cpp.o -MF CMakeFiles/ost_gui.dir/data_viewer/moc_overlay_manager_gui.cpp.o.d -o CMakeFiles/ost_gui.dir/data_viewer/moc_overlay_manager_gui.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_overlay_manager_gui.cpp +[ 74%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_data_viewer_panel_base.cpp.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_data_viewer_panel_base.cpp.o -MF CMakeFiles/ost_gui.dir/data_viewer/moc_data_viewer_panel_base.cpp.o.d -o CMakeFiles/ost_gui.dir/data_viewer/moc_data_viewer_panel_base.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_data_viewer_panel_base.cpp In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool.hh:30, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/tools/../../../../../modules/gui/src/tools/tool_manager.hh:24, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/tools/moc_tool_manager.cpp:10: @@ -20303,17 +20144,37 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/mol/alg/pymod/export_clash.cc:19: + from /build/openstructure-2.3.1/modules/gfx/pymod/export_gfx_node.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 75%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_gfx_obj.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_gfx_obj.cc.o -MF CMakeFiles/_ost_gfx.dir/export_gfx_obj.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_gfx_obj.cc.o -c /build/openstructure-2.3.1/modules/gfx/pymod/export_gfx_obj.cc -[ 75%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_entity.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_entity.cc.o -MF CMakeFiles/_ost_gfx.dir/export_entity.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_entity.cc.o -c /build/openstructure-2.3.1/modules/gfx/pymod/export_entity.cc +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/openstructure-2.3.1/modules/gfx/pymod/export_scene.cc:19: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 74%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_null_overlay.cpp.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_null_overlay.cpp.o -MF CMakeFiles/ost_gui.dir/data_viewer/moc_null_overlay.cpp.o.d -o CMakeFiles/ost_gui.dir/data_viewer/moc_null_overlay.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_null_overlay.cpp +[ 74%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_overlay_base.cpp.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_overlay_base.cpp.o -MF CMakeFiles/ost_gui.dir/data_viewer/moc_overlay_base.cpp.o.d -o CMakeFiles/ost_gui.dir/data_viewer/moc_overlay_base.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_overlay_base.cpp In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -20337,20 +20198,6 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 75%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_overlay_manager_gui.cpp.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_overlay_manager_gui.cpp.o -MF CMakeFiles/ost_gui.dir/data_viewer/moc_overlay_manager_gui.cpp.o.d -o CMakeFiles/ost_gui.dir/data_viewer/moc_overlay_manager_gui.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_overlay_manager_gui.cpp -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool.hh:30, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/tools/../../../../../modules/gui/src/tools/tool_options_win.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/tools/moc_tool_options_win.cpp:10: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:37:22: warning: 'Qt::MidButton' is deprecated: MidButton is deprecated. Use MiddleButton instead [-Wdeprecated-declarations] - 37 | MiddleButton=Qt::MidButton - | ^~~~~~~~~ -In file included from /usr/include/x86_64-linux-gnu/qt5/QtCore/qpoint.h:43, - from /usr/include/x86_64-linux-gnu/qt5/QtCore/QPoint:1, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:24: -/usr/include/x86_64-linux-gnu/qt5/QtCore/qnamespace.h:132:9: note: declared here - 132 | MidButton Q_DECL_ENUMERATOR_DEPRECATED_X("MidButton is deprecated. Use MiddleButton instead") = MiddleButton, - | ^~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -20374,16 +20221,14 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 75%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_data_viewer_panel_base.cpp.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_data_viewer_panel_base.cpp.o -MF CMakeFiles/ost_gui.dir/data_viewer/moc_data_viewer_panel_base.cpp.o.d -o CMakeFiles/ost_gui.dir/data_viewer/moc_data_viewer_panel_base.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_data_viewer_panel_base.cpp +[ 74%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_pointlist_overlay_base.cpp.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_pointlist_overlay_base.cpp.o -MF CMakeFiles/ost_gui.dir/data_viewer/moc_pointlist_overlay_base.cpp.o.d -o CMakeFiles/ost_gui.dir/data_viewer/moc_pointlist_overlay_base.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_pointlist_overlay_base.cpp In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/clash_score.hh:26, - from /build/openstructure-2.3.1/modules/mol/alg/pymod/export_clash.cc:23: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, + from /build/openstructure-2.3.1/modules/gfx/pymod/export_scene.cc:22: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -20405,6 +20250,8 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 74%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/thin_splitter.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/thin_splitter.cc.o -MF CMakeFiles/ost_gui.dir/thin_splitter.cc.o.d -o CMakeFiles/ost_gui.dir/thin_splitter.cc.o -c /build/openstructure-2.3.1/modules/gui/src/thin_splitter.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool.hh:30, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/tools/../../../../../modules/gui/src/tools/measure_tool.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/tools/moc_measure_tool.cpp:10: @@ -20417,8 +20264,20 @@ /usr/include/x86_64-linux-gnu/qt5/QtCore/qnamespace.h:132:9: note: declared here 132 | MidButton Q_DECL_ENUMERATOR_DEPRECATED_X("MidButton is deprecated. Use MiddleButton instead") = MiddleButton, | ^~~~~~~~~ -[ 75%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_null_overlay.cpp.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_null_overlay.cpp.o -MF CMakeFiles/ost_gui.dir/data_viewer/moc_null_overlay.cpp.o.d -o CMakeFiles/ost_gui.dir/data_viewer/moc_null_overlay.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_null_overlay.cpp +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool.hh:30, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/tools/../../../../../modules/gui/src/tools/tool_options_win.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/tools/moc_tool_options_win.cpp:10: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:37:22: warning: 'Qt::MidButton' is deprecated: MidButton is deprecated. Use MiddleButton instead [-Wdeprecated-declarations] + 37 | MiddleButton=Qt::MidButton + | ^~~~~~~~~ +In file included from /usr/include/x86_64-linux-gnu/qt5/QtCore/qpoint.h:43, + from /usr/include/x86_64-linux-gnu/qt5/QtCore/QPoint:1, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:24: +/usr/include/x86_64-linux-gnu/qt5/QtCore/qnamespace.h:132:9: note: declared here + 132 | MidButton Q_DECL_ENUMERATOR_DEPRECATED_X("MidButton is deprecated. Use MiddleButton instead") = MiddleButton, + | ^~~~~~~~~ +[ 74%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/perspective.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/perspective.cc.o -MF CMakeFiles/ost_gui.dir/perspective.cc.o.d -o CMakeFiles/ost_gui.dir/perspective.cc.o -c /build/openstructure-2.3.1/modules/gui/src/perspective.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -20444,28 +20303,6 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 75%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_overlay_base.cpp.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_overlay_base.cpp.o -MF CMakeFiles/ost_gui.dir/data_viewer/moc_overlay_base.cpp.o.d -o CMakeFiles/ost_gui.dir/data_viewer/moc_overlay_base.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_overlay_base.cpp -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color.hh:31, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/tools/../../../../../modules/gui/src/tools/measure_tool.hh:28: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/memory:63, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/tools/moc_measure_tool.cpp:9: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -20489,61 +20326,17 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 75%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_trajectory_analysis.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_trajectory_analysis.cc.o -MF CMakeFiles/_ost_mol_alg.dir/export_trajectory_analysis.cc.o.d -o CMakeFiles/_ost_mol_alg.dir/export_trajectory_analysis.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/pymod/export_trajectory_analysis.cc -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/../../../../../modules/gui/src/data_viewer/data_viewer.hh:37: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main_window.hh:46:55: warning: 'constexpr QFlags::QFlags(Zero) [with Enum = Qt::WindowType; Zero = int QFlags::Private::*]' is deprecated: Use default constructor instead [-Wdeprecated-declarations] - 46 | MainWindow(QWidget* parent=0, Qt::WindowFlags flags=0); - | ^ -In file included from /usr/include/x86_64-linux-gnu/qt5/QtCore/qglobal.h:1305, - from /usr/include/x86_64-linux-gnu/qt5/QtGui/qtguiglobal.h:43, - from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/qtwidgetsglobal.h:43, - from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/qmainwindow.h:43, - from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/QMainWindow:1, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main_window.hh:35: -/usr/include/x86_64-linux-gnu/qt5/QtCore/qflags.h:123:80: note: declared here - 123 | QT_DEPRECATED_X("Use default constructor instead") Q_DECL_CONSTEXPR inline QFlags(Zero) noexcept : i(0) {} - | ^~~~~~ -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/gfx/pymod/export_gfx_node.cc:19: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 75%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_pointlist_overlay_base.cpp.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_pointlist_overlay_base.cpp.o -MF CMakeFiles/ost_gui.dir/data_viewer/moc_pointlist_overlay_base.cpp.o.d -o CMakeFiles/ost_gui.dir/data_viewer/moc_pointlist_overlay_base.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_pointlist_overlay_base.cpp -[ 75%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/thin_splitter.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/thin_splitter.cc.o -MF CMakeFiles/ost_gui.dir/thin_splitter.cc.o.d -o CMakeFiles/ost_gui.dir/thin_splitter.cc.o -c /build/openstructure-2.3.1/modules/gui/src/thin_splitter.cc -[ 75%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_structure_analysis.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_structure_analysis.cc.o -MF CMakeFiles/_ost_mol_alg.dir/export_structure_analysis.cc.o.d -o CMakeFiles/_ost_mol_alg.dir/export_structure_analysis.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/pymod/export_structure_analysis.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/extent.hh:34, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/../../../../../modules/gui/src/data_viewer/data_viewer_panel_base.hh:34, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_data_viewer_panel_base.cpp:10: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color.hh:31, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/tools/../../../../../modules/gui/src/tools/measure_tool.hh:28: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_data_viewer_panel_base.cpp:9: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/tools/moc_measure_tool.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -20553,47 +20346,22 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/gfx/pymod/export_symmetry_node.cc:19: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 75%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/perspective.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/perspective.cc.o -MF CMakeFiles/ost_gui.dir/perspective.cc.o.d -o CMakeFiles/ost_gui.dir/perspective.cc.o -c /build/openstructure-2.3.1/modules/gui/src/perspective.cc -[ 76%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/widget_registry.cc.o +[ 75%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/widget_registry.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/widget_registry.cc.o -MF CMakeFiles/ost_gui.dir/widget_registry.cc.o.d -o CMakeFiles/ost_gui.dir/widget_registry.cc.o -c /build/openstructure-2.3.1/modules/gui/src/widget_registry.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/symmetry_node.hh:22, - from /build/openstructure-2.3.1/modules/gfx/pymod/export_symmetry_node.cc:23: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/extent.hh:34, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/../../../../../modules/gui/src/data_viewer/data_viewer_panel_base.hh:34, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_data_viewer_panel_base.cpp:10: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/specfun.h:45, - from /usr/include/c++/12/cmath:1935, - from /usr/include/c++/12/math.h:36, - from /usr/include/python3.11/pyport.h:218, - from /usr/include/python3.11/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8: + from /usr/include/c++/12/memory:63, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_data_viewer_panel_base.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -20603,32 +20371,6 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 76%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_contact_overlap.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_contact_overlap.cc.o -MF CMakeFiles/_ost_mol_alg.dir/export_contact_overlap.cc.o.d -o CMakeFiles/_ost_mol_alg.dir/export_contact_overlap.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/pymod/export_contact_overlap.cc -[ 76%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/file_browser.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/file_browser.cc.o -MF CMakeFiles/ost_gui.dir/file_browser.cc.o.d -o CMakeFiles/ost_gui.dir/file_browser.cc.o -c /build/openstructure-2.3.1/modules/gui/src/file_browser.cc -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/gfx/pymod/export_gfx_obj.cc:19: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 76%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/file_type_dialog.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/file_type_dialog.cc.o -MF CMakeFiles/ost_gui.dir/file_type_dialog.cc.o.d -o CMakeFiles/ost_gui.dir/file_type_dialog.cc.o -c /build/openstructure-2.3.1/modules/gui/src/file_type_dialog.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -20651,368 +20393,16 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, - from /build/openstructure-2.3.1/modules/gfx/pymod/export_gfx_obj.cc:22: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/specfun.h:45, - from /usr/include/c++/12/cmath:1935, - from /usr/include/c++/12/math.h:36, - from /usr/include/python3.11/pyport.h:218, - from /usr/include/python3.11/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -[ 76%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/file_viewer.cc.o +[ 75%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/file_browser.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/file_browser.cc.o -MF CMakeFiles/ost_gui.dir/file_browser.cc.o.d -o CMakeFiles/ost_gui.dir/file_browser.cc.o -c /build/openstructure-2.3.1/modules/gui/src/file_browser.cc +[ 75%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/file_type_dialog.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/file_type_dialog.cc.o -MF CMakeFiles/ost_gui.dir/file_type_dialog.cc.o.d -o CMakeFiles/ost_gui.dir/file_type_dialog.cc.o -c /build/openstructure-2.3.1/modules/gui/src/file_type_dialog.cc +[ 75%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/file_viewer.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/file_viewer.cc.o -MF CMakeFiles/ost_gui.dir/file_viewer.cc.o.d -o CMakeFiles/ost_gui.dir/file_viewer.cc.o -c /build/openstructure-2.3.1/modules/gui/src/file_viewer.cc -[ 76%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/main.cc.o +[ 75%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/main.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/main.cc.o -MF CMakeFiles/ost_gui.dir/main.cc.o.d -o CMakeFiles/ost_gui.dir/main.cc.o -c /build/openstructure-2.3.1/modules/gui/src/main.cc -[ 76%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/gl_canvas.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/gl_canvas.cc.o -MF CMakeFiles/ost_gui.dir/gl_canvas.cc.o.d -o CMakeFiles/ost_gui.dir/gl_canvas.cc.o -c /build/openstructure-2.3.1/modules/gui/src/gl_canvas.cc -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/gfx/pymod/export_entity.cc:19: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/file_browser.hh:23, - from /build/openstructure-2.3.1/modules/gui/src/perspective.cc:26: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/specfun.h:45, - from /usr/include/c++/12/cmath:1935, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/module_config.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/platform.hh:22, - from /build/openstructure-2.3.1/modules/gui/src/perspective.cc:20: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/mol/alg/pymod/export_structure_analysis.cc:19: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:29, - from /build/openstructure-2.3.1/modules/gfx/pymod/export_entity.cc:23: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/specfun.h:45, - from /usr/include/c++/12/cmath:1935, - from /usr/include/c++/12/math.h:36, - from /usr/include/python3.11/pyport.h:218, - from /usr/include/python3.11/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/mol/alg/pymod/export_trajectory_analysis.cc:19: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/structure_analysis.hh:28, - from /build/openstructure-2.3.1/modules/mol/alg/pymod/export_structure_analysis.cc:22: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/specfun.h:45, - from /usr/include/c++/12/cmath:1935, - from /usr/include/c++/12/math.h:36, - from /usr/include/python3.11/pyport.h:218, - from /usr/include/python3.11/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -[ 76%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/dock_widget.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/dock_widget.cc.o -MF CMakeFiles/ost_gui.dir/dock_widget.cc.o.d -o CMakeFiles/ost_gui.dir/dock_widget.cc.o -c /build/openstructure-2.3.1/modules/gui/src/dock_widget.cc -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, - from /build/openstructure-2.3.1/modules/gui/src/file_type_dialog.hh:31, - from /build/openstructure-2.3.1/modules/gui/src/file_type_dialog.cc:19: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 32 | : public std::iterator{ - | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/specfun.h:45, - from /usr/include/c++/12/cmath:1935, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/module_config.hh:26, - from /build/openstructure-2.3.1/modules/gui/src/file_type_dialog.hh:26: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/trajectory_analysis.hh:29, - from /build/openstructure-2.3.1/modules/mol/alg/pymod/export_trajectory_analysis.cc:22: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/specfun.h:45, - from /usr/include/c++/12/cmath:1935, - from /usr/include/c++/12/math.h:36, - from /usr/include/python3.11/pyport.h:218, - from /usr/include/python3.11/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -[ 76%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/main_window.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/main_window.cc.o -MF CMakeFiles/ost_gui.dir/main_window.cc.o.d -o CMakeFiles/ost_gui.dir/main_window.cc.o -c /build/openstructure-2.3.1/modules/gui/src/main_window.cc -[ 76%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/gl_win.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/gl_win.cc.o -MF CMakeFiles/ost_gui.dir/gl_win.cc.o.d -o CMakeFiles/ost_gui.dir/gl_win.cc.o -c /build/openstructure-2.3.1/modules/gui/src/gl_win.cc -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/mol/alg/pymod/export_contact_overlap.cc:1: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 76%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_menu.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_menu.cc.o -MF CMakeFiles/ost_gui.dir/scene_menu.cc.o.d -o CMakeFiles/ost_gui.dir/scene_menu.cc.o -c /build/openstructure-2.3.1/modules/gui/src/scene_menu.cc -[ 76%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_surface.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_surface.cc.o -MF CMakeFiles/_ost_gfx.dir/export_surface.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_surface.cc.o -c /build/openstructure-2.3.1/modules/gfx/pymod/export_surface.cc -[ 76%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_accessibility.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_accessibility.cc.o -MF CMakeFiles/_ost_mol_alg.dir/export_accessibility.cc.o.d -o CMakeFiles/_ost_mol_alg.dir/export_accessibility.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/pymod/export_accessibility.cc -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/contact_overlap.hh:6, - from /build/openstructure-2.3.1/modules/mol/alg/pymod/export_contact_overlap.cc:4: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/specfun.h:45, - from /usr/include/c++/12/cmath:1935, - from /usr/include/c++/12/math.h:36, - from /usr/include/python3.11/pyport.h:218, - from /usr/include/python3.11/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/contact_overlap.hh:8: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 32 | : public std::iterator{ - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -[ 78%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_sec_structure.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_sec_structure.cc.o -MF CMakeFiles/_ost_mol_alg.dir/export_sec_structure.cc.o.d -o CMakeFiles/_ost_mol_alg.dir/export_sec_structure.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/pymod/export_sec_structure.cc -In file included from /build/openstructure-2.3.1/modules/gui/src/dock_widget.cc:25: -/build/openstructure-2.3.1/modules/gui/src/dock_widget.hh:38:77: warning: 'constexpr QFlags::QFlags(Zero) [with Enum = Qt::WindowType; Zero = int QFlags::Private::*]' is deprecated: Use default constructor instead [-Wdeprecated-declarations] - 38 | DockWidget(const QString& title, QWidget* parent=0, Qt::WindowFlags flags=0); - | ^ -In file included from /usr/include/x86_64-linux-gnu/qt5/QtCore/qglobal.h:1305, - from /usr/include/x86_64-linux-gnu/qt5/QtGui/qtguiglobal.h:43, - from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/qtwidgetsglobal.h:43, - from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/qdockwidget.h:43, - from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/QDockWidget:1, - from /build/openstructure-2.3.1/modules/gui/src/dock_widget.hh:31: -/usr/include/x86_64-linux-gnu/qt5/QtCore/qflags.h:123:80: note: declared here - 123 | QT_DEPRECATED_X("Use default constructor instead") Q_DECL_CONSTEXPR inline QFlags(Zero) noexcept : i(0) {} - | ^~~~~~ -[ 78%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_primitives.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_primitives.cc.o -MF CMakeFiles/_ost_gfx.dir/export_primitives.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_primitives.cc.o -c /build/openstructure-2.3.1/modules/gfx/pymod/export_primitives.cc -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool.hh:30, - from /build/openstructure-2.3.1/modules/gui/src/gl_canvas.hh:23, - from /build/openstructure-2.3.1/modules/gui/src/gl_canvas.cc:22: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:37:22: warning: 'Qt::MidButton' is deprecated: MidButton is deprecated. Use MiddleButton instead [-Wdeprecated-declarations] - 37 | MiddleButton=Qt::MidButton - | ^~~~~~~~~ -In file included from /usr/include/x86_64-linux-gnu/qt5/QtCore/qpoint.h:43, - from /usr/include/x86_64-linux-gnu/qt5/QtCore/QPoint:1, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:24: -/usr/include/x86_64-linux-gnu/qt5/QtCore/qnamespace.h:132:9: note: declared here - 132 | MidButton Q_DECL_ENUMERATOR_DEPRECATED_X("MidButton is deprecated. Use MiddleButton instead") = MiddleButton, - | ^~~~~~~~~ -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main.hh:23, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, - from /build/openstructure-2.3.1/modules/gui/src/file_browser.cc:20: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/openstructure-2.3.1/modules/gui/src/main_window.cc:25: -/build/openstructure-2.3.1/modules/gui/src/main_window.hh:46:55: warning: 'constexpr QFlags::QFlags(Zero) [with Enum = Qt::WindowType; Zero = int QFlags::Private::*]' is deprecated: Use default constructor instead [-Wdeprecated-declarations] +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/../../../../../modules/gui/src/data_viewer/data_viewer.hh:37: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main_window.hh:46:55: warning: 'constexpr QFlags::QFlags(Zero) [with Enum = Qt::WindowType; Zero = int QFlags::Private::*]' is deprecated: Use default constructor instead [-Wdeprecated-declarations] 46 | MainWindow(QWidget* parent=0, Qt::WindowFlags flags=0); | ^ In file included from /usr/include/x86_64-linux-gnu/qt5/QtCore/qglobal.h:1305, @@ -21020,668 +20410,53 @@ from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/qtwidgetsglobal.h:43, from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/qmainwindow.h:43, from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/QMainWindow:1, - from /build/openstructure-2.3.1/modules/gui/src/main_window.hh:35: -/usr/include/x86_64-linux-gnu/qt5/QtCore/qflags.h:123:80: note: declared here - 123 | QT_DEPRECATED_X("Use default constructor instead") Q_DECL_CONSTEXPR inline QFlags(Zero) noexcept : i(0) {} - | ^~~~~~ -In file included from /build/openstructure-2.3.1/modules/gui/src/main_window.cc:26: -/build/openstructure-2.3.1/modules/gui/src/dock_widget.hh:38:77: warning: 'constexpr QFlags::QFlags(Zero) [with Enum = Qt::WindowType; Zero = int QFlags::Private::*]' is deprecated: Use default constructor instead [-Wdeprecated-declarations] - 38 | DockWidget(const QString& title, QWidget* parent=0, Qt::WindowFlags flags=0); - | ^ -/usr/include/x86_64-linux-gnu/qt5/QtCore/qflags.h:123:80: note: declared here - 123 | QT_DEPRECATED_X("Use default constructor instead") Q_DECL_CONSTEXPR inline QFlags(Zero) noexcept : i(0) {} - | ^~~~~~ -/build/openstructure-2.3.1/modules/gui/src/dock_widget.hh: In member function 'void ost::gui::MainWindow::AddDockWidget(QWidget*, const QString&, bool, int)': -/build/openstructure-2.3.1/modules/gui/src/dock_widget.hh:38:77: warning: 'constexpr QFlags::QFlags(Zero) [with Enum = Qt::WindowType; Zero = int QFlags::Private::*]' is deprecated: Use default constructor instead [-Wdeprecated-declarations] - 38 | DockWidget(const QString& title, QWidget* parent=0, Qt::WindowFlags flags=0); - | ^ + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main_window.hh:35: /usr/include/x86_64-linux-gnu/qt5/QtCore/qflags.h:123:80: note: declared here 123 | QT_DEPRECATED_X("Use default constructor instead") Q_DECL_CONSTEXPR inline QFlags(Zero) noexcept : i(0) {} | ^~~~~~ -/build/openstructure-2.3.1/modules/gui/src/main_window.cc:71:33: warning: 'QVariant qVariantFromValue(const T&) [with T = QDockWidget*]' is deprecated: Use QVariant::fromValue() instead. [-Wdeprecated-declarations] - 71 | act->setData(qVariantFromValue((QDockWidget*)dock)); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/qaction.h:47, - from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/qmenu.h:47, - from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/QMenu:1, - from /build/openstructure-2.3.1/modules/gui/src/main_window.hh:36: -/usr/include/x86_64-linux-gnu/qt5/QtCore/qvariant.h:530:17: note: declared here - 530 | inline QVariant qVariantFromValue(const T &t) - | ^~~~~~~~~~~~~~~~~ -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main.hh:23, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, - from /build/openstructure-2.3.1/modules/gui/src/main.cc:19: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color.hh:31, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/scene.hh:37, - from /build/openstructure-2.3.1/modules/gui/src/gl_canvas.cc:25: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/specfun.h:45, - from /usr/include/c++/12/cmath:1935, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/module_config.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/glwin_base.hh:28, - from /build/openstructure-2.3.1/modules/gui/src/gl_canvas.hh:22: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -[ 78%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_primlist.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_primlist.cc.o -MF CMakeFiles/_ost_gfx.dir/export_primlist.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_primlist.cc.o -c /build/openstructure-2.3.1/modules/gfx/pymod/export_primlist.cc -[ 78%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_non_standard.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_non_standard.cc.o -MF CMakeFiles/_ost_mol_alg.dir/export_non_standard.cc.o.d -o CMakeFiles/_ost_mol_alg.dir/export_non_standard.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/pymod/export_non_standard.cc -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/smart_ptr/weak_ptr.hpp:17, - from /usr/include/boost/smart_ptr/enable_shared_from_this.hpp:16, - from /usr/include/boost/enable_shared_from_this.hpp:16, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_node.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool.hh:29: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/mol/alg/pymod/export_sec_structure.cc:21: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 78%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_scene_observer.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_scene_observer.cc.o -MF CMakeFiles/_ost_gfx.dir/export_scene_observer.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_scene_observer.cc.o -c /build/openstructure-2.3.1/modules/gfx/pymod/export_scene_observer.cc -/build/openstructure-2.3.1/modules/gui/src/gl_canvas.cc: In member function 'void ost::gui::GLCanvas::HandleMouseMoveEvent(QMouseEvent*)': -/build/openstructure-2.3.1/modules/gui/src/gl_canvas.cc:373:32: warning: 'Qt::MidButton' is deprecated: MidButton is deprecated. Use MiddleButton instead [-Wdeprecated-declarations] - 373 | if (event->buttons() & Qt::MidButton) { - | ^~~~~~~~~ -/usr/include/x86_64-linux-gnu/qt5/QtCore/qnamespace.h:132:9: note: declared here - 132 | MidButton Q_DECL_ENUMERATOR_DEPRECATED_X("MidButton is deprecated. Use MiddleButton instead") = MiddleButton, - | ^~~~~~~~~ -/build/openstructure-2.3.1/modules/gui/src/gl_canvas.cc:399:37: warning: 'Qt::MidButton' is deprecated: MidButton is deprecated. Use MiddleButton instead [-Wdeprecated-declarations] - 399 | } else if (event->buttons() & Qt::MidButton) { - | ^~~~~~~~~ -/usr/include/x86_64-linux-gnu/qt5/QtCore/qnamespace.h:132:9: note: declared here - 132 | MidButton Q_DECL_ENUMERATOR_DEPRECATED_X("MidButton is deprecated. Use MiddleButton instead") = MiddleButton, - | ^~~~~~~~~ -/build/openstructure-2.3.1/modules/gui/src/gl_canvas.cc: In member function 'virtual void ost::gui::GLCanvas::wheelEvent(QWheelEvent*)': -/build/openstructure-2.3.1/modules/gui/src/gl_canvas.cc:488:50: warning: 'int QWheelEvent::delta() const' is deprecated: Use angleDelta() [-Wdeprecated-declarations] - 488 | 0.2*static_cast(-event->delta())); - | ~~~~~~~~~~~~^~ -In file included from /usr/include/x86_64-linux-gnu/qt5/QtGui/QMouseEvent:1, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:25: -/usr/include/x86_64-linux-gnu/qt5/QtGui/qevent.h:219:16: note: declared here - 219 | inline int delta() const { return qt4D; } - | ^~~~~ -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/gfx/pymod/export_surface.cc:19: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/mol/alg/pymod/export_accessibility.cc:21: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/sec_struct.hh:25, - from /build/openstructure-2.3.1/modules/mol/alg/pymod/export_sec_structure.cc:24: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/specfun.h:45, - from /usr/include/c++/12/cmath:1935, - from /usr/include/c++/12/math.h:36, - from /usr/include/python3.11/pyport.h:218, - from /usr/include/python3.11/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main.hh:23, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, - from /build/openstructure-2.3.1/modules/gui/src/gl_win.cc:19: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/file_loader.hh:24, - from /build/openstructure-2.3.1/modules/gui/src/main.cc:27: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/specfun.h:45, - from /usr/include/c++/12/cmath:1935, - from /usr/include/c++/12/math.h:36, - from /usr/include/python3.11/pyport.h:218, - from /usr/include/python3.11/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/surface_prop.hh:25, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/surface_handle.hh:24, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/surface.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/surface.hh:31, - from /build/openstructure-2.3.1/modules/gfx/pymod/export_surface.cc:22: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/specfun.h:45, - from /usr/include/c++/12/cmath:1935, - from /usr/include/c++/12/math.h:36, - from /usr/include/python3.11/pyport.h:218, - from /usr/include/python3.11/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, - from /build/openstructure-2.3.1/modules/gui/src/file_browser.cc:23: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/specfun.h:45, - from /usr/include/c++/12/cmath:1935, - from /usr/include/c++/12/math.h:36, - from /usr/include/python3.11/pyport.h:218, - from /usr/include/python3.11/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/file_loader.hh:30: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 32 | : public std::iterator{ - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/accessibility.hh:23, - from /build/openstructure-2.3.1/modules/mol/alg/pymod/export_accessibility.cc:23: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/specfun.h:45, - from /usr/include/c++/12/cmath:1935, - from /usr/include/c++/12/math.h:36, - from /usr/include/python3.11/pyport.h:218, - from /usr/include/python3.11/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main.hh:23, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, - from /build/openstructure-2.3.1/modules/gui/src/scene_menu.cc:19: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool.hh:30, - from /build/openstructure-2.3.1/modules/gui/src/tools/tool_options_win.hh:27, - from /build/openstructure-2.3.1/modules/gui/src/main.cc:31: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:37:22: warning: 'Qt::MidButton' is deprecated: MidButton is deprecated. Use MiddleButton instead [-Wdeprecated-declarations] - 37 | MiddleButton=Qt::MidButton - | ^~~~~~~~~ -In file included from /usr/include/x86_64-linux-gnu/qt5/QtCore/qbytearray.h:45, - from /usr/include/x86_64-linux-gnu/qt5/QtCore/qstring.h:50, - from /usr/include/x86_64-linux-gnu/qt5/QtCore/qdatetime.h:44, - from /usr/include/x86_64-linux-gnu/qt5/QtCore/QTime:1, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/output_redirector.hh:30, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:33: -/usr/include/x86_64-linux-gnu/qt5/QtCore/qnamespace.h:132:9: note: declared here - 132 | MidButton Q_DECL_ENUMERATOR_DEPRECATED_X("MidButton is deprecated. Use MiddleButton instead") = MiddleButton, - | ^~~~~~~~~ -/build/openstructure-2.3.1/modules/gui/src/main.cc: In static member function 'static QSize ost::gui::GostyMainWindow::GetDefaultSize()': -/build/openstructure-2.3.1/modules/gui/src/main.cc:59:64: warning: 'const QRect QDesktopWidget::availableGeometry(int) const' is deprecated: Use QGuiApplication::screens() [-Wdeprecated-declarations] - 59 | QRect desktop_geom=QApplication::desktop()->availableGeometry(); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ -In file included from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/QDesktopWidget:1, - from /build/openstructure-2.3.1/modules/gui/src/main.cc:35: -/usr/include/x86_64-linux-gnu/qt5/QtWidgets/qdesktopwidget.h:88:67: note: declared here - 88 | QT_DEPRECATED_X("Use QGuiApplication::screens()") const QRect availableGeometry(int screen = -1) const; - | ^~~~~~~~~~~~~~~~~ -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/gfx/pymod/export_primitives.cc:19: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main.hh:28: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/widget_state_saver.hh: In instantiation of 'ost::gui::WidgetStateSaver::~WidgetStateSaver() [with BASE = QMainWindow]': -/build/openstructure-2.3.1/modules/gui/src/main.cc:69:69: required from here -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/widget_state_saver.hh:323:8: warning: the address of 'ost::gui::WidgetStateSaver::' will never be NULL [-Waddress] - 323 | if(dynamic_cast(this)){ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/widget_state_saver.hh:263:7: note: 'ost::gui::WidgetStateSaver::' declared here - 263 | class WidgetStateSaver: public BASE - | ^~~~~~~~~~~~~~~~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/widget_state_saver.hh: In instantiation of 'void ost::gui::WidgetStateSaver::set_state_() [with BASE = QMainWindow]': -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/widget_state_saver.hh:286:5: required from 'ost::gui::WidgetStateSaver::WidgetStateSaver(const QString&, QPoint, QSize, QWidget*) [with BASE = QMainWindow]' -/build/openstructure-2.3.1/modules/gui/src/main.cc:69:69: required from here -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/widget_state_saver.hh:305:10: warning: the address of 'ost::gui::WidgetStateSaver::' will never be NULL [-Waddress] - 305 | if(dynamic_cast(this)){ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/widget_state_saver.hh:263:7: note: 'ost::gui::WidgetStateSaver::' declared here - 263 | class WidgetStateSaver: public BASE - | ^~~~~~~~~~~~~~~~~~~~~~ +[ 75%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/gl_canvas.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/gl_canvas.cc.o -MF CMakeFiles/ost_gui.dir/gl_canvas.cc.o.d -o CMakeFiles/ost_gui.dir/gl_canvas.cc.o -c /build/openstructure-2.3.1/modules/gui/src/gl_canvas.cc +[ 75%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/dock_widget.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/dock_widget.cc.o -MF CMakeFiles/ost_gui.dir/dock_widget.cc.o.d -o CMakeFiles/ost_gui.dir/dock_widget.cc.o -c /build/openstructure-2.3.1/modules/gui/src/dock_widget.cc +[ 75%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/main_window.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/main_window.cc.o -MF CMakeFiles/ost_gui.dir/main_window.cc.o.d -o CMakeFiles/ost_gui.dir/main_window.cc.o -c /build/openstructure-2.3.1/modules/gui/src/main_window.cc +[ 75%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/gl_win.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/gl_win.cc.o -MF CMakeFiles/ost_gui.dir/gl_win.cc.o.d -o CMakeFiles/ost_gui.dir/gl_win.cc.o -c /build/openstructure-2.3.1/modules/gui/src/gl_win.cc +[ 75%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_menu.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_menu.cc.o -MF CMakeFiles/ost_gui.dir/scene_menu.cc.o.d -o CMakeFiles/ost_gui.dir/scene_menu.cc.o -c /build/openstructure-2.3.1/modules/gui/src/scene_menu.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/file_loader.hh:30, - from /build/openstructure-2.3.1/modules/gui/src/file_browser.cc:34: + from /build/openstructure-2.3.1/modules/gui/src/file_type_dialog.hh:31, + from /build/openstructure-2.3.1/modules/gui/src/file_type_dialog.cc:19: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/primitives.hh:22, - from /build/openstructure-2.3.1/modules/gfx/pymod/export_primitives.cc:22: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/specfun.h:45, - from /usr/include/c++/12/cmath:1935, - from /usr/include/c++/12/math.h:36, - from /usr/include/python3.11/pyport.h:218, - from /usr/include/python3.11/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -[ 79%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/widget.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/widget.cc.o -MF CMakeFiles/ost_gui.dir/widget.cc.o.d -o CMakeFiles/ost_gui.dir/widget.cc.o -c /build/openstructure-2.3.1/modules/gui/src/widget.cc -/build/openstructure-2.3.1/modules/gui/src/file_browser.cc: In constructor 'ost::gui::FileBrowser::FileBrowser(QWidget*)': -/build/openstructure-2.3.1/modules/gui/src/file_browser.cc:62:13: warning: 'QDirModel::QDirModel(QObject*)' is deprecated: Use QFileSystemModel [-Wdeprecated-declarations] - 62 | model_(new QDirModel), - | ^~~~~~~~~ -In file included from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/QDirModel:1, - from /build/openstructure-2.3.1/modules/gui/src/file_browser.cc:53: -/usr/include/x86_64-linux-gnu/qt5/QtWidgets/qdirmodel.h:73:67: note: declared here - 73 | QT_DEPRECATED_VERSION_X_5_15("Use QFileSystemModel") explicit QDirModel(QObject *parent = nullptr); - | ^~~~~~~~~ -/build/openstructure-2.3.1/modules/gui/src/file_browser.cc: In constructor 'ost::gui::FileBrowser::FileBrowser(const QString&, QWidget*)': -/build/openstructure-2.3.1/modules/gui/src/file_browser.cc:102:13: warning: 'QDirModel::QDirModel(QObject*)' is deprecated: Use QFileSystemModel [-Wdeprecated-declarations] - 102 | model_(new QDirModel), - | ^~~~~~~~~ -/usr/include/x86_64-linux-gnu/qt5/QtWidgets/qdirmodel.h:73:67: note: declared here - 73 | QT_DEPRECATED_VERSION_X_5_15("Use QFileSystemModel") explicit QDirModel(QObject *parent = nullptr); - | ^~~~~~~~~ -[ 79%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_render_options.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_render_options.cc.o -MF CMakeFiles/_ost_gfx.dir/export_render_options.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_render_options.cc.o -c /build/openstructure-2.3.1/modules/gfx/pymod/export_render_options.cc -[ 79%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/admin.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/admin.cc.o -MF CMakeFiles/ost_gui.dir/admin.cc.o.d -o CMakeFiles/ost_gui.dir/admin.cc.o -c /build/openstructure-2.3.1/modules/gui/src/admin.cc -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color.hh:31, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/scene.hh:37, - from /build/openstructure-2.3.1/modules/gui/src/gl_win.cc:22: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, - from /usr/include/c++/12/math.h:36, - from /usr/include/python3.11/pyport.h:218, - from /usr/include/python3.11/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool.hh:30, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/gl_canvas.hh:23, - from /build/openstructure-2.3.1/modules/gui/src/gl_win.cc:25: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:37:22: warning: 'Qt::MidButton' is deprecated: MidButton is deprecated. Use MiddleButton instead [-Wdeprecated-declarations] - 37 | MiddleButton=Qt::MidButton - | ^~~~~~~~~ -In file included from /usr/include/x86_64-linux-gnu/qt5/QtCore/qbytearray.h:45, - from /usr/include/x86_64-linux-gnu/qt5/QtCore/qstring.h:50, - from /usr/include/x86_64-linux-gnu/qt5/QtCore/qdatetime.h:44, - from /usr/include/x86_64-linux-gnu/qt5/QtCore/QTime:1, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/output_redirector.hh:30, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:33: -/usr/include/x86_64-linux-gnu/qt5/QtCore/qnamespace.h:132:9: note: declared here - 132 | MidButton Q_DECL_ENUMERATOR_DEPRECATED_X("MidButton is deprecated. Use MiddleButton instead") = MiddleButton, - | ^~~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/view_op.hh:29, - from /build/openstructure-2.3.1/modules/gui/src/scene_menu.cc:21: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/specfun.h:45, - from /usr/include/c++/12/cmath:1935, - from /usr/include/c++/12/math.h:36, - from /usr/include/python3.11/pyport.h:218, - from /usr/include/python3.11/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -[ 79%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/widget_pool.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/widget_pool.cc.o -MF CMakeFiles/ost_gui.dir/widget_pool.cc.o.d -o CMakeFiles/ost_gui.dir/widget_pool.cc.o -c /build/openstructure-2.3.1/modules/gui/src/widget_pool.cc -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/gfx/pymod/export_scene_observer.cc:1: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/mol/alg/pymod/export_non_standard.cc:19: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 79%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_molck.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_molck.cc.o -MF CMakeFiles/_ost_mol_alg.dir/export_molck.cc.o.d -o CMakeFiles/_ost_mol_alg.dir/export_molck.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/pymod/export_molck.cc -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/gfx/pymod/export_primlist.cc:19: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 79%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/messages/message_widget.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/messages/message_widget.cc.o -MF CMakeFiles/ost_gui.dir/messages/message_widget.cc.o.d -o CMakeFiles/ost_gui.dir/messages/message_widget.cc.o -c /build/openstructure-2.3.1/modules/gui/src/messages/message_widget.cc -[ 79%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/messages/message_box_widget.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/messages/message_box_widget.cc.o -MF CMakeFiles/ost_gui.dir/messages/message_box_widget.cc.o.d -o CMakeFiles/ost_gui.dir/messages/message_box_widget.cc.o -c /build/openstructure-2.3.1/modules/gui/src/messages/message_box_widget.cc + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/module_config.hh:26, + from /build/openstructure-2.3.1/modules/gui/src/file_type_dialog.hh:26: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, - from /build/openstructure-2.3.1/modules/mol/alg/pymod/export_non_standard.cc:20: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/file_browser.hh:23, + from /build/openstructure-2.3.1/modules/gui/src/perspective.cc:26: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, - from /usr/include/c++/12/math.h:36, - from /usr/include/python3.11/pyport.h:218, - from /usr/include/python3.11/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/module_config.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/platform.hh:22, + from /build/openstructure-2.3.1/modules/gui/src/perspective.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -21694,20 +20469,14 @@ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/prim_list.hh:28, - from /build/openstructure-2.3.1/modules/gfx/pymod/export_primlist.cc:25: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/specfun.h:45, - from /usr/include/c++/12/cmath:1935, - from /usr/include/c++/12/math.h:36, - from /usr/include/python3.11/pyport.h:218, - from /usr/include/python3.11/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -21717,62 +20486,72 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 79%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_color.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_color.cc.o -MF CMakeFiles/_ost_gfx.dir/export_color.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_color.cc.o -c /build/openstructure-2.3.1/modules/gfx/pymod/export_color.cc -[ 79%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/messages/log_reader.cc.o +[ 76%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/widget.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/widget.cc.o -MF CMakeFiles/ost_gui.dir/widget.cc.o.d -o CMakeFiles/ost_gui.dir/widget.cc.o -c /build/openstructure-2.3.1/modules/gui/src/widget.cc +[ 76%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/admin.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/admin.cc.o -MF CMakeFiles/ost_gui.dir/admin.cc.o.d -o CMakeFiles/ost_gui.dir/admin.cc.o -c /build/openstructure-2.3.1/modules/gui/src/admin.cc +[ 76%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_symmetry_node.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_symmetry_node.cc.o -MF CMakeFiles/_ost_gfx.dir/export_symmetry_node.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_symmetry_node.cc.o -c /build/openstructure-2.3.1/modules/gfx/pymod/export_symmetry_node.cc +In file included from /build/openstructure-2.3.1/modules/gui/src/dock_widget.cc:25: +/build/openstructure-2.3.1/modules/gui/src/dock_widget.hh:38:77: warning: 'constexpr QFlags::QFlags(Zero) [with Enum = Qt::WindowType; Zero = int QFlags::Private::*]' is deprecated: Use default constructor instead [-Wdeprecated-declarations] + 38 | DockWidget(const QString& title, QWidget* parent=0, Qt::WindowFlags flags=0); + | ^ +In file included from /usr/include/x86_64-linux-gnu/qt5/QtCore/qglobal.h:1305, + from /usr/include/x86_64-linux-gnu/qt5/QtGui/qtguiglobal.h:43, + from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/qtwidgetsglobal.h:43, + from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/qdockwidget.h:43, + from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/QDockWidget:1, + from /build/openstructure-2.3.1/modules/gui/src/dock_widget.hh:31: +/usr/include/x86_64-linux-gnu/qt5/QtCore/qflags.h:123:80: note: declared here + 123 | QT_DEPRECATED_X("Use default constructor instead") Q_DECL_CONSTEXPR inline QFlags(Zero) noexcept : i(0) {} + | ^~~~~~ +In file included from /build/openstructure-2.3.1/modules/gui/src/main_window.cc:25: +/build/openstructure-2.3.1/modules/gui/src/main_window.hh:46:55: warning: 'constexpr QFlags::QFlags(Zero) [with Enum = Qt::WindowType; Zero = int QFlags::Private::*]' is deprecated: Use default constructor instead [-Wdeprecated-declarations] + 46 | MainWindow(QWidget* parent=0, Qt::WindowFlags flags=0); + | ^ +In file included from /usr/include/x86_64-linux-gnu/qt5/QtCore/qglobal.h:1305, + from /usr/include/x86_64-linux-gnu/qt5/QtGui/qtguiglobal.h:43, + from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/qtwidgetsglobal.h:43, + from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/qmainwindow.h:43, + from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/QMainWindow:1, + from /build/openstructure-2.3.1/modules/gui/src/main_window.hh:35: +/usr/include/x86_64-linux-gnu/qt5/QtCore/qflags.h:123:80: note: declared here + 123 | QT_DEPRECATED_X("Use default constructor instead") Q_DECL_CONSTEXPR inline QFlags(Zero) noexcept : i(0) {} + | ^~~~~~ +In file included from /build/openstructure-2.3.1/modules/gui/src/main_window.cc:26: +/build/openstructure-2.3.1/modules/gui/src/dock_widget.hh:38:77: warning: 'constexpr QFlags::QFlags(Zero) [with Enum = Qt::WindowType; Zero = int QFlags::Private::*]' is deprecated: Use default constructor instead [-Wdeprecated-declarations] + 38 | DockWidget(const QString& title, QWidget* parent=0, Qt::WindowFlags flags=0); + | ^ +/usr/include/x86_64-linux-gnu/qt5/QtCore/qflags.h:123:80: note: declared here + 123 | QT_DEPRECATED_X("Use default constructor instead") Q_DECL_CONSTEXPR inline QFlags(Zero) noexcept : i(0) {} + | ^~~~~~ +/build/openstructure-2.3.1/modules/gui/src/dock_widget.hh: In member function 'void ost::gui::MainWindow::AddDockWidget(QWidget*, const QString&, bool, int)': +/build/openstructure-2.3.1/modules/gui/src/dock_widget.hh:38:77: warning: 'constexpr QFlags::QFlags(Zero) [with Enum = Qt::WindowType; Zero = int QFlags::Private::*]' is deprecated: Use default constructor instead [-Wdeprecated-declarations] + 38 | DockWidget(const QString& title, QWidget* parent=0, Qt::WindowFlags flags=0); + | ^ +/usr/include/x86_64-linux-gnu/qt5/QtCore/qflags.h:123:80: note: declared here + 123 | QT_DEPRECATED_X("Use default constructor instead") Q_DECL_CONSTEXPR inline QFlags(Zero) noexcept : i(0) {} + | ^~~~~~ +/build/openstructure-2.3.1/modules/gui/src/main_window.cc:71:33: warning: 'QVariant qVariantFromValue(const T&) [with T = QDockWidget*]' is deprecated: Use QVariant::fromValue() instead. [-Wdeprecated-declarations] + 71 | act->setData(qVariantFromValue((QDockWidget*)dock)); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/qaction.h:47, + from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/qmenu.h:47, + from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/QMenu:1, + from /build/openstructure-2.3.1/modules/gui/src/main_window.hh:36: +/usr/include/x86_64-linux-gnu/qt5/QtCore/qvariant.h:530:17: note: declared here + 530 | inline QVariant qVariantFromValue(const T &t) + | ^~~~~~~~~~~~~~~~~ +[ 76%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/widget_pool.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/widget_pool.cc.o -MF CMakeFiles/ost_gui.dir/widget_pool.cc.o.d -o CMakeFiles/ost_gui.dir/widget_pool.cc.o -c /build/openstructure-2.3.1/modules/gui/src/widget_pool.cc +[ 76%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/messages/message_widget.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/messages/message_widget.cc.o -MF CMakeFiles/ost_gui.dir/messages/message_widget.cc.o.d -o CMakeFiles/ost_gui.dir/messages/message_widget.cc.o -c /build/openstructure-2.3.1/modules/gui/src/messages/message_widget.cc +[ 76%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/messages/message_box_widget.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/messages/message_box_widget.cc.o -MF CMakeFiles/ost_gui.dir/messages/message_box_widget.cc.o.d -o CMakeFiles/ost_gui.dir/messages/message_box_widget.cc.o -c /build/openstructure-2.3.1/modules/gui/src/messages/message_box_widget.cc +[ 76%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/messages/log_reader.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/messages/log_reader.cc.o -MF CMakeFiles/ost_gui.dir/messages/log_reader.cc.o.d -o CMakeFiles/ost_gui.dir/messages/log_reader.cc.o -c /build/openstructure-2.3.1/modules/gui/src/messages/log_reader.cc -[ 79%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_membrane.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_membrane.cc.o -MF CMakeFiles/_ost_mol_alg.dir/export_membrane.cc.o.d -o CMakeFiles/_ost_mol_alg.dir/export_membrane.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/pymod/export_membrane.cc -[ 79%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_entity_to_density.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_entity_to_density.cc.o -MF CMakeFiles/_ost_mol_alg.dir/export_entity_to_density.cc.o.d -o CMakeFiles/_ost_mol_alg.dir/export_entity_to_density.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/pymod/export_entity_to_density.cc -[ 79%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_gradient.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_gradient.cc.o -MF CMakeFiles/_ost_gfx.dir/export_gradient.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_gradient.cc.o -c /build/openstructure-2.3.1/modules/gfx/pymod/export_gradient.cc -[ 79%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/align_properties_painter.cc.o +[ 76%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/align_properties_painter.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/align_properties_painter.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/align_properties_painter.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/align_properties_painter.cc.o -c /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/align_properties_painter.cc -[ 79%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_color_ops.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_color_ops.cc.o -MF CMakeFiles/_ost_gfx.dir/export_color_ops.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_color_ops.cc.o -c /build/openstructure-2.3.1/modules/gfx/pymod/export_color_ops.cc -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/gfx/pymod/export_render_options.cc:19: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 79%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_glwin_base.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_glwin_base.cc.o -MF CMakeFiles/_ost_gfx.dir/export_glwin_base.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_glwin_base.cc.o -c /build/openstructure-2.3.1/modules/gfx/pymod/export_glwin_base.cc -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/mol/alg/pymod/export_molck.cc:20: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -21791,36 +20570,13 @@ from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, - from /build/openstructure-2.3.1/modules/gui/src/messages/message_widget.cc:23: + from /build/openstructure-2.3.1/modules/gui/src/file_browser.cc:20: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/molck.hh:23, - from /build/openstructure-2.3.1/modules/mol/alg/pymod/export_molck.cc:25: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/12/string:45, - from /usr/include/c++/12/stdexcept:39, - from /build/openstructure-2.3.1/modules/mol/alg/pymod/export_molck.cc:19: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -21834,34 +20590,42 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/mol/alg/pymod/export_membrane.cc:21: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main.hh:23, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, + from /build/openstructure-2.3.1/modules/gui/src/main.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 80%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_exporter.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_exporter.cc.o -MF CMakeFiles/_ost_gfx.dir/export_exporter.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_exporter.cc.o -c /build/openstructure-2.3.1/modules/gfx/pymod/export_exporter.cc +[ 76%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/base_row.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/base_row.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/base_row.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/base_row.cc.o -c /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/base_row.cc +[ 76%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/background_painter.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/background_painter.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/background_painter.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/background_painter.cc.o -c /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/background_painter.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, - from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/painter.hh:27, - from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/align_properties_painter.hh:27, - from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/align_properties_painter.cc:26: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, + from /build/openstructure-2.3.1/modules/gui/src/file_browser.cc:23: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: + from /usr/include/c++/12/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -21871,6 +20635,18 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool.hh:30, + from /build/openstructure-2.3.1/modules/gui/src/gl_canvas.hh:23, + from /build/openstructure-2.3.1/modules/gui/src/gl_canvas.cc:22: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:37:22: warning: 'Qt::MidButton' is deprecated: MidButton is deprecated. Use MiddleButton instead [-Wdeprecated-declarations] + 37 | MiddleButton=Qt::MidButton + | ^~~~~~~~~ +In file included from /usr/include/x86_64-linux-gnu/qt5/QtCore/qpoint.h:43, + from /usr/include/x86_64-linux-gnu/qt5/QtCore/QPoint:1, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:24: +/usr/include/x86_64-linux-gnu/qt5/QtCore/qnamespace.h:132:9: note: declared here + 132 | MidButton Q_DECL_ENUMERATOR_DEPRECATED_X("MidButton is deprecated. Use MiddleButton instead") = MiddleButton, + | ^~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -21889,7 +20665,7 @@ from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, - from /build/openstructure-2.3.1/modules/gui/src/messages/message_box_widget.cc:23: + from /build/openstructure-2.3.1/modules/gui/src/scene_menu.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ @@ -21909,34 +20685,47 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/gfx/pymod/export_color.cc:19: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main.hh:23, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, + from /build/openstructure-2.3.1/modules/gui/src/gl_win.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/file_loader.hh:30, + from /build/openstructure-2.3.1/modules/gui/src/file_browser.cc:34: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 32 | : public std::iterator{ + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/find_membrane.hh:22, - from /build/openstructure-2.3.1/modules/mol/alg/pymod/export_membrane.cc:23: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, + from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/painter.hh:27, + from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/align_properties_painter.hh:27, + from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/align_properties_painter.cc:26: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, - from /usr/include/c++/12/math.h:36, - from /usr/include/python3.11/pyport.h:218, - from /usr/include/python3.11/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -21946,28 +20735,6 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 80%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/base_row.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/base_row.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/base_row.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/base_row.cc.o -c /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/base_row.cc -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/mol/alg/pymod/export_entity_to_density.cc:23: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -21981,18 +20748,36 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/gfx/pymod/export_gradient.cc:24: + from /build/openstructure-2.3.1/modules/gfx/pymod/export_symmetry_node.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +/build/openstructure-2.3.1/modules/gui/src/file_browser.cc: In constructor 'ost::gui::FileBrowser::FileBrowser(QWidget*)': +/build/openstructure-2.3.1/modules/gui/src/file_browser.cc:62:13: warning: 'QDirModel::QDirModel(QObject*)' is deprecated: Use QFileSystemModel [-Wdeprecated-declarations] + 62 | model_(new QDirModel), + | ^~~~~~~~~ +In file included from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/QDirModel:1, + from /build/openstructure-2.3.1/modules/gui/src/file_browser.cc:53: +/usr/include/x86_64-linux-gnu/qt5/QtWidgets/qdirmodel.h:73:67: note: declared here + 73 | QT_DEPRECATED_VERSION_X_5_15("Use QFileSystemModel") explicit QDirModel(QObject *parent = nullptr); + | ^~~~~~~~~ +/build/openstructure-2.3.1/modules/gui/src/file_browser.cc: In constructor 'ost::gui::FileBrowser::FileBrowser(const QString&, QWidget*)': +/build/openstructure-2.3.1/modules/gui/src/file_browser.cc:102:13: warning: 'QDirModel::QDirModel(QObject*)' is deprecated: Use QFileSystemModel [-Wdeprecated-declarations] + 102 | model_(new QDirModel), + | ^~~~~~~~~ +/usr/include/x86_64-linux-gnu/qt5/QtWidgets/qdirmodel.h:73:67: note: declared here + 73 | QT_DEPRECATED_VERSION_X_5_15("Use QFileSystemModel") explicit QDirModel(QObject *parent = nullptr); + | ^~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color.hh:31, - from /build/openstructure-2.3.1/modules/gfx/pymod/export_color.cc:23: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/file_loader.hh:24, + from /build/openstructure-2.3.1/modules/gui/src/main.cc:27: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -22014,46 +20799,52 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/gfx/pymod/export_color_ops.cc:19: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color.hh:31, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/scene.hh:37, + from /build/openstructure-2.3.1/modules/gui/src/gl_canvas.cc:25: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/bits/specfun.h:45, + from /usr/include/c++/12/cmath:1935, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/module_config.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/glwin_base.hh:28, + from /build/openstructure-2.3.1/modules/gui/src/gl_canvas.hh:22: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 76%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/conservation_painter.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/conservation_painter.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/conservation_painter.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/conservation_painter.cc.o -c /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/conservation_painter.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/entity_to_density.hh:4, - from /build/openstructure-2.3.1/modules/mol/alg/pymod/export_entity_to_density.cc:26: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, + from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/painter.hh:27, + from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/base_row.hh:27, + from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/base_row.cc:26: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, - from /usr/include/c++/12/math.h:36, - from /usr/include/python3.11/pyport.h:218, - from /usr/include/python3.11/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -22063,12 +20854,20 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/file_loader.hh:30: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 32 | : public std::iterator{ + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color.hh:31, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gradient.hh:28, - from /build/openstructure-2.3.1/modules/gfx/pymod/export_gradient.cc:29: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/symmetry_node.hh:22, + from /build/openstructure-2.3.1/modules/gfx/pymod/export_symmetry_node.cc:23: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -22090,6 +20889,72 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 76%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/secstr_row.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/secstr_row.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/secstr_row.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/secstr_row.cc.o -c /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/secstr_row.cc +[ 78%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_gfx_obj.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_gfx_obj.cc.o -MF CMakeFiles/_ost_gfx.dir/export_gfx_obj.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_gfx_obj.cc.o -c /build/openstructure-2.3.1/modules/gfx/pymod/export_gfx_obj.cc +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, + from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/painter.hh:27, + from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/background_painter.hh:27, + from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/background_painter.cc:26: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/bits/specfun.h:45, + from /usr/include/c++/12/cmath:1935, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/smart_ptr/weak_ptr.hpp:17, + from /usr/include/boost/smart_ptr/enable_shared_from_this.hpp:16, + from /usr/include/boost/enable_shared_from_this.hpp:16, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_node.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool.hh:29: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool.hh:30, + from /build/openstructure-2.3.1/modules/gui/src/tools/tool_options_win.hh:27, + from /build/openstructure-2.3.1/modules/gui/src/main.cc:31: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:37:22: warning: 'Qt::MidButton' is deprecated: MidButton is deprecated. Use MiddleButton instead [-Wdeprecated-declarations] + 37 | MiddleButton=Qt::MidButton + | ^~~~~~~~~ +In file included from /usr/include/x86_64-linux-gnu/qt5/QtCore/qbytearray.h:45, + from /usr/include/x86_64-linux-gnu/qt5/QtCore/qstring.h:50, + from /usr/include/x86_64-linux-gnu/qt5/QtCore/qdatetime.h:44, + from /usr/include/x86_64-linux-gnu/qt5/QtCore/QTime:1, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/output_redirector.hh:30, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:33: +/usr/include/x86_64-linux-gnu/qt5/QtCore/qnamespace.h:132:9: note: declared here + 132 | MidButton Q_DECL_ENUMERATOR_DEPRECATED_X("MidButton is deprecated. Use MiddleButton instead") = MiddleButton, + | ^~~~~~~~~ +[ 79%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/seq_secstr_painter.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/seq_secstr_painter.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/seq_secstr_painter.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/seq_secstr_painter.cc.o -c /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/seq_secstr_painter.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -22103,24 +20968,35 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/gfx/pymod/export_glwin_base.cc:19: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main.hh:23, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, + from /build/openstructure-2.3.1/modules/gui/src/messages/message_box_widget.cc:23: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ +/build/openstructure-2.3.1/modules/gui/src/main.cc: In static member function 'static QSize ost::gui::GostyMainWindow::GetDefaultSize()': +/build/openstructure-2.3.1/modules/gui/src/main.cc:59:64: warning: 'const QRect QDesktopWidget::availableGeometry(int) const' is deprecated: Use QGuiApplication::screens() [-Wdeprecated-declarations] + 59 | QRect desktop_geom=QApplication::desktop()->availableGeometry(); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ +In file included from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/QDesktopWidget:1, + from /build/openstructure-2.3.1/modules/gui/src/main.cc:35: +/usr/include/x86_64-linux-gnu/qt5/QtWidgets/qdesktopwidget.h:88:67: note: declared here + 88 | QT_DEPRECATED_X("Use QGuiApplication::screens()") const QRect availableGeometry(int screen = -1) const; + | ^~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 80%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/background_painter.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/background_painter.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/background_painter.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/background_painter.cc.o -c /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/background_painter.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/color_op.hh:24, - from /build/openstructure-2.3.1/modules/gfx/pymod/export_color_ops.cc:23: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/view_op.hh:29, + from /build/openstructure-2.3.1/modules/gui/src/scene_menu.cc:21: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -22142,16 +21018,6 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 80%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/conservation_painter.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/conservation_painter.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/conservation_painter.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/conservation_painter.cc.o -c /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/conservation_painter.cc -[ 80%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/secstr_row.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/secstr_row.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/secstr_row.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/secstr_row.cc.o -c /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/secstr_row.cc -[ 82%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/seq_secstr_painter.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/seq_secstr_painter.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/seq_secstr_painter.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/seq_secstr_painter.cc.o -c /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/seq_secstr_painter.cc -[ 82%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_bitmap.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_bitmap.cc.o -MF CMakeFiles/_ost_gfx.dir/export_bitmap.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_bitmap.cc.o -c /build/openstructure-2.3.1/modules/gfx/pymod/export_bitmap.cc -[ 82%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_map.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_map.cc.o -MF CMakeFiles/_ost_gfx.dir/export_map.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_map.cc.o -c /build/openstructure-2.3.1/modules/gfx/pymod/export_map.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -22165,34 +21031,76 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/gfx/pymod/export_exporter.cc:19: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main.hh:23, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, + from /build/openstructure-2.3.1/modules/gui/src/messages/message_widget.cc:23: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 82%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/seq_selection_painter.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/seq_selection_painter.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/seq_selection_painter.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/seq_selection_painter.cc.o -c /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/seq_selection_painter.cc +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main.hh:28: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/widget_state_saver.hh: In instantiation of 'ost::gui::WidgetStateSaver::~WidgetStateSaver() [with BASE = QMainWindow]': +/build/openstructure-2.3.1/modules/gui/src/main.cc:69:69: required from here +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/widget_state_saver.hh:323:8: warning: the address of 'ost::gui::WidgetStateSaver::' will never be NULL [-Waddress] + 323 | if(dynamic_cast(this)){ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/widget_state_saver.hh:263:7: note: 'ost::gui::WidgetStateSaver::' declared here + 263 | class WidgetStateSaver: public BASE + | ^~~~~~~~~~~~~~~~~~~~~~ +/build/openstructure-2.3.1/modules/gui/src/gl_canvas.cc: In member function 'void ost::gui::GLCanvas::HandleMouseMoveEvent(QMouseEvent*)': +/build/openstructure-2.3.1/modules/gui/src/gl_canvas.cc:373:32: warning: 'Qt::MidButton' is deprecated: MidButton is deprecated. Use MiddleButton instead [-Wdeprecated-declarations] + 373 | if (event->buttons() & Qt::MidButton) { + | ^~~~~~~~~ +/usr/include/x86_64-linux-gnu/qt5/QtCore/qnamespace.h:132:9: note: declared here + 132 | MidButton Q_DECL_ENUMERATOR_DEPRECATED_X("MidButton is deprecated. Use MiddleButton instead") = MiddleButton, + | ^~~~~~~~~ +/build/openstructure-2.3.1/modules/gui/src/gl_canvas.cc:399:37: warning: 'Qt::MidButton' is deprecated: MidButton is deprecated. Use MiddleButton instead [-Wdeprecated-declarations] + 399 | } else if (event->buttons() & Qt::MidButton) { + | ^~~~~~~~~ +/usr/include/x86_64-linux-gnu/qt5/QtCore/qnamespace.h:132:9: note: declared here + 132 | MidButton Q_DECL_ENUMERATOR_DEPRECATED_X("MidButton is deprecated. Use MiddleButton instead") = MiddleButton, + | ^~~~~~~~~ +/build/openstructure-2.3.1/modules/gui/src/gl_canvas.cc: In member function 'virtual void ost::gui::GLCanvas::wheelEvent(QWheelEvent*)': +/build/openstructure-2.3.1/modules/gui/src/gl_canvas.cc:488:50: warning: 'int QWheelEvent::delta() const' is deprecated: Use angleDelta() [-Wdeprecated-declarations] + 488 | 0.2*static_cast(-event->delta())); + | ~~~~~~~~~~~~^~ +In file included from /usr/include/x86_64-linux-gnu/qt5/QtGui/QMouseEvent:1, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:25: +/usr/include/x86_64-linux-gnu/qt5/QtGui/qevent.h:219:16: note: declared here + 219 | inline int delta() const { return qt4D; } + | ^~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/widget_state_saver.hh: In instantiation of 'void ost::gui::WidgetStateSaver::set_state_() [with BASE = QMainWindow]': +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/widget_state_saver.hh:286:5: required from 'ost::gui::WidgetStateSaver::WidgetStateSaver(const QString&, QPoint, QSize, QWidget*) [with BASE = QMainWindow]' +/build/openstructure-2.3.1/modules/gui/src/main.cc:69:69: required from here +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/widget_state_saver.hh:305:10: warning: the address of 'ost::gui::WidgetStateSaver::' will never be NULL [-Waddress] + 305 | if(dynamic_cast(this)){ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/widget_state_saver.hh:263:7: note: 'ost::gui::WidgetStateSaver::' declared here + 263 | class WidgetStateSaver: public BASE + | ^~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, - from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/painter.hh:27, - from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/base_row.hh:27, - from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/base_row.cc:26: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color.hh:31, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/scene.hh:37, + from /build/openstructure-2.3.1/modules/gui/src/gl_win.cc:22: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: + from /usr/include/c++/12/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -22202,6 +21110,23 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool.hh:30, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/gl_canvas.hh:23, + from /build/openstructure-2.3.1/modules/gui/src/gl_win.cc:25: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:37:22: warning: 'Qt::MidButton' is deprecated: MidButton is deprecated. Use MiddleButton instead [-Wdeprecated-declarations] + 37 | MiddleButton=Qt::MidButton + | ^~~~~~~~~ +In file included from /usr/include/x86_64-linux-gnu/qt5/QtCore/qbytearray.h:45, + from /usr/include/x86_64-linux-gnu/qt5/QtCore/qstring.h:50, + from /usr/include/x86_64-linux-gnu/qt5/QtCore/qdatetime.h:44, + from /usr/include/x86_64-linux-gnu/qt5/QtCore/QTime:1, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/output_redirector.hh:30, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:33: +/usr/include/x86_64-linux-gnu/qt5/QtCore/qnamespace.h:132:9: note: declared here + 132 | MidButton Q_DECL_ENUMERATOR_DEPRECATED_X("MidButton is deprecated. Use MiddleButton instead") = MiddleButton, + | ^~~~~~~~~ +[ 79%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/seq_selection_painter.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/seq_selection_painter.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/seq_selection_painter.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/seq_selection_painter.cc.o -c /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/seq_selection_painter.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -22210,8 +21135,8 @@ from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/painter.hh:27, - from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/background_painter.hh:27, - from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/background_painter.cc:26: + from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/conservation_painter.hh:27, + from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/conservation_painter.cc:26: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -22230,6 +21155,12 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 79%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/seq_text_painter.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/seq_text_painter.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/seq_text_painter.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/seq_text_painter.cc.o -c /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/seq_text_painter.cc +[ 79%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_delegate.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_delegate.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/sequence_delegate.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/sequence_delegate.cc.o -c /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_delegate.cc +[ 79%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_model.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_model.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/sequence_model.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/sequence_model.cc.o -c /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_model.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -22258,38 +21189,10 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, - from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/painter.hh:27, - from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/conservation_painter.hh:27, - from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/conservation_painter.cc:26: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/specfun.h:45, - from /usr/include/c++/12/cmath:1935, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -[ 82%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/seq_text_painter.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/seq_text_painter.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/seq_text_painter.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/seq_text_painter.cc.o -c /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/seq_text_painter.cc -[ 82%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_delegate.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_delegate.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/sequence_delegate.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/sequence_delegate.cc.o -c /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_delegate.cc +[ 79%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_row.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_row.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/sequence_row.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/sequence_row.cc.o -c /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_row.cc +[ 79%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_search_bar.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_search_bar.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/sequence_search_bar.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/sequence_search_bar.cc.o -c /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_search_bar.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -22316,6 +21219,8 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 79%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_table_view.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_table_view.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/sequence_table_view.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/sequence_table_view.cc.o -c /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_table_view.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -22344,12 +21249,8 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 82%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_model.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_model.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/sequence_model.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/sequence_model.cc.o -c /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_model.cc -[ 82%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_row.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_row.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/sequence_row.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/sequence_row.cc.o -c /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_row.cc -[ 82%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_search_bar.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_search_bar.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/sequence_search_bar.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/sequence_search_bar.cc.o -c /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_search_bar.cc +[ 79%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_viewer.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_viewer.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/sequence_viewer.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/sequence_viewer.cc.o -c /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_viewer.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -22363,7 +21264,7 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/gfx/pymod/export_bitmap.cc:19: + from /build/openstructure-2.3.1/modules/gfx/pymod/export_gfx_obj.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ @@ -22398,42 +21299,24 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/gfx/pymod/export_map.cc:19: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/chain_view.hh:23, - from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_model.hh:28, - from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_delegate.hh:28, - from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_delegate.cc:25: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, + from /build/openstructure-2.3.1/modules/gfx/pymod/export_gfx_obj.cc:22: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/chain_view.hh:22: + from /usr/include/c++/12/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -22443,16 +21326,8 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 82%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_table_view.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_table_view.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/sequence_table_view.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/sequence_table_view.cc.o -c /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_table_view.cc -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, - from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_model.hh:30: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 32 | : public std::iterator{ - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ +[ 79%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/tick_painter.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/tick_painter.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/tick_painter.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/tick_painter.cc.o -c /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/tick_painter.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -22475,33 +21350,38 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 32 | : public std::iterator{ + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 79%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/title_row.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/title_row.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/title_row.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/title_row.cc.o -c /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/title_row.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/map.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/map_iso.hh:28, - from /build/openstructure-2.3.1/modules/gfx/pymod/export_map.cc:23: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/chain_view.hh:23, + from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_model.hh:28, + from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_delegate.hh:28, + from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_delegate.cc:25: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, - from /usr/include/c++/12/math.h:36, - from /usr/include/python3.11/pyport.h:218, - from /usr/include/python3.11/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/chain_view.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -22512,19 +21392,13 @@ 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: + from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_model.hh:30: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 82%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_viewer.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_viewer.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/sequence_viewer.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/sequence_viewer.cc.o -c /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_viewer.cc -[ 82%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/tick_painter.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/tick_painter.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/tick_painter.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/tick_painter.cc.o -c /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/tick_painter.cc -[ 82%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/title_row.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/title_row.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/title_row.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/title_row.cc.o -c /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/title_row.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -22551,17 +21425,6 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 83%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/alignment_view_object.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/alignment_view_object.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/alignment_view_object.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/alignment_view_object.cc.o -c /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/alignment_view_object.cc -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, - from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_view_object.hh:32, - from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_row.cc:31: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 32 | : public std::iterator{ - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -22591,6 +21454,8 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 79%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_entity.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_entity.cc.o -MF CMakeFiles/_ost_gfx.dir/export_entity.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_entity.cc.o -c /build/openstructure-2.3.1/modules/gfx/pymod/export_entity.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -22618,37 +21483,26 @@ 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, - from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_model.hh:30: + from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_view_object.hh:32, + from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_row.cc:31: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/chain_view.hh:23, - from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_model.hh:28, - from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/title_row.cc:26: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/specfun.h:45, - from /usr/include/c++/12/cmath:1935, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/chain_view.hh:22: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, + from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_model.hh:30: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 32 | : public std::iterator{ + | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 80%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/alignment_view_object.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/alignment_view_object.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/alignment_view_object.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/alignment_view_object.cc.o -c /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/alignment_view_object.cc +[ 80%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/base_view_object.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/base_view_object.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/base_view_object.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/base_view_object.cc.o -c /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/base_view_object.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_model.hh:30, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_model.cc:30: @@ -22658,16 +21512,12 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 83%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/base_view_object.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/base_view_object.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/base_view_object.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/base_view_object.cc.o -c /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/base_view_object.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, - from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/alignment_view_object.cc:26: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/chain_view.hh:23, + from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_model.hh:28, + from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/title_row.cc:26: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -22676,7 +21526,7 @@ from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/chain_view.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -22686,28 +21536,9 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 83%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_view_object.cc.o +[ 80%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_view_object.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_view_object.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/sequence_view_object.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/sequence_view_object.cc.o -c /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_view_object.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_region.hh:26, - from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/alignment_view_object.cc:29: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 32 | : public std::iterator{ - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_region.hh:27: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_column_iterator.hh:29:43: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 29 | class AlignedColumnIterator : public std::iterator struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ @@ -22715,8 +21546,33 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 83%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/main_area.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/main_area.cc.o -MF CMakeFiles/ost_gui.dir/main_area.cc.o.d -o CMakeFiles/ost_gui.dir/main_area.cc.o -c /build/openstructure-2.3.1/modules/gui/src/main_area.cc +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main.hh:23, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, + from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_viewer.cc:23: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 80%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/gosty_app.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/gosty_app.cc.o -MF CMakeFiles/ost_gui.dir/gosty_app.cc.o.d -o CMakeFiles/ost_gui.dir/gosty_app.cc.o -c /build/openstructure-2.3.1/modules/gui/src/gosty_app.cc /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_table_view.cc: In member function 'virtual int ost::gui::SequenceTableView::sizeHintForColumn(int) const': /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_table_view.cc:480:35: warning: 'int QFontMetrics::width(QChar) const' is deprecated: Use QFontMetrics::horizontalAdvance [-Wdeprecated-declarations] 480 | return this->fontMetrics().width('W'); @@ -22730,10 +21586,6 @@ /usr/include/x86_64-linux-gnu/qt5/QtGui/qfontmetrics.h:110:9: note: declared here 110 | int width(QChar) const; | ^~~~~ -[ 83%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/widget_state_saver.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/widget_state_saver.cc.o -MF CMakeFiles/ost_gui.dir/widget_state_saver.cc.o.d -o CMakeFiles/ost_gui.dir/widget_state_saver.cc.o -c /build/openstructure-2.3.1/modules/gui/src/widget_state_saver.cc -[ 83%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_selection.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_selection.cc.o -MF CMakeFiles/ost_gui.dir/scene_selection.cc.o.d -o CMakeFiles/ost_gui.dir/scene_selection.cc.o -c /build/openstructure-2.3.1/modules/gui/src/scene_selection.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -22763,31 +21615,10 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main.hh:23, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, - from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_viewer.cc:23: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 80%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/main_area.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/main_area.cc.o -MF CMakeFiles/ost_gui.dir/main_area.cc.o.d -o CMakeFiles/ost_gui.dir/main_area.cc.o -c /build/openstructure-2.3.1/modules/gui/src/main_area.cc +[ 80%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/widget_state_saver.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/widget_state_saver.cc.o -MF CMakeFiles/ost_gui.dir/widget_state_saver.cc.o.d -o CMakeFiles/ost_gui.dir/widget_state_saver.cc.o -c /build/openstructure-2.3.1/modules/gui/src/widget_state_saver.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -22820,20 +21651,20 @@ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, - from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_view_object.cc:26: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/chain_view.hh:23, + from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_viewer.cc:28: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: + from /usr/include/c++/12/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -22843,31 +21674,23 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 83%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/widget_geom_handler.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/widget_geom_handler.cc.o -MF CMakeFiles/ost_gui.dir/widget_geom_handler.cc.o.d -o CMakeFiles/ost_gui.dir/widget_geom_handler.cc.o -c /build/openstructure-2.3.1/modules/gui/src/widget_geom_handler.cc -[ 83%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/file_loader.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/file_loader.cc.o -MF CMakeFiles/ost_gui.dir/file_loader.cc.o.d -o CMakeFiles/ost_gui.dir/file_loader.cc.o -c /build/openstructure-2.3.1/modules/gui/src/file_loader.cc -[ 83%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/button_bar.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/button_bar.cc.o -MF CMakeFiles/ost_gui.dir/panels/button_bar.cc.o.d -o CMakeFiles/ost_gui.dir/panels/button_bar.cc.o -c /build/openstructure-2.3.1/modules/gui/src/panels/button_bar.cc -[ 83%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/drop_box.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/drop_box.cc.o -MF CMakeFiles/ost_gui.dir/panels/drop_box.cc.o.d -o CMakeFiles/ost_gui.dir/panels/drop_box.cc.o -c /build/openstructure-2.3.1/modules/gui/src/panels/drop_box.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/chain_view.hh:23, - from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_viewer.cc:28: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, + from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/alignment_view_object.cc:26: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, - from /usr/include/c++/12/math.h:36, - from /usr/include/python3.11/pyport.h:218, - from /usr/include/python3.11/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -22877,10 +21700,25 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 84%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/panel_bar.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/panel_bar.cc.o -MF CMakeFiles/ost_gui.dir/panels/panel_bar.cc.o.d -o CMakeFiles/ost_gui.dir/panels/panel_bar.cc.o -c /build/openstructure-2.3.1/modules/gui/src/panels/panel_bar.cc -[ 84%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/bottom_bar.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/bottom_bar.cc.o -MF CMakeFiles/ost_gui.dir/panels/bottom_bar.cc.o.d -o CMakeFiles/ost_gui.dir/panels/bottom_bar.cc.o -c /build/openstructure-2.3.1/modules/gui/src/panels/bottom_bar.cc +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_region.hh:26, + from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/alignment_view_object.cc:29: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 32 | : public std::iterator{ + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_region.hh:27: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_column_iterator.hh:29:43: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 29 | class AlignedColumnIterator : public std::iterator + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, - from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_view_object.hh:32, - from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_view_object.cc:32: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 32 | : public std::iterator{ - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ @@ -22924,6 +21748,34 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 80%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/widget_geom_handler.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/widget_geom_handler.cc.o -MF CMakeFiles/ost_gui.dir/widget_geom_handler.cc.o.d -o CMakeFiles/ost_gui.dir/widget_geom_handler.cc.o -c /build/openstructure-2.3.1/modules/gui/src/widget_geom_handler.cc +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, + from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_view_object.cc:26: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/bits/specfun.h:45, + from /usr/include/c++/12/cmath:1935, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_viewer.cc: In member function 'void ost::gui::SequenceViewer::MouseWheelEvent(QWheelEvent*)': /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_viewer.cc:298:27: warning: 'int QWheelEvent::delta() const' is deprecated: Use angleDelta() [-Wdeprecated-declarations] 298 | int delta = event->delta(); @@ -22940,10 +21792,82 @@ /usr/include/x86_64-linux-gnu/qt5/QtGui/qevent.h:222:28: note: declared here 222 | inline Qt::Orientation orientation() const { return qt4O; } | ^~~~~~~~~~~ -[ 84%] Linking CXX shared module ../../../stage/lib/python3.11/dist-packages/ost/gfx/_ost_gfx.so -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/pymod/gradients.xml /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/share/openstructure/scene/gradients.xml -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_gfx.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -o ../../../stage/lib/python3.11/dist-packages/ost/gfx/_ost_gfx.so CMakeFiles/_ost_gfx.dir/wrap_gfx.cc.o CMakeFiles/_ost_gfx.dir/export_scene.cc.o CMakeFiles/_ost_gfx.dir/export_gfx_node.cc.o CMakeFiles/_ost_gfx.dir/export_symmetry_node.cc.o CMakeFiles/_ost_gfx.dir/export_gfx_obj.cc.o CMakeFiles/_ost_gfx.dir/export_entity.cc.o CMakeFiles/_ost_gfx.dir/export_surface.cc.o CMakeFiles/_ost_gfx.dir/export_primitives.cc.o CMakeFiles/_ost_gfx.dir/export_primlist.cc.o CMakeFiles/_ost_gfx.dir/export_scene_observer.cc.o CMakeFiles/_ost_gfx.dir/export_render_options.cc.o CMakeFiles/_ost_gfx.dir/export_color.cc.o CMakeFiles/_ost_gfx.dir/export_gradient.cc.o CMakeFiles/_ost_gfx.dir/export_color_ops.cc.o CMakeFiles/_ost_gfx.dir/export_glwin_base.cc.o CMakeFiles/_ost_gfx.dir/export_exporter.cc.o CMakeFiles/_ost_gfx.dir/export_bitmap.cc.o CMakeFiles/_ost_gfx.dir/export_map.cc.o -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib: ../../../stage/lib/libost_gfx.so.2.3.1 /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so ../../../stage/lib/libost_conop.so.2.3.1 ../../../stage/lib/libost_db.so.2.3.1 /usr/lib/x86_64-linux-gnu/libsqlite3.so ../../../stage/lib/libost_seq.so.2.3.1 ../../../stage/lib/libost_mol.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so ../../../stage/lib/libost_img_alg.so.2.3.1 ../../../stage/lib/libost_img.so.2.3.1 ../../../stage/lib/libost_info.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 ../../../stage/lib/libost_base.so.2.3.1 ../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libfftw3f_threads.so /usr/lib/x86_64-linux-gnu/libOpenGL.so /usr/lib/x86_64-linux-gnu/libGLX.so /usr/lib/x86_64-linux-gnu/libGLU.so /usr/lib/x86_64-linux-gnu/libpng.so /usr/lib/x86_64-linux-gnu/libz.so +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:29, + from /build/openstructure-2.3.1/modules/gfx/pymod/export_entity.cc:23: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/bits/specfun.h:45, + from /usr/include/c++/12/cmath:1935, + from /usr/include/c++/12/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 80%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/file_loader.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/file_loader.cc.o -MF CMakeFiles/ost_gui.dir/file_loader.cc.o.d -o CMakeFiles/ost_gui.dir/file_loader.cc.o -c /build/openstructure-2.3.1/modules/gui/src/file_loader.cc +[ 80%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/button_bar.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/button_bar.cc.o -MF CMakeFiles/ost_gui.dir/panels/button_bar.cc.o.d -o CMakeFiles/ost_gui.dir/panels/button_bar.cc.o -c /build/openstructure-2.3.1/modules/gui/src/panels/button_bar.cc +[ 80%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/drop_box.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/drop_box.cc.o -MF CMakeFiles/ost_gui.dir/panels/drop_box.cc.o.d -o CMakeFiles/ost_gui.dir/panels/drop_box.cc.o -c /build/openstructure-2.3.1/modules/gui/src/panels/drop_box.cc +[ 82%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/panel_bar.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/panel_bar.cc.o -MF CMakeFiles/ost_gui.dir/panels/panel_bar.cc.o.d -o CMakeFiles/ost_gui.dir/panels/panel_bar.cc.o -c /build/openstructure-2.3.1/modules/gui/src/panels/panel_bar.cc +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, + from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_view_object.hh:32, + from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_view_object.cc:32: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 32 | : public std::iterator{ + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 82%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_surface.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_surface.cc.o -MF CMakeFiles/_ost_gfx.dir/export_surface.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_surface.cc.o -c /build/openstructure-2.3.1/modules/gfx/pymod/export_surface.cc +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main.hh:23, + from /build/openstructure-2.3.1/modules/gui/src/gosty_app.hh:28, + from /build/openstructure-2.3.1/modules/gui/src/gosty_app.cc:19: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 82%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/bottom_bar.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/bottom_bar.cc.o -MF CMakeFiles/ost_gui.dir/panels/bottom_bar.cc.o.d -o CMakeFiles/ost_gui.dir/panels/bottom_bar.cc.o -c /build/openstructure-2.3.1/modules/gui/src/panels/bottom_bar.cc +[ 82%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/button_box.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/button_box.cc.o -MF CMakeFiles/ost_gui.dir/panels/button_box.cc.o.d -o CMakeFiles/ost_gui.dir/panels/button_box.cc.o -c /build/openstructure-2.3.1/modules/gui/src/panels/button_box.cc +[ 82%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/event_button.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/event_button.cc.o -MF CMakeFiles/ost_gui.dir/panels/event_button.cc.o.d -o CMakeFiles/ost_gui.dir/panels/event_button.cc.o -c /build/openstructure-2.3.1/modules/gui/src/panels/event_button.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -22967,12 +21891,10 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 84%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/button_box.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/button_box.cc.o -MF CMakeFiles/ost_gui.dir/panels/button_box.cc.o.d -o CMakeFiles/ost_gui.dir/panels/button_box.cc.o -c /build/openstructure-2.3.1/modules/gui/src/panels/button_box.cc -[ 84%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/event_button.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/event_button.cc.o -MF CMakeFiles/ost_gui.dir/panels/event_button.cc.o.d -o CMakeFiles/ost_gui.dir/panels/event_button.cc.o -c /build/openstructure-2.3.1/modules/gui/src/panels/event_button.cc -[ 84%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/panel_manager.cc.o +[ 82%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/panel_manager.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/panel_manager.cc.o -MF CMakeFiles/ost_gui.dir/panels/panel_manager.cc.o.d -o CMakeFiles/ost_gui.dir/panels/panel_manager.cc.o -c /build/openstructure-2.3.1/modules/gui/src/panels/panel_manager.cc +[ 82%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/panel_widget_container.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/panel_widget_container.cc.o -MF CMakeFiles/ost_gui.dir/panels/panel_widget_container.cc.o.d -o CMakeFiles/ost_gui.dir/panels/panel_widget_container.cc.o -c /build/openstructure-2.3.1/modules/gui/src/panels/panel_widget_container.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -23013,8 +21935,6 @@ /usr/include/x86_64-linux-gnu/qt5/QtCore/qnamespace.h:132:9: note: declared here 132 | MidButton Q_DECL_ENUMERATOR_DEPRECATED_X("MidButton is deprecated. Use MiddleButton instead") = MiddleButton, | ^~~~~~~~~ -[ 84%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/panel_widget_container.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/panel_widget_container.cc.o -MF CMakeFiles/ost_gui.dir/panels/panel_widget_container.cc.o.d -o CMakeFiles/ost_gui.dir/panels/panel_widget_container.cc.o -c /build/openstructure-2.3.1/modules/gui/src/panels/panel_widget_container.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -23045,6 +21965,8 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 82%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/panel_bar_widget_holder.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/panel_bar_widget_holder.cc.o -MF CMakeFiles/ost_gui.dir/panels/panel_bar_widget_holder.cc.o.d -o CMakeFiles/ost_gui.dir/panels/panel_bar_widget_holder.cc.o -c /build/openstructure-2.3.1/modules/gui/src/panels/panel_bar_widget_holder.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_viewer.hh:28, @@ -23055,22 +21977,44 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 84%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/panel_bar_widget_holder.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/panel_bar_widget_holder.cc.o -MF CMakeFiles/ost_gui.dir/panels/panel_bar_widget_holder.cc.o.d -o CMakeFiles/ost_gui.dir/panels/panel_bar_widget_holder.cc.o -c /build/openstructure-2.3.1/modules/gui/src/panels/panel_bar_widget_holder.cc -[ 84%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/side_bar.cc.o +[ 82%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/side_bar.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/side_bar.cc.o -MF CMakeFiles/ost_gui.dir/panels/side_bar.cc.o.d -o CMakeFiles/ost_gui.dir/panels/side_bar.cc.o -c /build/openstructure-2.3.1/modules/gui/src/panels/side_bar.cc -[ 84%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/splitter_panel_bar.cc.o +/build/openstructure-2.3.1/modules/gui/src/panels/event_button.cc: In member function 'virtual void ost::gui::EventButton::mouseMoveEvent(QMouseEvent*)': +/build/openstructure-2.3.1/modules/gui/src/panels/event_button.cc:50:15: warning: 'Qt::DropAction QDrag::start(Qt::DropActions)' is deprecated: Use QDrag::exec() instead [-Wdeprecated-declarations] + 50 | drag->start(Qt::MoveAction); + | ~~~~~~~~~~~^~~~~~~~~~~~~~~~ +In file included from /usr/include/x86_64-linux-gnu/qt5/QtGui/QDrag:1, + from /build/openstructure-2.3.1/modules/gui/src/panels/event_button.cc:22: +/usr/include/x86_64-linux-gnu/qt5/QtGui/qdrag.h:79:20: note: declared here + 79 | Qt::DropAction start(Qt::DropActions supportedActions = Qt::CopyAction); + | ^~~~~ +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main.hh:23, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, + from /build/openstructure-2.3.1/modules/gui/src/file_loader.cc:19: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 82%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/splitter_panel_bar.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/splitter_panel_bar.cc.o -MF CMakeFiles/ost_gui.dir/panels/splitter_panel_bar.cc.o.d -o CMakeFiles/ost_gui.dir/panels/splitter_panel_bar.cc.o -c /build/openstructure-2.3.1/modules/gui/src/panels/splitter_panel_bar.cc -[ 84%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/tabbed_panel_bar.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/tabbed_panel_bar.cc.o -MF CMakeFiles/ost_gui.dir/panels/tabbed_panel_bar.cc.o.d -o CMakeFiles/ost_gui.dir/panels/tabbed_panel_bar.cc.o -c /build/openstructure-2.3.1/modules/gui/src/panels/tabbed_panel_bar.cc -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gfx/pymod/__init__.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gfx/./__init__.pyc\",\"__init__.py\",doraise=True)" -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gfx/pymod/py_gfx_obj.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gfx/./py_gfx_obj.pyc\",\"py_gfx_obj.py\",doraise=True)" -make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 84%] Built target _ost_gfx -[ 85%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/tool_option_group.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/tool_option_group.cc.o -MF CMakeFiles/ost_gui.dir/tools/tool_option_group.cc.o.d -o CMakeFiles/ost_gui.dir/tools/tool_option_group.cc.o -c /build/openstructure-2.3.1/modules/gui/src/tools/tool_option_group.cc -[ 85%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/tool_options.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/tool_options.cc.o -MF CMakeFiles/ost_gui.dir/tools/tool_options.cc.o.d -o CMakeFiles/ost_gui.dir/tools/tool_options.cc.o -c /build/openstructure-2.3.1/modules/gui/src/tools/tool_options.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/data_viewer.hh:37, from /build/openstructure-2.3.1/modules/gui/src/gosty_app.cc:31: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main_window.hh:46:55: warning: 'constexpr QFlags::QFlags(Zero) [with Enum = Qt::WindowType; Zero = int QFlags::Private::*]' is deprecated: Use default constructor instead [-Wdeprecated-declarations] @@ -23100,15 +22044,15 @@ from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, - from /build/openstructure-2.3.1/modules/gui/src/file_loader.cc:19: + from /build/openstructure-2.3.1/modules/gui/src/panels/panel_bar.cc:21: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 85%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/tool_option.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/tool_option.cc.o -MF CMakeFiles/ost_gui.dir/tools/tool_option.cc.o.d -o CMakeFiles/ost_gui.dir/tools/tool_option.cc.o -c /build/openstructure-2.3.1/modules/gui/src/tools/tool_option.cc +[ 82%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/tabbed_panel_bar.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/tabbed_panel_bar.cc.o -MF CMakeFiles/ost_gui.dir/panels/tabbed_panel_bar.cc.o.d -o CMakeFiles/ost_gui.dir/panels/tabbed_panel_bar.cc.o -c /build/openstructure-2.3.1/modules/gui/src/panels/tabbed_panel_bar.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -23138,17 +22082,8 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 85%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/tool_manager.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/tool_manager.cc.o -MF CMakeFiles/ost_gui.dir/tools/tool_manager.cc.o.d -o CMakeFiles/ost_gui.dir/tools/tool_manager.cc.o -c /build/openstructure-2.3.1/modules/gui/src/tools/tool_manager.cc -/build/openstructure-2.3.1/modules/gui/src/panels/event_button.cc: In member function 'virtual void ost::gui::EventButton::mouseMoveEvent(QMouseEvent*)': -/build/openstructure-2.3.1/modules/gui/src/panels/event_button.cc:50:15: warning: 'Qt::DropAction QDrag::start(Qt::DropActions)' is deprecated: Use QDrag::exec() instead [-Wdeprecated-declarations] - 50 | drag->start(Qt::MoveAction); - | ~~~~~~~~~~~^~~~~~~~~~~~~~~~ -In file included from /usr/include/x86_64-linux-gnu/qt5/QtGui/QDrag:1, - from /build/openstructure-2.3.1/modules/gui/src/panels/event_button.cc:22: -/usr/include/x86_64-linux-gnu/qt5/QtGui/qdrag.h:79:20: note: declared here - 79 | Qt::DropAction start(Qt::DropActions supportedActions = Qt::CopyAction); - | ^~~~~ +[ 83%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/tool_option_group.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/tool_option_group.cc.o -MF CMakeFiles/ost_gui.dir/tools/tool_option_group.cc.o.d -o CMakeFiles/ost_gui.dir/tools/tool_option_group.cc.o -c /build/openstructure-2.3.1/modules/gui/src/tools/tool_option_group.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -23162,22 +22097,15 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main.hh:23, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, - from /build/openstructure-2.3.1/modules/gui/src/panels/panel_bar.cc:21: + from /build/openstructure-2.3.1/modules/gfx/pymod/export_surface.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 85%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/tool.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/tool.cc.o -MF CMakeFiles/ost_gui.dir/tools/tool.cc.o.d -o CMakeFiles/ost_gui.dir/tools/tool.cc.o -c /build/openstructure-2.3.1/modules/gui/src/tools/tool.cc -[ 85%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/tool_options_win.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/tool_options_win.cc.o -MF CMakeFiles/ost_gui.dir/tools/tool_options_win.cc.o.d -o CMakeFiles/ost_gui.dir/tools/tool_options_win.cc.o -c /build/openstructure-2.3.1/modules/gui/src/tools/tool_options_win.cc +[ 83%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/tool_options.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/tool_options.cc.o -MF CMakeFiles/ost_gui.dir/tools/tool_options.cc.o.d -o CMakeFiles/ost_gui.dir/tools/tool_options.cc.o -c /build/openstructure-2.3.1/modules/gui/src/tools/tool_options.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/data_viewer.hh:37, from /build/openstructure-2.3.1/modules/gui/src/scene_selection.cc:34: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main_window.hh:46:55: warning: 'constexpr QFlags::QFlags(Zero) [with Enum = Qt::WindowType; Zero = int QFlags::Private::*]' is deprecated: Use default constructor instead [-Wdeprecated-declarations] @@ -23193,15 +22121,44 @@ /usr/include/x86_64-linux-gnu/qt5/QtCore/qflags.h:123:80: note: declared here 123 | QT_DEPRECATED_X("Use default constructor instead") Q_DECL_CONSTEXPR inline QFlags(Zero) noexcept : i(0) {} | ^~~~~~ -[ 85%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/mouse_event.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/mouse_event.cc.o -MF CMakeFiles/ost_gui.dir/tools/mouse_event.cc.o.d -o CMakeFiles/ost_gui.dir/tools/mouse_event.cc.o -c /build/openstructure-2.3.1/modules/gui/src/tools/mouse_event.cc +[ 83%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/tool_option.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/tool_option.cc.o -MF CMakeFiles/ost_gui.dir/tools/tool_option.cc.o.d -o CMakeFiles/ost_gui.dir/tools/tool_option.cc.o -c /build/openstructure-2.3.1/modules/gui/src/tools/tool_option.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, - from /build/openstructure-2.3.1/modules/gui/src/panels/drop_box.hh:22, - from /build/openstructure-2.3.1/modules/gui/src/panels/panel_bar.cc:26: + from /build/openstructure-2.3.1/modules/gui/src/file_loader.hh:24, + from /build/openstructure-2.3.1/modules/gui/src/file_loader.cc:20: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/bits/specfun.h:45, + from /usr/include/c++/12/cmath:1935, + from /usr/include/c++/12/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/surface_prop.hh:25, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/surface_handle.hh:24, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/surface.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/surface.hh:31, + from /build/openstructure-2.3.1/modules/gfx/pymod/export_surface.cc:22: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -23223,15 +22180,13 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 85%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/manipulator.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/manipulator.cc.o -MF CMakeFiles/ost_gui.dir/tools/manipulator.cc.o.d -o CMakeFiles/ost_gui.dir/tools/manipulator.cc.o -c /build/openstructure-2.3.1/modules/gui/src/tools/manipulator.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, - from /build/openstructure-2.3.1/modules/gui/src/file_loader.hh:24, - from /build/openstructure-2.3.1/modules/gui/src/file_loader.cc:20: + from /build/openstructure-2.3.1/modules/gui/src/panels/drop_box.hh:22, + from /build/openstructure-2.3.1/modules/gui/src/panels/panel_bar.cc:26: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -23253,8 +22208,8 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 85%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/tool_options_widget.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/tool_options_widget.cc.o -MF CMakeFiles/ost_gui.dir/tools/tool_options_widget.cc.o.d -o CMakeFiles/ost_gui.dir/tools/tool_options_widget.cc.o -c /build/openstructure-2.3.1/modules/gui/src/tools/tool_options_widget.cc +[ 83%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/tool_manager.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/tool_manager.cc.o -MF CMakeFiles/ost_gui.dir/tools/tool_manager.cc.o.d -o CMakeFiles/ost_gui.dir/tools/tool_manager.cc.o -c /build/openstructure-2.3.1/modules/gui/src/tools/tool_manager.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, from /build/openstructure-2.3.1/modules/gui/src/file_loader.hh:30: @@ -23264,20 +22219,35 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool.hh:30, - from /build/openstructure-2.3.1/modules/gui/src/tools/tool_manager.hh:24, - from /build/openstructure-2.3.1/modules/gui/src/tools/tool_manager.cc:19: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:37:22: warning: 'Qt::MidButton' is deprecated: MidButton is deprecated. Use MiddleButton instead [-Wdeprecated-declarations] - 37 | MiddleButton=Qt::MidButton - | ^~~~~~~~~ -In file included from /usr/include/x86_64-linux-gnu/qt5/QtCore/qpoint.h:43, - from /usr/include/x86_64-linux-gnu/qt5/QtCore/QPoint:1, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:24: -/usr/include/x86_64-linux-gnu/qt5/QtCore/qnamespace.h:132:9: note: declared here - 132 | MidButton Q_DECL_ENUMERATOR_DEPRECATED_X("MidButton is deprecated. Use MiddleButton instead") = MiddleButton, - | ^~~~~~~~~ -[ 85%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/tool_bar.cc.o +[ 83%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/tool_options_win.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/tool_options_win.cc.o -MF CMakeFiles/ost_gui.dir/tools/tool_options_win.cc.o.d -o CMakeFiles/ost_gui.dir/tools/tool_options_win.cc.o -c /build/openstructure-2.3.1/modules/gui/src/tools/tool_options_win.cc +[ 83%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/tool.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/tool.cc.o -MF CMakeFiles/ost_gui.dir/tools/tool.cc.o.d -o CMakeFiles/ost_gui.dir/tools/tool.cc.o -c /build/openstructure-2.3.1/modules/gui/src/tools/tool.cc +[ 83%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/mouse_event.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/mouse_event.cc.o -MF CMakeFiles/ost_gui.dir/tools/mouse_event.cc.o.d -o CMakeFiles/ost_gui.dir/tools/mouse_event.cc.o -c /build/openstructure-2.3.1/modules/gui/src/tools/mouse_event.cc +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/data_viewer.hh:37, + from /build/openstructure-2.3.1/modules/gui/src/file_loader.cc:51: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main_window.hh:46:55: warning: 'constexpr QFlags::QFlags(Zero) [with Enum = Qt::WindowType; Zero = int QFlags::Private::*]' is deprecated: Use default constructor instead [-Wdeprecated-declarations] + 46 | MainWindow(QWidget* parent=0, Qt::WindowFlags flags=0); + | ^ +In file included from /usr/include/x86_64-linux-gnu/qt5/QtCore/qglobal.h:1305, + from /usr/include/x86_64-linux-gnu/qt5/QtCore/qchar.h:43, + from /usr/include/x86_64-linux-gnu/qt5/QtCore/qstring.h:49, + from /usr/include/x86_64-linux-gnu/qt5/QtCore/qdatetime.h:44, + from /usr/include/x86_64-linux-gnu/qt5/QtCore/QTime:1, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/output_redirector.hh:30, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:33: +/usr/include/x86_64-linux-gnu/qt5/QtCore/qflags.h:123:80: note: declared here + 123 | QT_DEPRECATED_X("Use default constructor instead") Q_DECL_CONSTEXPR inline QFlags(Zero) noexcept : i(0) {} + | ^~~~~~ +[ 83%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/manipulator.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/manipulator.cc.o -MF CMakeFiles/ost_gui.dir/tools/manipulator.cc.o.d -o CMakeFiles/ost_gui.dir/tools/manipulator.cc.o -c /build/openstructure-2.3.1/modules/gui/src/tools/manipulator.cc +[ 83%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/tool_options_widget.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/tool_options_widget.cc.o -MF CMakeFiles/ost_gui.dir/tools/tool_options_widget.cc.o.d -o CMakeFiles/ost_gui.dir/tools/tool_options_widget.cc.o -c /build/openstructure-2.3.1/modules/gui/src/tools/tool_options_widget.cc +[ 83%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/tool_bar.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/tool_bar.cc.o -MF CMakeFiles/ost_gui.dir/tools/tool_bar.cc.o.d -o CMakeFiles/ost_gui.dir/tools/tool_bar.cc.o -c /build/openstructure-2.3.1/modules/gui/src/tools/tool_bar.cc +[ 83%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/selection_tool.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/selection_tool.cc.o -MF CMakeFiles/ost_gui.dir/tools/selection_tool.cc.o.d -o CMakeFiles/ost_gui.dir/tools/selection_tool.cc.o -c /build/openstructure-2.3.1/modules/gui/src/tools/selection_tool.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -23303,29 +22273,9 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 85%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/selection_tool.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/selection_tool.cc.o -MF CMakeFiles/ost_gui.dir/tools/selection_tool.cc.o.d -o CMakeFiles/ost_gui.dir/tools/selection_tool.cc.o -c /build/openstructure-2.3.1/modules/gui/src/tools/selection_tool.cc -[ 87%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/measure_tool.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/measure_tool.cc.o -MF CMakeFiles/ost_gui.dir/tools/measure_tool.cc.o.d -o CMakeFiles/ost_gui.dir/tools/measure_tool.cc.o -c /build/openstructure-2.3.1/modules/gui/src/tools/measure_tool.cc -[ 87%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/gutter.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/gutter.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/gutter.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/gutter.cc.o -c /build/openstructure-2.3.1/modules/gui/src/python_shell/gutter.cc -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/data_viewer.hh:37, - from /build/openstructure-2.3.1/modules/gui/src/file_loader.cc:51: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main_window.hh:46:55: warning: 'constexpr QFlags::QFlags(Zero) [with Enum = Qt::WindowType; Zero = int QFlags::Private::*]' is deprecated: Use default constructor instead [-Wdeprecated-declarations] - 46 | MainWindow(QWidget* parent=0, Qt::WindowFlags flags=0); - | ^ -In file included from /usr/include/x86_64-linux-gnu/qt5/QtCore/qglobal.h:1305, - from /usr/include/x86_64-linux-gnu/qt5/QtCore/qchar.h:43, - from /usr/include/x86_64-linux-gnu/qt5/QtCore/qstring.h:49, - from /usr/include/x86_64-linux-gnu/qt5/QtCore/qdatetime.h:44, - from /usr/include/x86_64-linux-gnu/qt5/QtCore/QTime:1, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/output_redirector.hh:30, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:33: -/usr/include/x86_64-linux-gnu/qt5/QtCore/qflags.h:123:80: note: declared here - 123 | QT_DEPRECATED_X("Use default constructor instead") Q_DECL_CONSTEXPR inline QFlags(Zero) noexcept : i(0) {} - | ^~~~~~ -In file included from /build/openstructure-2.3.1/modules/gui/src/tools/tool.hh:30, - from /build/openstructure-2.3.1/modules/gui/src/tools/tool.cc:19: +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool.hh:30, + from /build/openstructure-2.3.1/modules/gui/src/tools/tool_manager.hh:24, + from /build/openstructure-2.3.1/modules/gui/src/tools/tool_manager.cc:19: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:37:22: warning: 'Qt::MidButton' is deprecated: MidButton is deprecated. Use MiddleButton instead [-Wdeprecated-declarations] 37 | MiddleButton=Qt::MidButton | ^~~~~~~~~ @@ -23335,20 +22285,8 @@ /usr/include/x86_64-linux-gnu/qt5/QtCore/qnamespace.h:132:9: note: declared here 132 | MidButton Q_DECL_ENUMERATOR_DEPRECATED_X("MidButton is deprecated. Use MiddleButton instead") = MiddleButton, | ^~~~~~~~~ -In file included from /build/openstructure-2.3.1/modules/gui/src/tools/mouse_event.cc:19: -/build/openstructure-2.3.1/modules/gui/src/tools/mouse_event.hh:37:22: warning: 'Qt::MidButton' is deprecated: MidButton is deprecated. Use MiddleButton instead [-Wdeprecated-declarations] - 37 | MiddleButton=Qt::MidButton - | ^~~~~~~~~ -In file included from /usr/include/x86_64-linux-gnu/qt5/QtCore/qpoint.h:43, - from /usr/include/x86_64-linux-gnu/qt5/QtCore/QPoint:1, - from /build/openstructure-2.3.1/modules/gui/src/tools/mouse_event.hh:24: -/usr/include/x86_64-linux-gnu/qt5/QtCore/qnamespace.h:132:9: note: declared here - 132 | MidButton Q_DECL_ENUMERATOR_DEPRECATED_X("MidButton is deprecated. Use MiddleButton instead") = MiddleButton, - | ^~~~~~~~~ -[ 87%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/main_thread_runner.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/main_thread_runner.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/main_thread_runner.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/main_thread_runner.cc.o -c /build/openstructure-2.3.1/modules/gui/src/python_shell/main_thread_runner.cc -[ 87%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/output_redirector.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/output_redirector.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/output_redirector.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/output_redirector.cc.o -c /build/openstructure-2.3.1/modules/gui/src/python_shell/output_redirector.cc +[ 84%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/measure_tool.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/measure_tool.cc.o -MF CMakeFiles/ost_gui.dir/tools/measure_tool.cc.o.d -o CMakeFiles/ost_gui.dir/tools/measure_tool.cc.o -c /build/openstructure-2.3.1/modules/gui/src/tools/measure_tool.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -23371,15 +22309,78 @@ /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ +In file included from /build/openstructure-2.3.1/modules/gui/src/tools/tool.hh:30, + from /build/openstructure-2.3.1/modules/gui/src/tools/tool.cc:19: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:37:22: warning: 'Qt::MidButton' is deprecated: MidButton is deprecated. Use MiddleButton instead [-Wdeprecated-declarations] + 37 | MiddleButton=Qt::MidButton + | ^~~~~~~~~ +In file included from /usr/include/x86_64-linux-gnu/qt5/QtCore/qpoint.h:43, + from /usr/include/x86_64-linux-gnu/qt5/QtCore/QPoint:1, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:24: +/usr/include/x86_64-linux-gnu/qt5/QtCore/qnamespace.h:132:9: note: declared here + 132 | MidButton Q_DECL_ENUMERATOR_DEPRECATED_X("MidButton is deprecated. Use MiddleButton instead") = MiddleButton, + | ^~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 87%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/completer_base.cc.o +In file included from /build/openstructure-2.3.1/modules/gui/src/tools/mouse_event.cc:19: +/build/openstructure-2.3.1/modules/gui/src/tools/mouse_event.hh:37:22: warning: 'Qt::MidButton' is deprecated: MidButton is deprecated. Use MiddleButton instead [-Wdeprecated-declarations] + 37 | MiddleButton=Qt::MidButton + | ^~~~~~~~~ +In file included from /usr/include/x86_64-linux-gnu/qt5/QtCore/qpoint.h:43, + from /usr/include/x86_64-linux-gnu/qt5/QtCore/QPoint:1, + from /build/openstructure-2.3.1/modules/gui/src/tools/mouse_event.hh:24: +/usr/include/x86_64-linux-gnu/qt5/QtCore/qnamespace.h:132:9: note: declared here + 132 | MidButton Q_DECL_ENUMERATOR_DEPRECATED_X("MidButton is deprecated. Use MiddleButton instead") = MiddleButton, + | ^~~~~~~~~ +[ 84%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/gutter.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/gutter.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/gutter.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/gutter.cc.o -c /build/openstructure-2.3.1/modules/gui/src/python_shell/gutter.cc +[ 84%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/main_thread_runner.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/main_thread_runner.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/main_thread_runner.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/main_thread_runner.cc.o -c /build/openstructure-2.3.1/modules/gui/src/python_shell/main_thread_runner.cc +[ 84%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/output_redirector.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/output_redirector.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/output_redirector.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/output_redirector.cc.o -c /build/openstructure-2.3.1/modules/gui/src/python_shell/output_redirector.cc +[ 84%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/completer_base.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/completer_base.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/completer_base.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/completer_base.cc.o -c /build/openstructure-2.3.1/modules/gui/src/python_shell/completer_base.cc -[ 87%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/dir_model.cc.o +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool.hh:30, + from /build/openstructure-2.3.1/modules/gui/src/tools/selection_tool.hh:26, + from /build/openstructure-2.3.1/modules/gui/src/tools/selection_tool.cc:22: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:37:22: warning: 'Qt::MidButton' is deprecated: MidButton is deprecated. Use MiddleButton instead [-Wdeprecated-declarations] + 37 | MiddleButton=Qt::MidButton + | ^~~~~~~~~ +In file included from /usr/include/x86_64-linux-gnu/qt5/QtCore/qpoint.h:43, + from /usr/include/x86_64-linux-gnu/qt5/QtCore/QPoint:1, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:24: +/usr/include/x86_64-linux-gnu/qt5/QtCore/qnamespace.h:132:9: note: declared here + 132 | MidButton Q_DECL_ENUMERATOR_DEPRECATED_X("MidButton is deprecated. Use MiddleButton instead") = MiddleButton, + | ^~~~~~~~~ +[ 84%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/dir_model.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/dir_model.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/dir_model.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/dir_model.cc.o -c /build/openstructure-2.3.1/modules/gui/src/python_shell/dir_model.cc -[ 87%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/path_completer.cc.o +/build/openstructure-2.3.1/modules/gui/src/python_shell/output_redirector.cc: In member function 'void ost::gui::OutputRedirector::Write(const String&)': +/build/openstructure-2.3.1/modules/gui/src/python_shell/output_redirector.cc:42:22: warning: 'int QTime::elapsed() const' is deprecated: Use QElapsedTimer instead [-Wdeprecated-declarations] + 42 | if(timer_.elapsed()>1000){ + | ~~~~~~~~~~~~~~^~ +In file included from /usr/include/x86_64-linux-gnu/qt5/QtCore/QTime:1, + from /build/openstructure-2.3.1/modules/gui/src/python_shell/output_redirector.hh:30, + from /build/openstructure-2.3.1/modules/gui/src/python_shell/output_redirector.cc:25: +/usr/include/x86_64-linux-gnu/qt5/QtCore/qdatetime.h:237:54: note: declared here + 237 | QT_DEPRECATED_X("Use QElapsedTimer instead") int elapsed() const; + | ^~~~~~~ +/build/openstructure-2.3.1/modules/gui/src/python_shell/output_redirector.cc:46:21: warning: 'int QTime::restart()' is deprecated: Use QElapsedTimer instead [-Wdeprecated-declarations] + 46 | timer_.restart(); + | ~~~~~~~~~~~~~~^~ +/usr/include/x86_64-linux-gnu/qt5/QtCore/qdatetime.h:236:54: note: declared here + 236 | QT_DEPRECATED_X("Use QElapsedTimer instead") int restart(); + | ^~~~~~~ +/build/openstructure-2.3.1/modules/gui/src/python_shell/output_redirector.cc:52:17: warning: 'void QTime::start()' is deprecated: Use QElapsedTimer instead [-Wdeprecated-declarations] + 52 | timer_.start(); + | ~~~~~~~~~~~~^~ +/usr/include/x86_64-linux-gnu/qt5/QtCore/qdatetime.h:235:55: note: declared here + 235 | QT_DEPRECATED_X("Use QElapsedTimer instead") void start(); + | ^~~~~ +[ 84%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/path_completer.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/path_completer.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/path_completer.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/path_completer.cc.o -c /build/openstructure-2.3.1/modules/gui/src/python_shell/path_completer.cc +[ 84%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_context_parser.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_context_parser.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/python_context_parser.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/python_context_parser.cc.o -c /build/openstructure-2.3.1/modules/gui/src/python_shell/python_context_parser.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -23405,30 +22406,29 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -/build/openstructure-2.3.1/modules/gui/src/python_shell/output_redirector.cc: In member function 'void ost::gui::OutputRedirector::Write(const String&)': -/build/openstructure-2.3.1/modules/gui/src/python_shell/output_redirector.cc:42:22: warning: 'int QTime::elapsed() const' is deprecated: Use QElapsedTimer instead [-Wdeprecated-declarations] - 42 | if(timer_.elapsed()>1000){ - | ~~~~~~~~~~~~~~^~ -In file included from /usr/include/x86_64-linux-gnu/qt5/QtCore/QTime:1, - from /build/openstructure-2.3.1/modules/gui/src/python_shell/output_redirector.hh:30, - from /build/openstructure-2.3.1/modules/gui/src/python_shell/output_redirector.cc:25: -/usr/include/x86_64-linux-gnu/qt5/QtCore/qdatetime.h:237:54: note: declared here - 237 | QT_DEPRECATED_X("Use QElapsedTimer instead") int elapsed() const; - | ^~~~~~~ -/build/openstructure-2.3.1/modules/gui/src/python_shell/output_redirector.cc:46:21: warning: 'int QTime::restart()' is deprecated: Use QElapsedTimer instead [-Wdeprecated-declarations] - 46 | timer_.restart(); - | ~~~~~~~~~~~~~~^~ -/usr/include/x86_64-linux-gnu/qt5/QtCore/qdatetime.h:236:54: note: declared here - 236 | QT_DEPRECATED_X("Use QElapsedTimer instead") int restart(); - | ^~~~~~~ -/build/openstructure-2.3.1/modules/gui/src/python_shell/output_redirector.cc:52:17: warning: 'void QTime::start()' is deprecated: Use QElapsedTimer instead [-Wdeprecated-declarations] - 52 | timer_.start(); - | ~~~~~~~~~~~~^~ -/usr/include/x86_64-linux-gnu/qt5/QtCore/qdatetime.h:235:55: note: declared here - 235 | QT_DEPRECATED_X("Use QElapsedTimer instead") void start(); - | ^~~~~ -[ 87%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_context_parser.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_context_parser.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/python_context_parser.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/python_context_parser.cc.o -c /build/openstructure-2.3.1/modules/gui/src/python_shell/python_context_parser.cc +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color.hh:31, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/scene.hh:37, + from /build/openstructure-2.3.1/modules/gui/src/tools/selection_tool.cc:26: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/vector:60, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool.hh:25: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 84%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_primitives.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_primitives.cc.o -MF CMakeFiles/_ost_gfx.dir/export_primitives.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_primitives.cc.o -c /build/openstructure-2.3.1/modules/gfx/pymod/export_primitives.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool.hh:30, from /build/openstructure-2.3.1/modules/gui/src/tools/measure_tool.hh:26, from /build/openstructure-2.3.1/modules/gui/src/tools/measure_tool.cc:22: @@ -23441,10 +22441,6 @@ /usr/include/x86_64-linux-gnu/qt5/QtCore/qnamespace.h:132:9: note: declared here 132 | MidButton Q_DECL_ENUMERATOR_DEPRECATED_X("MidButton is deprecated. Use MiddleButton instead") = MiddleButton, | ^~~~~~~~~ -[ 87%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_completer.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_completer.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/python_completer.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/python_completer.cc.o -c /build/openstructure-2.3.1/modules/gui/src/python_shell/python_completer.cc -[ 87%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_interpreter.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_interpreter.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/python_interpreter.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/python_interpreter.cc.o -c /build/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -23470,18 +22466,6 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool.hh:30, - from /build/openstructure-2.3.1/modules/gui/src/tools/selection_tool.hh:26, - from /build/openstructure-2.3.1/modules/gui/src/tools/selection_tool.cc:22: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:37:22: warning: 'Qt::MidButton' is deprecated: MidButton is deprecated. Use MiddleButton instead [-Wdeprecated-declarations] - 37 | MiddleButton=Qt::MidButton - | ^~~~~~~~~ -In file included from /usr/include/x86_64-linux-gnu/qt5/QtCore/qpoint.h:43, - from /usr/include/x86_64-linux-gnu/qt5/QtCore/QPoint:1, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:24: -/usr/include/x86_64-linux-gnu/qt5/QtCore/qnamespace.h:132:9: note: declared here - 132 | MidButton Q_DECL_ENUMERATOR_DEPRECATED_X("MidButton is deprecated. Use MiddleButton instead") = MiddleButton, - | ^~~~~~~~~ /build/openstructure-2.3.1/modules/gui/src/python_shell/dir_model.cc: In constructor 'ost::gui::OstDirModel::OstDirModel(QObject*)': /build/openstructure-2.3.1/modules/gui/src/python_shell/dir_model.cc:31:18: warning: 'QDirModel::QDirModel(QObject*)' is deprecated: Use QFileSystemModel [-Wdeprecated-declarations] 31 | QDirModel(parent) @@ -23492,26 +22476,8 @@ /usr/include/x86_64-linux-gnu/qt5/QtWidgets/qdirmodel.h:73:67: note: declared here 73 | QT_DEPRECATED_VERSION_X_5_15("Use QFileSystemModel") explicit QDirModel(QObject *parent = nullptr); | ^~~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color.hh:31, - from /build/openstructure-2.3.1/modules/gui/src/tools/measure_tool.hh:28: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/vector:60, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool.hh:25: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ +[ 84%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_completer.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_completer.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/python_completer.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/python_completer.cc.o -c /build/openstructure-2.3.1/modules/gui/src/python_shell/python_completer.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -23537,29 +22503,19 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool.hh:30, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool_options_win.hh:27, - from /build/openstructure-2.3.1/modules/gui/src/tools/tool_options_win.cc:21: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:37:22: warning: 'Qt::MidButton' is deprecated: MidButton is deprecated. Use MiddleButton instead [-Wdeprecated-declarations] - 37 | MiddleButton=Qt::MidButton - | ^~~~~~~~~ -In file included from /usr/include/x86_64-linux-gnu/qt5/QtCore/qbytearray.h:45, - from /usr/include/x86_64-linux-gnu/qt5/QtCore/qstring.h:50, - from /usr/include/x86_64-linux-gnu/qt5/QtCore/qdatetime.h:44, - from /usr/include/x86_64-linux-gnu/qt5/QtCore/QTime:1, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/output_redirector.hh:30, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:33: -/usr/include/x86_64-linux-gnu/qt5/QtCore/qnamespace.h:132:9: note: declared here - 132 | MidButton Q_DECL_ENUMERATOR_DEPRECATED_X("MidButton is deprecated. Use MiddleButton instead") = MiddleButton, - | ^~~~~~~~~ -[ 87%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_interpreter_worker.cc.o +[ 84%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_interpreter.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_interpreter.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/python_interpreter.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/python_interpreter.cc.o -c /build/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter.cc +[ 84%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_interpreter_worker.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_interpreter_worker.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/python_interpreter_worker.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/python_interpreter_worker.cc.o -c /build/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter_worker.cc +[ 85%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_namespace_tree_model.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_namespace_tree_model.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/python_namespace_tree_model.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/python_namespace_tree_model.cc.o -c /build/openstructure-2.3.1/modules/gui/src/python_shell/python_namespace_tree_model.cc +[ 85%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_namespace_tree_item.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_namespace_tree_item.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/python_namespace_tree_item.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/python_namespace_tree_item.cc.o -c /build/openstructure-2.3.1/modules/gui/src/python_shell/python_namespace_tree_item.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color.hh:31, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/scene.hh:37, - from /build/openstructure-2.3.1/modules/gui/src/tools/selection_tool.cc:26: + from /build/openstructure-2.3.1/modules/gui/src/tools/measure_tool.hh:28: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -23575,8 +22531,68 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 88%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_namespace_tree_model.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_namespace_tree_model.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/python_namespace_tree_model.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/python_namespace_tree_model.cc.o -c /build/openstructure-2.3.1/modules/gui/src/python_shell/python_namespace_tree_model.cc +[ 85%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_shell.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_shell.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/python_shell.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/python_shell.cc.o -c /build/openstructure-2.3.1/modules/gui/src/python_shell/python_shell.cc +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool.hh:30, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool_options_win.hh:27, + from /build/openstructure-2.3.1/modules/gui/src/tools/tool_options_win.cc:21: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:37:22: warning: 'Qt::MidButton' is deprecated: MidButton is deprecated. Use MiddleButton instead [-Wdeprecated-declarations] + 37 | MiddleButton=Qt::MidButton + | ^~~~~~~~~ +In file included from /usr/include/x86_64-linux-gnu/qt5/QtCore/qbytearray.h:45, + from /usr/include/x86_64-linux-gnu/qt5/QtCore/qstring.h:50, + from /usr/include/x86_64-linux-gnu/qt5/QtCore/qdatetime.h:44, + from /usr/include/x86_64-linux-gnu/qt5/QtCore/QTime:1, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/output_redirector.hh:30, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:33: +/usr/include/x86_64-linux-gnu/qt5/QtCore/qnamespace.h:132:9: note: declared here + 132 | MidButton Q_DECL_ENUMERATOR_DEPRECATED_X("MidButton is deprecated. Use MiddleButton instead") = MiddleButton, + | ^~~~~~~~~ +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/openstructure-2.3.1/modules/gui/src/python_shell/main_thread_runner.cc:25: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter_worker.hh:29, + from /build/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter.hh:31, + from /build/openstructure-2.3.1/modules/gui/src/python_shell/python_shell_widget.hh:28, + from /build/openstructure-2.3.1/modules/gui/src/python_shell/gutter.cc:22: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 85%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_shell_widget.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_shell_widget.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/python_shell_widget.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/python_shell_widget.cc.o -c /build/openstructure-2.3.1/modules/gui/src/python_shell/python_shell_widget.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -23606,48 +22622,7 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/gui/src/python_shell/main_thread_runner.cc:25: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -[ 88%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_namespace_tree_item.cc.o -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_namespace_tree_item.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/python_namespace_tree_item.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/python_namespace_tree_item.cc.o -c /build/openstructure-2.3.1/modules/gui/src/python_shell/python_namespace_tree_item.cc -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool.hh:30, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool_manager.hh:24, - from /build/openstructure-2.3.1/modules/gui/src/tools/tool_bar.cc:22: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:37:22: warning: 'Qt::MidButton' is deprecated: MidButton is deprecated. Use MiddleButton instead [-Wdeprecated-declarations] - 37 | MiddleButton=Qt::MidButton - | ^~~~~~~~~ -In file included from /usr/include/x86_64-linux-gnu/qt5/QtCore/qbytearray.h:45, - from /usr/include/x86_64-linux-gnu/qt5/QtCore/qstring.h:50, - from /usr/include/x86_64-linux-gnu/qt5/QtCore/qdatetime.h:44, - from /usr/include/x86_64-linux-gnu/qt5/QtCore/QTime:1, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/output_redirector.hh:30, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:33: -/usr/include/x86_64-linux-gnu/qt5/QtCore/qnamespace.h:132:9: note: declared here - 132 | MidButton Q_DECL_ENUMERATOR_DEPRECATED_X("MidButton is deprecated. Use MiddleButton instead") = MiddleButton, - | ^~~~~~~~~ -[ 88%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_shell.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_shell.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/python_shell.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/python_shell.cc.o -c /build/openstructure-2.3.1/modules/gui/src/python_shell/python_shell.cc -[ 88%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_shell_widget.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_shell_widget.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/python_shell_widget.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/python_shell_widget.cc.o -c /build/openstructure-2.3.1/modules/gui/src/python_shell/python_shell_widget.cc -[ 88%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_shell_text_document_layout.cc.o +[ 85%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_shell_text_document_layout.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_shell_text_document_layout.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/python_shell_text_document_layout.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/python_shell_text_document_layout.cc.o -c /build/openstructure-2.3.1/modules/gui/src/python_shell/python_shell_text_document_layout.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, @@ -23676,10 +22651,21 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 88%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_tokenizer.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_tokenizer.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/python_tokenizer.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/python_tokenizer.cc.o -c /build/openstructure-2.3.1/modules/gui/src/python_shell/python_tokenizer.cc -[ 88%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_syntax_highlighter.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_syntax_highlighter.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/python_syntax_highlighter.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/python_syntax_highlighter.cc.o -c /build/openstructure-2.3.1/modules/gui/src/python_shell/python_syntax_highlighter.cc +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool.hh:30, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool_manager.hh:24, + from /build/openstructure-2.3.1/modules/gui/src/tools/tool_bar.cc:22: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:37:22: warning: 'Qt::MidButton' is deprecated: MidButton is deprecated. Use MiddleButton instead [-Wdeprecated-declarations] + 37 | MiddleButton=Qt::MidButton + | ^~~~~~~~~ +In file included from /usr/include/x86_64-linux-gnu/qt5/QtCore/qbytearray.h:45, + from /usr/include/x86_64-linux-gnu/qt5/QtCore/qstring.h:50, + from /usr/include/x86_64-linux-gnu/qt5/QtCore/qdatetime.h:44, + from /usr/include/x86_64-linux-gnu/qt5/QtCore/QTime:1, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/output_redirector.hh:30, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:33: +/usr/include/x86_64-linux-gnu/qt5/QtCore/qnamespace.h:132:9: note: declared here + 132 | MidButton Q_DECL_ENUMERATOR_DEPRECATED_X("MidButton is deprecated. Use MiddleButton instead") = MiddleButton, + | ^~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool.hh:30, from /build/openstructure-2.3.1/modules/gui/src/tools/manipulator.hh:29, from /build/openstructure-2.3.1/modules/gui/src/tools/manipulator.cc:29: @@ -23695,6 +22681,10 @@ /usr/include/x86_64-linux-gnu/qt5/QtCore/qnamespace.h:132:9: note: declared here 132 | MidButton Q_DECL_ENUMERATOR_DEPRECATED_X("MidButton is deprecated. Use MiddleButton instead") = MiddleButton, | ^~~~~~~~~ +[ 85%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_tokenizer.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_tokenizer.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/python_tokenizer.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/python_tokenizer.cc.o -c /build/openstructure-2.3.1/modules/gui/src/python_shell/python_tokenizer.cc +[ 85%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_syntax_highlighter.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_syntax_highlighter.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/python_syntax_highlighter.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/python_syntax_highlighter.cc.o -c /build/openstructure-2.3.1/modules/gui/src/python_shell/python_syntax_highlighter.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -23708,28 +22698,41 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter_worker.hh:29, - from /build/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter.hh:31, - from /build/openstructure-2.3.1/modules/gui/src/python_shell/python_shell_widget.hh:28, - from /build/openstructure-2.3.1/modules/gui/src/python_shell/gutter.cc:22: + from /build/openstructure-2.3.1/modules/gfx/pymod/export_primitives.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 88%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/shell_history.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/shell_history.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/shell_history.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/shell_history.cc.o -c /build/openstructure-2.3.1/modules/gui/src/python_shell/shell_history.cc -[ 88%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/string_literal_positions.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/string_literal_positions.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/string_literal_positions.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/string_literal_positions.cc.o -c /build/openstructure-2.3.1/modules/gui/src/python_shell/string_literal_positions.cc -[ 88%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/text_logger.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/text_logger.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/text_logger.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/text_logger.cc.o -c /build/openstructure-2.3.1/modules/gui/src/python_shell/text_logger.cc -[ 88%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/state_machine.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/state_machine.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/state_machine.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/state_machine.cc.o -c /build/openstructure-2.3.1/modules/gui/src/python_shell/state_machine.cc -[ 89%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/state.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/state.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/state.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/state.cc.o -c /build/openstructure-2.3.1/modules/gui/src/python_shell/state.cc -[ 89%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/transition.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/transition.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/transition.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/transition.cc.o -c /build/openstructure-2.3.1/modules/gui/src/python_shell/transition.cc +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/primitives.hh:22, + from /build/openstructure-2.3.1/modules/gfx/pymod/export_primitives.cc:22: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/bits/specfun.h:45, + from /usr/include/c++/12/cmath:1935, + from /usr/include/c++/12/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 85%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_primlist.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_primlist.cc.o -MF CMakeFiles/_ost_gfx.dir/export_primlist.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_primlist.cc.o -c /build/openstructure-2.3.1/modules/gfx/pymod/export_primlist.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -23744,13 +22747,16 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter_worker.hh:29, - from /build/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter_worker.cc:21: + from /build/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter.hh:31, + from /build/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter.cc:25: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 85%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/shell_history.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/shell_history.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/shell_history.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/shell_history.cc.o -c /build/openstructure-2.3.1/modules/gui/src/python_shell/shell_history.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -23765,18 +22771,15 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter_worker.hh:29, - from /build/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter.hh:31, - from /build/openstructure-2.3.1/modules/gui/src/python_shell/python_namespace_tree_model.cc:19: + from /build/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter_worker.cc:21: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 89%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/transition_guard.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/transition_guard.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/transition_guard.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/transition_guard.cc.o -c /build/openstructure-2.3.1/modules/gui/src/python_shell/transition_guard.cc -[ 89%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/context_menu.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/context_menu.cc.o -MF CMakeFiles/ost_gui.dir/scene_win/context_menu.cc.o.d -o CMakeFiles/ost_gui.dir/scene_win/context_menu.cc.o -c /build/openstructure-2.3.1/modules/gui/src/scene_win/context_menu.cc +[ 85%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/string_literal_positions.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/string_literal_positions.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/string_literal_positions.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/string_literal_positions.cc.o -c /build/openstructure-2.3.1/modules/gui/src/python_shell/string_literal_positions.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -23792,15 +22795,19 @@ from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter_worker.hh:29, from /build/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter.hh:31, - from /build/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter.cc:25: + from /build/openstructure-2.3.1/modules/gui/src/python_shell/python_namespace_tree_model.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 89%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/current_selection_node.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/current_selection_node.cc.o -MF CMakeFiles/ost_gui.dir/scene_win/current_selection_node.cc.o.d -o CMakeFiles/ost_gui.dir/scene_win/current_selection_node.cc.o -c /build/openstructure-2.3.1/modules/gui/src/scene_win/current_selection_node.cc +[ 85%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/state_machine.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/state_machine.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/state_machine.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/state_machine.cc.o -c /build/openstructure-2.3.1/modules/gui/src/python_shell/state_machine.cc +[ 85%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/text_logger.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/text_logger.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/text_logger.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/text_logger.cc.o -c /build/openstructure-2.3.1/modules/gui/src/python_shell/text_logger.cc +[ 87%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/state.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/state.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/state.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/state.cc.o -c /build/openstructure-2.3.1/modules/gui/src/python_shell/state.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -23814,16 +22821,18 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter_worker.hh:29, - from /build/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter.hh:31, - from /build/openstructure-2.3.1/modules/gui/src/python_shell/python_shell_widget.hh:28, - from /build/openstructure-2.3.1/modules/gui/src/python_shell/python_shell.cc:24: + from /build/openstructure-2.3.1/modules/gui/src/python_shell/python_namespace_tree_item.hh:25, + from /build/openstructure-2.3.1/modules/gui/src/python_shell/python_namespace_tree_item.cc:20: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 87%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/transition.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/transition.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/transition.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/transition.cc.o -c /build/openstructure-2.3.1/modules/gui/src/python_shell/transition.cc +[ 87%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/transition_guard.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/transition_guard.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/transition_guard.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/transition_guard.cc.o -c /build/openstructure-2.3.1/modules/gui/src/python_shell/transition_guard.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -23837,16 +22846,16 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/gui/src/python_shell/python_namespace_tree_item.hh:25, - from /build/openstructure-2.3.1/modules/gui/src/python_shell/python_namespace_tree_item.cc:20: + from /build/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter_worker.hh:29, + from /build/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter.hh:31, + from /build/openstructure-2.3.1/modules/gui/src/python_shell/python_shell_widget.hh:28, + from /build/openstructure-2.3.1/modules/gui/src/python_shell/python_shell.cc:24: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 89%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/custom_part_node.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/custom_part_node.cc.o -MF CMakeFiles/ost_gui.dir/scene_win/custom_part_node.cc.o.d -o CMakeFiles/ost_gui.dir/scene_win/custom_part_node.cc.o -c /build/openstructure-2.3.1/modules/gui/src/scene_win/custom_part_node.cc /build/openstructure-2.3.1/modules/gui/src/python_shell/python_namespace_tree_model.cc: In member function 'virtual Qt::ItemFlags ost::gui::PythonNamespaceTreeModel::flags(const QModelIndex&) const': /build/openstructure-2.3.1/modules/gui/src/python_shell/python_namespace_tree_model.cc:110:12: warning: 'constexpr QFlags::QFlags(Zero) [with Enum = Qt::ItemFlag; Zero = int QFlags::Private::*]' is deprecated: Use default constructor instead [-Wdeprecated-declarations] 110 | return 0; @@ -23861,6 +22870,8 @@ /usr/include/x86_64-linux-gnu/qt5/QtCore/qflags.h:123:80: note: declared here 123 | QT_DEPRECATED_X("Use default constructor instead") Q_DECL_CONSTEXPR inline QFlags(Zero) noexcept : i(0) {} | ^~~~~~ +[ 87%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_scene_observer.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_scene_observer.cc.o -MF CMakeFiles/_ost_gfx.dir/export_scene_observer.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_scene_observer.cc.o -c /build/openstructure-2.3.1/modules/gfx/pymod/export_scene_observer.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -23884,37 +22895,20 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 89%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/scene_node.cc.o +[ 87%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/context_menu.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/context_menu.cc.o -MF CMakeFiles/ost_gui.dir/scene_win/context_menu.cc.o.d -o CMakeFiles/ost_gui.dir/scene_win/context_menu.cc.o -c /build/openstructure-2.3.1/modules/gui/src/scene_win/context_menu.cc +[ 87%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/current_selection_node.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/current_selection_node.cc.o -MF CMakeFiles/ost_gui.dir/scene_win/current_selection_node.cc.o.d -o CMakeFiles/ost_gui.dir/scene_win/current_selection_node.cc.o -c /build/openstructure-2.3.1/modules/gui/src/scene_win/current_selection_node.cc +[ 87%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/custom_part_node.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/custom_part_node.cc.o -MF CMakeFiles/ost_gui.dir/scene_win/custom_part_node.cc.o.d -o CMakeFiles/ost_gui.dir/scene_win/custom_part_node.cc.o -c /build/openstructure-2.3.1/modules/gui/src/scene_win/custom_part_node.cc +[ 87%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/scene_node.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/scene_node.cc.o -MF CMakeFiles/ost_gui.dir/scene_win/scene_node.cc.o.d -o CMakeFiles/ost_gui.dir/scene_win/scene_node.cc.o -c /build/openstructure-2.3.1/modules/gui/src/scene_win/scene_node.cc -[ 89%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/label_node.cc.o +[ 87%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/label_node.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/label_node.cc.o -MF CMakeFiles/ost_gui.dir/scene_win/label_node.cc.o.d -o CMakeFiles/ost_gui.dir/scene_win/label_node.cc.o -c /build/openstructure-2.3.1/modules/gui/src/scene_win/label_node.cc -[ 89%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/entity_node.cc.o +[ 87%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/entity_node.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/entity_node.cc.o -MF CMakeFiles/ost_gui.dir/scene_win/entity_node.cc.o.d -o CMakeFiles/ost_gui.dir/scene_win/entity_node.cc.o -c /build/openstructure-2.3.1/modules/gui/src/scene_win/entity_node.cc -[ 89%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/entity_part_node.cc.o +[ 87%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/entity_part_node.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/entity_part_node.cc.o -MF CMakeFiles/ost_gui.dir/scene_win/entity_part_node.cc.o.d -o CMakeFiles/ost_gui.dir/scene_win/entity_part_node.cc.o -c /build/openstructure-2.3.1/modules/gui/src/scene_win/entity_part_node.cc -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter_worker.hh:29, - from /build/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter.hh:31, - from /build/openstructure-2.3.1/modules/gui/src/python_shell/text_logger.hh:26, - from /build/openstructure-2.3.1/modules/gui/src/python_shell/text_logger.cc:19: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ /build/openstructure-2.3.1/modules/gui/src/python_shell/python_shell_widget.cc: In constructor 'ost::gui::PythonShellWidget::PythonShellWidget(QWidget*)': /build/openstructure-2.3.1/modules/gui/src/python_shell/python_shell_widget.cc:79:34: warning: 'int QFontMetrics::width(const QString&, int) const' is deprecated: Use QFontMetrics::horizontalAdvance [-Wdeprecated-declarations] 79 | setTabStopWidth(2*metrics.width(" ")); @@ -23935,6 +22929,19 @@ /usr/include/x86_64-linux-gnu/qt5/QtWidgets/qplaintextedit.h:179:24: note: declared here 179 | QT_DEPRECATED void setTabStopWidth(int width); | ^~~~~~~~~~~~~~~ +/build/openstructure-2.3.1/modules/gui/src/python_shell/python_shell_widget.cc: In member function 'void ost::gui::PythonShellWidget::SetTabWidth(int)': +/build/openstructure-2.3.1/modules/gui/src/python_shell/python_shell_widget.cc:537:43: warning: 'int QFontMetrics::width(const QString&, int) const' is deprecated: Use QFontMetrics::horizontalAdvance [-Wdeprecated-declarations] + 537 | setTabStopWidth(tab_width_*metrics.width(" ")); + | ~~~~~~~~~~~~~^~~~~ +/usr/include/x86_64-linux-gnu/qt5/QtGui/qfontmetrics.h:106:9: note: declared here + 106 | int width(const QString &, int len = -1) const; + | ^~~~~ +/build/openstructure-2.3.1/modules/gui/src/python_shell/python_shell_widget.cc:537:18: warning: 'void QPlainTextEdit::setTabStopWidth(int)' is deprecated [-Wdeprecated-declarations] + 537 | setTabStopWidth(tab_width_*metrics.width(" ")); + | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/x86_64-linux-gnu/qt5/QtWidgets/qplaintextedit.h:179:24: note: declared here + 179 | QT_DEPRECATED void setTabStopWidth(int width); + | ^~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -23948,29 +22955,37 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter_worker.hh:29, - from /build/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter.hh:31, - from /build/openstructure-2.3.1/modules/gui/src/python_shell/transition_guard.hh:24, - from /build/openstructure-2.3.1/modules/gui/src/python_shell/transition_guard.cc:21: + from /build/openstructure-2.3.1/modules/gfx/pymod/export_primlist.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -/build/openstructure-2.3.1/modules/gui/src/python_shell/python_shell_widget.cc: In member function 'void ost::gui::PythonShellWidget::SetTabWidth(int)': -/build/openstructure-2.3.1/modules/gui/src/python_shell/python_shell_widget.cc:537:43: warning: 'int QFontMetrics::width(const QString&, int) const' is deprecated: Use QFontMetrics::horizontalAdvance [-Wdeprecated-declarations] - 537 | setTabStopWidth(tab_width_*metrics.width(" ")); - | ~~~~~~~~~~~~~^~~~~ -/usr/include/x86_64-linux-gnu/qt5/QtGui/qfontmetrics.h:106:9: note: declared here - 106 | int width(const QString &, int len = -1) const; - | ^~~~~ -/build/openstructure-2.3.1/modules/gui/src/python_shell/python_shell_widget.cc:537:18: warning: 'void QPlainTextEdit::setTabStopWidth(int)' is deprecated [-Wdeprecated-declarations] - 537 | setTabStopWidth(tab_width_*metrics.width(" ")); - | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/x86_64-linux-gnu/qt5/QtWidgets/qplaintextedit.h:179:24: note: declared here - 179 | QT_DEPRECATED void setTabStopWidth(int width); - | ^~~~~~~~~~~~~~~ +[ 88%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/gfx_scene_node.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/gfx_scene_node.cc.o -MF CMakeFiles/ost_gui.dir/scene_win/gfx_scene_node.cc.o.d -o CMakeFiles/ost_gui.dir/scene_win/gfx_scene_node.cc.o -c /build/openstructure-2.3.1/modules/gui/src/scene_win/gfx_scene_node.cc +[ 88%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/render_mode_node.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/render_mode_node.cc.o -MF CMakeFiles/ost_gui.dir/scene_win/render_mode_node.cc.o.d -o CMakeFiles/ost_gui.dir/scene_win/render_mode_node.cc.o -c /build/openstructure-2.3.1/modules/gui/src/scene_win/render_mode_node.cc +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter_worker.hh:29, + from /build/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter.hh:31, + from /build/openstructure-2.3.1/modules/gui/src/python_shell/text_logger.hh:26, + from /build/openstructure-2.3.1/modules/gui/src/python_shell/text_logger.cc:19: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -23994,21 +23009,26 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 91%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/gfx_scene_node.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/gfx_scene_node.cc.o -MF CMakeFiles/ost_gui.dir/scene_win/gfx_scene_node.cc.o.d -o CMakeFiles/ost_gui.dir/scene_win/gfx_scene_node.cc.o -c /build/openstructure-2.3.1/modules/gui/src/scene_win/gfx_scene_node.cc +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color.hh:31, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/scene.hh:37, - from /build/openstructure-2.3.1/modules/gui/src/scene_win/context_menu.cc:27: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/prim_list.hh:28, + from /build/openstructure-2.3.1/modules/gfx/pymod/export_primlist.cc:25: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/memory:63, - from /usr/include/boost/pointer_cast.hpp:52, - from /build/openstructure-2.3.1/modules/gui/src/scene_win/context_menu.cc:22: + from /usr/include/c++/12/bits/specfun.h:45, + from /usr/include/c++/12/cmath:1935, + from /usr/include/c++/12/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -24018,33 +23038,6 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 91%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/render_mode_node.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/render_mode_node.cc.o -MF CMakeFiles/ost_gui.dir/scene_win/render_mode_node.cc.o.d -o CMakeFiles/ost_gui.dir/scene_win/render_mode_node.cc.o -c /build/openstructure-2.3.1/modules/gui/src/scene_win/render_mode_node.cc -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter_worker.hh:29, - from /build/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter.hh:31, - from /build/openstructure-2.3.1/modules/gui/src/python_shell/python_shell_widget.hh:28, - from /build/openstructure-2.3.1/modules/gui/src/python_shell/transition.cc:20: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 91%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/render_modes_node.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/render_modes_node.cc.o -MF CMakeFiles/ost_gui.dir/scene_win/render_modes_node.cc.o.d -o CMakeFiles/ost_gui.dir/scene_win/render_modes_node.cc.o -c /build/openstructure-2.3.1/modules/gui/src/scene_win/render_modes_node.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -24074,6 +23067,28 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color.hh:31, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/scene.hh:37, + from /build/openstructure-2.3.1/modules/gui/src/scene_win/context_menu.cc:27: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/memory:63, + from /usr/include/boost/pointer_cast.hpp:52, + from /build/openstructure-2.3.1/modules/gui/src/scene_win/context_menu.cc:22: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -24087,53 +23102,39 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main.hh:23, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, - from /build/openstructure-2.3.1/modules/gui/src/scene_win/current_selection_node.cc:20: + from /build/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter_worker.hh:29, + from /build/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter.hh:31, + from /build/openstructure-2.3.1/modules/gui/src/python_shell/python_shell_widget.hh:28, + from /build/openstructure-2.3.1/modules/gui/src/python_shell/transition.cc:20: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[ 91%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/root_node.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/root_node.cc.o -MF CMakeFiles/ost_gui.dir/scene_win/root_node.cc.o.d -o CMakeFiles/ost_gui.dir/scene_win/root_node.cc.o -c /build/openstructure-2.3.1/modules/gui/src/scene_win/root_node.cc /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 91%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/scene_win.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/scene_win.cc.o -MF CMakeFiles/ost_gui.dir/scene_win/scene_win.cc.o.d -o CMakeFiles/ost_gui.dir/scene_win/scene_win.cc.o -c /build/openstructure-2.3.1/modules/gui/src/scene_win/scene_win.cc -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, - from /build/openstructure-2.3.1/modules/gui/src/scene_win/entity_part_node.hh:23, - from /build/openstructure-2.3.1/modules/gui/src/scene_win/entity_part_node.cc:20: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/memory:63, - from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, - from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/view_type_fw.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:22: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -[ 91%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/scene_win_model.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/scene_win_model.cc.o -MF CMakeFiles/ost_gui.dir/scene_win/scene_win_model.cc.o.d -o CMakeFiles/ost_gui.dir/scene_win/scene_win_model.cc.o -c /build/openstructure-2.3.1/modules/gui/src/scene_win/scene_win_model.cc + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter_worker.hh:29, + from /build/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter.hh:31, + from /build/openstructure-2.3.1/modules/gui/src/python_shell/transition_guard.hh:24, + from /build/openstructure-2.3.1/modules/gui/src/python_shell/transition_guard.cc:21: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -24158,6 +23159,26 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/openstructure-2.3.1/modules/gfx/pymod/export_scene_observer.cc:1: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -24165,19 +23186,19 @@ from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, - from /build/openstructure-2.3.1/modules/gui/src/scene_win/current_selection_node.cc:21: + from /build/openstructure-2.3.1/modules/gui/src/scene_win/entity_part_node.hh:23, + from /build/openstructure-2.3.1/modules/gui/src/scene_win/entity_part_node.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/specfun.h:45, - from /usr/include/c++/12/cmath:1935, - from /usr/include/c++/12/math.h:36, - from /usr/include/python3.11/pyport.h:218, - from /usr/include/python3.11/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8: + from /usr/include/c++/12/memory:63, + from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, + from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, + from /usr/include/boost/shared_ptr.hpp:17, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/view_type_fw.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -24205,6 +23226,37 @@ from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, + from /build/openstructure-2.3.1/modules/gui/src/scene_win/current_selection_node.cc:20: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 88%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/render_modes_node.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/render_modes_node.cc.o -MF CMakeFiles/ost_gui.dir/scene_win/render_modes_node.cc.o.d -o CMakeFiles/ost_gui.dir/scene_win/render_modes_node.cc.o -c /build/openstructure-2.3.1/modules/gui/src/scene_win/render_modes_node.cc +[ 88%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/root_node.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/root_node.cc.o -MF CMakeFiles/ost_gui.dir/scene_win/root_node.cc.o.d -o CMakeFiles/ost_gui.dir/scene_win/root_node.cc.o -c /build/openstructure-2.3.1/modules/gui/src/scene_win/root_node.cc +[ 88%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/scene_win.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/scene_win.cc.o -MF CMakeFiles/ost_gui.dir/scene_win/scene_win.cc.o.d -o CMakeFiles/ost_gui.dir/scene_win/scene_win.cc.o -c /build/openstructure-2.3.1/modules/gui/src/scene_win/scene_win.cc +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main.hh:23, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /build/openstructure-2.3.1/modules/gui/src/scene_win/entity_node.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( @@ -24212,10 +23264,6 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 91%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/map_tool.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/map_tool.cc.o -MF CMakeFiles/ost_gui.dir/tools/map_tool.cc.o.d -o CMakeFiles/ost_gui.dir/tools/map_tool.cc.o -c /build/openstructure-2.3.1/modules/gui/src/tools/map_tool.cc -[ 91%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/argand.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/argand.cc.o -MF CMakeFiles/ost_gui.dir/data_viewer/argand.cc.o.d -o CMakeFiles/ost_gui.dir/data_viewer/argand.cc.o -c /build/openstructure-2.3.1/modules/gui/src/data_viewer/argand.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -24244,10 +23292,6 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 91%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/data_viewer.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/data_viewer.cc.o -MF CMakeFiles/ost_gui.dir/data_viewer/data_viewer.cc.o.d -o CMakeFiles/ost_gui.dir/data_viewer/data_viewer.cc.o -c /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer.cc -[ 91%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/data_viewer_panel.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/data_viewer_panel.cc.o -MF CMakeFiles/ost_gui.dir/data_viewer/data_viewer_panel.cc.o.d -o CMakeFiles/ost_gui.dir/data_viewer/data_viewer_panel.cc.o -c /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -24274,22 +23318,32 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 88%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/scene_win_model.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/scene_win_model.cc.o -MF CMakeFiles/ost_gui.dir/scene_win/scene_win_model.cc.o.d -o CMakeFiles/ost_gui.dir/scene_win/scene_win_model.cc.o -c /build/openstructure-2.3.1/modules/gui/src/scene_win/scene_win_model.cc +[ 88%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_render_options.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_render_options.cc.o -MF CMakeFiles/_ost_gfx.dir/export_render_options.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_render_options.cc.o -c /build/openstructure-2.3.1/modules/gfx/pymod/export_render_options.cc +[ 88%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/map_tool.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/map_tool.cc.o -MF CMakeFiles/ost_gui.dir/tools/map_tool.cc.o.d -o CMakeFiles/ost_gui.dir/tools/map_tool.cc.o -c /build/openstructure-2.3.1/modules/gui/src/tools/map_tool.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color.hh:31, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/scene.hh:37, - from /build/openstructure-2.3.1/modules/gui/src/scene_win/root_node.cc:22: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, + from /build/openstructure-2.3.1/modules/gui/src/scene_win/current_selection_node.cc:21: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/module_config.hh:26, - from /build/openstructure-2.3.1/modules/gui/src/scene_win/root_node.hh:23, - from /build/openstructure-2.3.1/modules/gui/src/scene_win/root_node.cc:20: + from /usr/include/c++/12/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -24299,6 +23353,18 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 88%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_color.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_color.cc.o -MF CMakeFiles/_ost_gfx.dir/export_color.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_color.cc.o -c /build/openstructure-2.3.1/modules/gfx/pymod/export_color.cc +[ 88%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/argand.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/argand.cc.o -MF CMakeFiles/ost_gui.dir/data_viewer/argand.cc.o.d -o CMakeFiles/ost_gui.dir/data_viewer/argand.cc.o -c /build/openstructure-2.3.1/modules/gui/src/data_viewer/argand.cc +[ 88%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/data_viewer.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/data_viewer.cc.o -MF CMakeFiles/ost_gui.dir/data_viewer/data_viewer.cc.o.d -o CMakeFiles/ost_gui.dir/data_viewer/data_viewer.cc.o -c /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer.cc +[ 88%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/data_viewer_panel.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/data_viewer_panel.cc.o -MF CMakeFiles/ost_gui.dir/data_viewer/data_viewer_panel.cc.o.d -o CMakeFiles/ost_gui.dir/data_viewer/data_viewer_panel.cc.o -c /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel.cc +[ 88%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/data_viewer_panel_base.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/data_viewer_panel_base.cc.o -MF CMakeFiles/ost_gui.dir/data_viewer/data_viewer_panel_base.cc.o.d -o CMakeFiles/ost_gui.dir/data_viewer/data_viewer_panel_base.cc.o -c /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel_base.cc +[ 89%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/draw_overlay.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/draw_overlay.cc.o -MF CMakeFiles/ost_gui.dir/data_viewer/draw_overlay.cc.o.d -o CMakeFiles/ost_gui.dir/data_viewer/draw_overlay.cc.o -c /build/openstructure-2.3.1/modules/gui/src/data_viewer/draw_overlay.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -24326,8 +23392,31 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 91%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/data_viewer_panel_base.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/data_viewer_panel_base.cc.o -MF CMakeFiles/ost_gui.dir/data_viewer/data_viewer_panel_base.cc.o.d -o CMakeFiles/ost_gui.dir/data_viewer/data_viewer_panel_base.cc.o -c /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel_base.cc +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color.hh:31, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/scene.hh:37, + from /build/openstructure-2.3.1/modules/gui/src/scene_win/root_node.cc:22: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/bits/specfun.h:45, + from /usr/include/c++/12/cmath:1935, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/module_config.hh:26, + from /build/openstructure-2.3.1/modules/gui/src/scene_win/root_node.hh:23, + from /build/openstructure-2.3.1/modules/gui/src/scene_win/root_node.cc:20: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -24353,9 +23442,7 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 92%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/draw_overlay.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/draw_overlay.cc.o -MF CMakeFiles/ost_gui.dir/data_viewer/draw_overlay.cc.o.d -o CMakeFiles/ost_gui.dir/data_viewer/draw_overlay.cc.o -c /build/openstructure-2.3.1/modules/gui/src/data_viewer/draw_overlay.cc -[ 92%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/drawing_functions.cc.o +[ 89%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/drawing_functions.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/drawing_functions.cc.o -MF CMakeFiles/ost_gui.dir/data_viewer/drawing_functions.cc.o.d -o CMakeFiles/ost_gui.dir/data_viewer/drawing_functions.cc.o -c /build/openstructure-2.3.1/modules/gui/src/data_viewer/drawing_functions.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, @@ -24386,10 +23473,35 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 92%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/fft_panel.cc.o +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/extent.hh:34, + from /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel_base.hh:34, + from /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel.hh:24, + from /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel.cc:20: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/bits/specfun.h:45, + from /usr/include/c++/12/cmath:1935, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/module_config.hh:26, + from /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel.hh:23: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 89%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/fft_panel.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/fft_panel.cc.o -MF CMakeFiles/ost_gui.dir/data_viewer/fft_panel.cc.o.d -o CMakeFiles/ost_gui.dir/data_viewer/fft_panel.cc.o -c /build/openstructure-2.3.1/modules/gui/src/data_viewer/fft_panel.cc -[ 92%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/info_panel.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/info_panel.cc.o -MF CMakeFiles/ost_gui.dir/data_viewer/info_panel.cc.o.d -o CMakeFiles/ost_gui.dir/data_viewer/info_panel.cc.o -c /build/openstructure-2.3.1/modules/gui/src/data_viewer/info_panel.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -24412,9 +23524,6 @@ /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -24437,13 +23546,14 @@ /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[ 92%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/img2qt.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/img2qt.cc.o -MF CMakeFiles/ost_gui.dir/data_viewer/img2qt.cc.o.d -o CMakeFiles/ost_gui.dir/data_viewer/img2qt.cc.o -c /build/openstructure-2.3.1/modules/gui/src/data_viewer/img2qt.cc /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 92%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/mask_overlay.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/mask_overlay.cc.o -MF CMakeFiles/ost_gui.dir/data_viewer/mask_overlay.cc.o.d -o CMakeFiles/ost_gui.dir/data_viewer/mask_overlay.cc.o -c /build/openstructure-2.3.1/modules/gui/src/data_viewer/mask_overlay.cc +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 89%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/info_panel.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/info_panel.cc.o -MF CMakeFiles/ost_gui.dir/data_viewer/info_panel.cc.o.d -o CMakeFiles/ost_gui.dir/data_viewer/info_panel.cc.o -c /build/openstructure-2.3.1/modules/gui/src/data_viewer/info_panel.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -24452,7 +23562,7 @@ from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/extent.hh:34, from /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel_base.hh:34, from /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel.hh:24, - from /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel.cc:20: + from /build/openstructure-2.3.1/modules/gui/src/data_viewer/draw_overlay.cc:26: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -24471,17 +23581,48 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/openstructure-2.3.1/modules/gfx/pymod/export_render_options.cc:19: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/modules/gui/src/data_viewer/drawing_functions.hh:28, - from /build/openstructure-2.3.1/modules/gui/src/data_viewer/drawing_functions.cc:27: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/normalizer_impl.hh:32, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/norm_linear.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/norm.hh:30, + from /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel_base.cc:25: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/algorithm:60, - from /build/openstructure-2.3.1/modules/gui/src/data_viewer/drawing_functions.cc:25: + from /usr/include/c++/12/memory:63, + from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, + from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, + from /usr/include/boost/shared_ptr.hpp:17, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/normalizer_impl.hh:30: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -24491,26 +23632,17 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 92%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/null_overlay.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/null_overlay.cc.o -MF CMakeFiles/ost_gui.dir/data_viewer/null_overlay.cc.o.d -o CMakeFiles/ost_gui.dir/data_viewer/null_overlay.cc.o -c /build/openstructure-2.3.1/modules/gui/src/data_viewer/null_overlay.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/extent.hh:34, - from /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel_base.hh:34, - from /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel.hh:24, - from /build/openstructure-2.3.1/modules/gui/src/data_viewer/draw_overlay.cc:26: + from /build/openstructure-2.3.1/modules/gui/src/data_viewer/drawing_functions.hh:28, + from /build/openstructure-2.3.1/modules/gui/src/data_viewer/drawing_functions.cc:27: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/specfun.h:45, - from /usr/include/c++/12/cmath:1935, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/module_config.hh:26, - from /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel.hh:23: + from /usr/include/c++/12/algorithm:60, + from /build/openstructure-2.3.1/modules/gui/src/data_viewer/drawing_functions.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -24520,8 +23652,26 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 92%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/overlay_base.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/overlay_base.cc.o -MF CMakeFiles/ost_gui.dir/data_viewer/overlay_base.cc.o.d -o CMakeFiles/ost_gui.dir/data_viewer/overlay_base.cc.o -c /build/openstructure-2.3.1/modules/gui/src/data_viewer/overlay_base.cc +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/openstructure-2.3.1/modules/gfx/pymod/export_color.cc:19: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ /build/openstructure-2.3.1/modules/gui/src/scene_win/scene_win_model.cc: In member function 'virtual QMimeData* ost::gui::SceneWinModel::mimeData(const QModelIndexList&) const': /build/openstructure-2.3.1/modules/gui/src/scene_win/scene_win_model.cc:231:26: warning: 'QByteArray& QByteArray::append(const QString&)' is deprecated: Use QString's toUtf8(), toLatin1() or toLocal8Bit() [-Wdeprecated-declarations] 231 | encoded_data.append(text); @@ -24533,54 +23683,48 @@ /usr/include/x86_64-linux-gnu/qt5/QtCore/qstring.h:1511:20: note: declared here 1511 | inline QByteArray &QByteArray::append(const QString &s) | ^~~~~~~~~~ +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main.hh:23, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, + from /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer.cc:26: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 89%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/img2qt.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/img2qt.cc.o -MF CMakeFiles/ost_gui.dir/data_viewer/img2qt.cc.o.d -o CMakeFiles/ost_gui.dir/data_viewer/img2qt.cc.o -c /build/openstructure-2.3.1/modules/gui/src/data_viewer/img2qt.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/fft.hh:27, - from /build/openstructure-2.3.1/modules/gui/src/data_viewer/fft_panel.cc:25: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/12/string:45, - from /usr/include/c++/12/stdexcept:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/fft.hh:24: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/normalizer_impl.hh:32, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/norm_linear.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/norm.hh:30, - from /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel_base.cc:25: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/map_slab.hh:29, + from /build/openstructure-2.3.1/modules/gui/src/tools/map_tool.cc:21: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/memory:63, - from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, - from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, - from /usr/include/boost/shared_ptr.hpp:17, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/normalizer_impl.hh:30: + from /usr/include/c++/12/bits/specfun.h:45, + from /usr/include/c++/12/cmath:1935, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/module_config.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/platform.hh:22, + from /build/openstructure-2.3.1/modules/gui/src/tools/map_tool.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -24590,20 +23734,25 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 89%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/mask_overlay.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/mask_overlay.cc.o -MF CMakeFiles/ost_gui.dir/data_viewer/mask_overlay.cc.o.d -o CMakeFiles/ost_gui.dir/data_viewer/mask_overlay.cc.o -c /build/openstructure-2.3.1/modules/gui/src/data_viewer/mask_overlay.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, - from /build/openstructure-2.3.1/modules/gui/src/data_viewer/info_panel.cc:28: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color.hh:31, + from /build/openstructure-2.3.1/modules/gfx/pymod/export_color.cc:23: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/vector:60, - from /usr/include/boost/format.hpp:17, - from /build/openstructure-2.3.1/modules/gui/src/data_viewer/info_panel.cc:25: + from /usr/include/c++/12/bits/specfun.h:45, + from /usr/include/c++/12/cmath:1935, + from /usr/include/c++/12/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -24643,17 +23792,6 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -/build/openstructure-2.3.1/modules/gui/src/scene_win/scene_win.cc: In member function 'void ost::gui::SceneWin::RowsInserted(const QModelIndex&, int, int)': -/build/openstructure-2.3.1/modules/gui/src/scene_win/scene_win.cc:117:31: warning: 'QModelIndex QModelIndex::child(int, int) const' is deprecated: Use QAbstractItemModel::index [-Wdeprecated-declarations] - 117 | model->select(parent.child(start,0),QItemSelectionModel::ClearAndSelect|QItemSelectionModel::Rows); - | ~~~~~~~~~~~~^~~~~~~~~ -In file included from /usr/include/x86_64-linux-gnu/qt5/QtCore/QModelIndex:1, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/scene_node.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/scene_win_model.hh:34, - from /build/openstructure-2.3.1/modules/gui/src/scene_win/scene_win.cc:26: -/usr/include/x86_64-linux-gnu/qt5/QtCore/qabstractitemmodel.h:455:20: note: declared here - 455 | inline QModelIndex QModelIndex::child(int arow, int acolumn) const - | ^~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -24686,39 +23824,15 @@ from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, - from /build/openstructure-2.3.1/modules/gui/src/data_viewer/img2qt.cc:21: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/specfun.h:45, - from /usr/include/c++/12/cmath:1935, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:30: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/map_slab.hh:29, - from /build/openstructure-2.3.1/modules/gui/src/tools/map_tool.cc:21: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, + from /build/openstructure-2.3.1/modules/gui/src/data_viewer/info_panel.cc:28: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/specfun.h:45, - from /usr/include/c++/12/cmath:1935, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/module_config.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/platform.hh:22, - from /build/openstructure-2.3.1/modules/gui/src/tools/map_tool.cc:20: + from /usr/include/c++/12/vector:60, + from /usr/include/boost/format.hpp:17, + from /build/openstructure-2.3.1/modules/gui/src/data_viewer/info_panel.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -24728,56 +23842,45 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main.hh:23, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, - from /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer.cc:26: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ +/build/openstructure-2.3.1/modules/gui/src/scene_win/scene_win.cc: In member function 'void ost::gui::SceneWin::RowsInserted(const QModelIndex&, int, int)': +/build/openstructure-2.3.1/modules/gui/src/scene_win/scene_win.cc:117:31: warning: 'QModelIndex QModelIndex::child(int, int) const' is deprecated: Use QAbstractItemModel::index [-Wdeprecated-declarations] + 117 | model->select(parent.child(start,0),QItemSelectionModel::ClearAndSelect|QItemSelectionModel::Rows); + | ~~~~~~~~~~~~^~~~~~~~~ +In file included from /usr/include/x86_64-linux-gnu/qt5/QtCore/QModelIndex:1, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/scene_node.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/scene_win_model.hh:34, + from /build/openstructure-2.3.1/modules/gui/src/scene_win/scene_win.cc:26: +/usr/include/x86_64-linux-gnu/qt5/QtCore/qabstractitemmodel.h:455:20: note: declared here + 455 | inline QModelIndex QModelIndex::child(int arow, int acolumn) const + | ^~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/circle_mask.hh:25, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/mask_visitor.hh:28, - from /build/openstructure-2.3.1/modules/gui/src/data_viewer/mask_overlay.cc:26: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/fft.hh:27, + from /build/openstructure-2.3.1/modules/gui/src/data_viewer/fft_panel.cc:25: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/specfun.h:45, - from /usr/include/c++/12/cmath:1935, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:30: +In file included from /usr/include/c++/12/string:45, + from /usr/include/c++/12/stdexcept:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/fft.hh:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 92%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/overlay_manager.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/overlay_manager.cc.o -MF CMakeFiles/ost_gui.dir/data_viewer/overlay_manager.cc.o.d -o CMakeFiles/ost_gui.dir/data_viewer/overlay_manager.cc.o -c /build/openstructure-2.3.1/modules/gui/src/data_viewer/overlay_manager.cc /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 89%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/null_overlay.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/null_overlay.cc.o -MF CMakeFiles/ost_gui.dir/data_viewer/null_overlay.cc.o.d -o CMakeFiles/ost_gui.dir/data_viewer/null_overlay.cc.o -c /build/openstructure-2.3.1/modules/gui/src/data_viewer/null_overlay.cc /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel_base.cc: In member function 'virtual void ost::img::gui::DataViewerPanelBase::paintEvent(QPaintEvent*)': /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel_base.cc:440:56: warning: 'static bool QPixmapCache::find(const QString&, QPixmap&)' is deprecated: Use bool find(const QString &, QPixmap *) instead [-Wdeprecated-declarations] 440 | if (update_raster_image_ || ( !QPixmapCache::find(cache_key, pm))) { @@ -24823,10 +23926,8 @@ /usr/include/x86_64-linux-gnu/qt5/QtGui/qfontmetrics.h:106:9: note: declared here 106 | int width(const QString &, int len = -1) const; | ^~~~~ -[ 92%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/overlay_manager_gui.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/overlay_manager_gui.cc.o -MF CMakeFiles/ost_gui.dir/data_viewer/overlay_manager_gui.cc.o.d -o CMakeFiles/ost_gui.dir/data_viewer/overlay_manager_gui.cc.o -c /build/openstructure-2.3.1/modules/gui/src/data_viewer/overlay_manager_gui.cc -[ 92%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/pointlist_overlay.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/pointlist_overlay.cc.o -MF CMakeFiles/ost_gui.dir/data_viewer/pointlist_overlay.cc.o.d -o CMakeFiles/ost_gui.dir/data_viewer/pointlist_overlay.cc.o -c /build/openstructure-2.3.1/modules/gui/src/data_viewer/pointlist_overlay.cc +[ 89%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/overlay_base.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/overlay_base.cc.o -MF CMakeFiles/ost_gui.dir/data_viewer/overlay_base.cc.o.d -o CMakeFiles/ost_gui.dir/data_viewer/overlay_base.cc.o -c /build/openstructure-2.3.1/modules/gui/src/data_viewer/overlay_base.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -24841,8 +23942,6 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 93%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/pointlist_overlay_base.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/pointlist_overlay_base.cc.o -MF CMakeFiles/ost_gui.dir/data_viewer/pointlist_overlay_base.cc.o.d -o CMakeFiles/ost_gui.dir/data_viewer/pointlist_overlay_base.cc.o -c /build/openstructure-2.3.1/modules/gui/src/data_viewer/pointlist_overlay_base.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -24876,8 +23975,8 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 93%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/strategies.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/strategies.cc.o -MF CMakeFiles/ost_gui.dir/data_viewer/strategies.cc.o.d -o CMakeFiles/ost_gui.dir/data_viewer/strategies.cc.o -c /build/openstructure-2.3.1/modules/gui/src/data_viewer/strategies.cc +[ 89%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/overlay_manager.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/overlay_manager.cc.o -MF CMakeFiles/ost_gui.dir/data_viewer/overlay_manager.cc.o.d -o CMakeFiles/ost_gui.dir/data_viewer/overlay_manager.cc.o -c /build/openstructure-2.3.1/modules/gui/src/data_viewer/overlay_manager.cc In file included from /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer.cc:37: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/dock_widget.hh:38:77: warning: 'constexpr QFlags::QFlags(Zero) [with Enum = Qt::WindowType; Zero = int QFlags::Private::*]' is deprecated: Use default constructor instead [-Wdeprecated-declarations] 38 | DockWidget(const QString& title, QWidget* parent=0, Qt::WindowFlags flags=0); @@ -24900,8 +23999,29 @@ /usr/include/x86_64-linux-gnu/qt5/QtCore/qflags.h:123:80: note: declared here 123 | QT_DEPRECATED_X("Use default constructor instead") Q_DECL_CONSTEXPR inline QFlags(Zero) noexcept : i(0) {} | ^~~~~~ -[ 93%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/viewer_normalizer.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/viewer_normalizer.cc.o -MF CMakeFiles/ost_gui.dir/data_viewer/viewer_normalizer.cc.o.d -o CMakeFiles/ost_gui.dir/data_viewer/viewer_normalizer.cc.o -c /build/openstructure-2.3.1/modules/gui/src/data_viewer/viewer_normalizer.cc +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, + from /build/openstructure-2.3.1/modules/gui/src/data_viewer/img2qt.cc:21: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/bits/specfun.h:45, + from /usr/include/c++/12/cmath:1935, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:30: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer.cc: In constructor 'ost::img::gui::DataViewer::DataViewer(QWidget*, const ost::img::ImageHandle&, const QString&)': /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer.cc:75:14: warning: 'constexpr QFlags::QFlags(Zero) [with Enum = Qt::WindowType; Zero = int QFlags::Private::*]' is deprecated: Use default constructor instead [-Wdeprecated-declarations] 75 | lastmouse_() @@ -24918,6 +24038,37 @@ /usr/include/x86_64-linux-gnu/qt5/QtWidgets/qdesktopwidget.h:88:67: note: declared here 88 | QT_DEPRECATED_X("Use QGuiApplication::screens()") const QRect availableGeometry(int screen = -1) const; | ^~~~~~~~~~~~~~~~~ +[ 89%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/overlay_manager_gui.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/overlay_manager_gui.cc.o -MF CMakeFiles/ost_gui.dir/data_viewer/overlay_manager_gui.cc.o.d -o CMakeFiles/ost_gui.dir/data_viewer/overlay_manager_gui.cc.o -c /build/openstructure-2.3.1/modules/gui/src/data_viewer/overlay_manager_gui.cc +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/circle_mask.hh:25, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/mask_visitor.hh:28, + from /build/openstructure-2.3.1/modules/gui/src/data_viewer/mask_overlay.cc:26: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/bits/specfun.h:45, + from /usr/include/c++/12/cmath:1935, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:30: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 89%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/pointlist_overlay.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/pointlist_overlay.cc.o -MF CMakeFiles/ost_gui.dir/data_viewer/pointlist_overlay.cc.o.d -o CMakeFiles/ost_gui.dir/data_viewer/pointlist_overlay.cc.o -c /build/openstructure-2.3.1/modules/gui/src/data_viewer/pointlist_overlay.cc +[ 91%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/pointlist_overlay_base.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/pointlist_overlay_base.cc.o -MF CMakeFiles/ost_gui.dir/data_viewer/pointlist_overlay_base.cc.o.d -o CMakeFiles/ost_gui.dir/data_viewer/pointlist_overlay_base.cc.o -c /build/openstructure-2.3.1/modules/gui/src/data_viewer/pointlist_overlay_base.cc +[ 91%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/strategies.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/strategies.cc.o -MF CMakeFiles/ost_gui.dir/data_viewer/strategies.cc.o.d -o CMakeFiles/ost_gui.dir/data_viewer/strategies.cc.o -c /build/openstructure-2.3.1/modules/gui/src/data_viewer/strategies.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool.hh:30, from /build/openstructure-2.3.1/modules/gui/src/tools/map_tool.hh:26, from /build/openstructure-2.3.1/modules/gui/src/tools/map_tool.cc:28: @@ -24938,6 +24089,36 @@ /usr/include/x86_64-linux-gnu/qt5/QtCore/qnamespace.h:132:9: note: declared here 132 | MidButton Q_DECL_ENUMERATOR_DEPRECATED_X("MidButton is deprecated. Use MiddleButton instead") = MiddleButton, | ^~~~~~~~~ +[ 91%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/viewer_normalizer.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/viewer_normalizer.cc.o -MF CMakeFiles/ost_gui.dir/data_viewer/viewer_normalizer.cc.o.d -o CMakeFiles/ost_gui.dir/data_viewer/viewer_normalizer.cc.o -c /build/openstructure-2.3.1/modules/gui/src/data_viewer/viewer_normalizer.cc +[ 91%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_gradient.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_gradient.cc.o -MF CMakeFiles/_ost_gfx.dir/export_gradient.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_gradient.cc.o -c /build/openstructure-2.3.1/modules/gfx/pymod/export_gradient.cc +[ 91%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_color_ops.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_color_ops.cc.o -MF CMakeFiles/_ost_gfx.dir/export_color_ops.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_color_ops.cc.o -c /build/openstructure-2.3.1/modules/gfx/pymod/export_color_ops.cc +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/openstructure-2.3.1/modules/gui/src/data_viewer/strategies.hh:29, + from /build/openstructure-2.3.1/modules/gui/src/data_viewer/strategies.cc:26: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/12/string:45, + from /usr/include/c++/12/stdexcept:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec2.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec.hh:24, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:24: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 91%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_glwin_base.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_glwin_base.cc.o -MF CMakeFiles/_ost_gfx.dir/export_glwin_base.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_glwin_base.cc.o -c /build/openstructure-2.3.1/modules/gfx/pymod/export_glwin_base.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -24990,6 +24171,48 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +make -f modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/build.make modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/depend +make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/alg/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/DependInfo.cmake --color= +make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +make -f modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/build.make modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/build +make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[ 91%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/wrap_mol_alg.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/wrap_mol_alg.cc.o -MF CMakeFiles/_ost_mol_alg.dir/wrap_mol_alg.cc.o.d -o CMakeFiles/_ost_mol_alg.dir/wrap_mol_alg.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/pymod/wrap_mol_alg.cc +[ 92%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_exporter.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_exporter.cc.o -MF CMakeFiles/_ost_gfx.dir/export_exporter.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_exporter.cc.o -c /build/openstructure-2.3.1/modules/gfx/pymod/export_exporter.cc +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/extent.hh:34, + from /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel_base.hh:34, + from /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel.hh:24, + from /build/openstructure-2.3.1/modules/gui/src/data_viewer/overlay_manager.cc:29: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/12/string:45, + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/ostream:38, + from /usr/include/c++/12/iostream:39, + from /build/openstructure-2.3.1/modules/gui/src/data_viewer/overlay_manager.cc:25: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 92%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_bitmap.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_bitmap.cc.o -MF CMakeFiles/_ost_gfx.dir/export_bitmap.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_bitmap.cc.o -c /build/openstructure-2.3.1/modules/gfx/pymod/export_bitmap.cc +[ 92%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_map.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_map.cc.o -MF CMakeFiles/_ost_gfx.dir/export_map.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_map.cc.o -c /build/openstructure-2.3.1/modules/gfx/pymod/export_map.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -25018,19 +24241,222 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 92%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_svd_superpose.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_svd_superpose.cc.o -MF CMakeFiles/_ost_mol_alg.dir/export_svd_superpose.cc.o.d -o CMakeFiles/_ost_mol_alg.dir/export_svd_superpose.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/pymod/export_svd_superpose.cc +[ 92%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_clash.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_clash.cc.o -MF CMakeFiles/_ost_mol_alg.dir/export_clash.cc.o.d -o CMakeFiles/_ost_mol_alg.dir/export_clash.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/pymod/export_clash.cc +[ 92%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_trajectory_analysis.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_trajectory_analysis.cc.o -MF CMakeFiles/_ost_mol_alg.dir/export_trajectory_analysis.cc.o.d -o CMakeFiles/_ost_mol_alg.dir/export_trajectory_analysis.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/pymod/export_trajectory_analysis.cc +[ 92%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_structure_analysis.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_structure_analysis.cc.o -MF CMakeFiles/_ost_mol_alg.dir/export_structure_analysis.cc.o.d -o CMakeFiles/_ost_mol_alg.dir/export_structure_analysis.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/pymod/export_structure_analysis.cc +[ 92%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_contact_overlap.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_contact_overlap.cc.o -MF CMakeFiles/_ost_mol_alg.dir/export_contact_overlap.cc.o.d -o CMakeFiles/_ost_mol_alg.dir/export_contact_overlap.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/pymod/export_contact_overlap.cc +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/openstructure-2.3.1/modules/gfx/pymod/export_gradient.cc:24: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/openstructure-2.3.1/modules/gfx/pymod/export_glwin_base.cc:19: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +[ 92%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_accessibility.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_accessibility.cc.o -MF CMakeFiles/_ost_mol_alg.dir/export_accessibility.cc.o.d -o CMakeFiles/_ost_mol_alg.dir/export_accessibility.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/pymod/export_accessibility.cc +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/openstructure-2.3.1/modules/gfx/pymod/export_color_ops.cc:19: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 93%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_sec_structure.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_sec_structure.cc.o -MF CMakeFiles/_ost_mol_alg.dir/export_sec_structure.cc.o.d -o CMakeFiles/_ost_mol_alg.dir/export_sec_structure.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/pymod/export_sec_structure.cc +[ 93%] Linking CXX shared library ../../../stage/lib/libost_gui.so +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_gui.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libost_gui.so.2.3 -o ../../../stage/lib/libost_gui.so.2.3.1 CMakeFiles/ost_gui.dir/moc_file_browser.cpp.o CMakeFiles/ost_gui.dir/moc_file_type_dialog.cpp.o CMakeFiles/ost_gui.dir/moc_file_viewer.cpp.o CMakeFiles/ost_gui.dir/moc_gl_canvas.cpp.o 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CMakeFiles/ost_gui.dir/data_viewer/pointlist_overlay_base.cc.o CMakeFiles/ost_gui.dir/data_viewer/strategies.cc.o CMakeFiles/ost_gui.dir/data_viewer/viewer_normalizer.cc.o -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib: /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so ../../../stage/lib/libost_gfx.so.2.3.1 ../../../stage/lib/libost_io.so.2.3.1 ../../../stage/lib/libost_mol_alg.so.2.3.1 ../../../stage/lib/libost_seq_alg.so.2.3.1 /usr/lib/x86_64-linux-gnu/libOpenGL.so /usr/lib/x86_64-linux-gnu/libGLX.so /usr/lib/x86_64-linux-gnu/libGLU.so /usr/lib/x86_64-linux-gnu/libboost_program_options.so /usr/lib/x86_64-linux-gnu/libboost_thread.so /usr/lib/x86_64-linux-gnu/libboost_chrono.so /usr/lib/x86_64-linux-gnu/libboost_date_time.so /usr/lib/x86_64-linux-gnu/libboost_atomic.so ../../../stage/lib/libost_conop.so.2.3.1 ../../../stage/lib/libost_db.so.2.3.1 /usr/lib/x86_64-linux-gnu/libsqlite3.so ../../../stage/lib/libost_seq.so.2.3.1 ../../../stage/lib/libost_mol.so.2.3.1 ../../../stage/lib/libost_img_alg.so.2.3.1 ../../../stage/lib/libost_img.so.2.3.1 ../../../stage/lib/libost_info.so.2.3.1 /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libfftw3f_threads.so ../../../stage/lib/libost_base.so.2.3.1 ../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libtiff.so /usr/lib/x86_64-linux-gnu/libpng.so /usr/lib/x86_64-linux-gnu/libz.so +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color.hh:31, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gradient.hh:28, + from /build/openstructure-2.3.1/modules/gfx/pymod/export_gradient.cc:29: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/bits/specfun.h:45, + from /usr/include/c++/12/cmath:1935, + from /usr/include/c++/12/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/modules/gui/src/data_viewer/strategies.hh:29, - from /build/openstructure-2.3.1/modules/gui/src/data_viewer/strategies.cc:26: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/color_op.hh:24, + from /build/openstructure-2.3.1/modules/gfx/pymod/export_color_ops.cc:23: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/12/string:45, - from /usr/include/c++/12/stdexcept:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec2.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec.hh:24, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:24: +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/bits/specfun.h:45, + from /usr/include/c++/12/cmath:1935, + from /usr/include/c++/12/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/openstructure-2.3.1/modules/mol/alg/pymod/wrap_mol_alg.cc:20: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/openstructure-2.3.1/modules/gfx/pymod/export_exporter.cc:19: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/openstructure-2.3.1/modules/gfx/pymod/export_bitmap.cc:19: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 93%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_non_standard.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_non_standard.cc.o -MF CMakeFiles/_ost_mol_alg.dir/export_non_standard.cc.o.d -o CMakeFiles/_ost_mol_alg.dir/export_non_standard.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/pymod/export_non_standard.cc +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/local_dist_diff_test.hh:23, + from /build/openstructure-2.3.1/modules/mol/alg/pymod/wrap_mol_alg.cc:25: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/bits/specfun.h:45, + from /usr/include/c++/12/cmath:1935, + from /usr/include/c++/12/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -25040,25 +24466,116 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/local_dist_diff_test.hh:24: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 32 | : public std::iterator{ + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/openstructure-2.3.1/modules/gfx/pymod/export_map.cc:19: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/openstructure-2.3.1/modules/mol/alg/pymod/export_trajectory_analysis.cc:19: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/openstructure-2.3.1/modules/mol/alg/pymod/export_svd_superpose.cc:23: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/openstructure-2.3.1/modules/mol/alg/pymod/export_structure_analysis.cc:19: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/extent.hh:34, - from /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel_base.hh:34, - from /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel.hh:24, - from /build/openstructure-2.3.1/modules/gui/src/data_viewer/overlay_manager.cc:29: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/map.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/map_iso.hh:28, + from /build/openstructure-2.3.1/modules/gfx/pymod/export_map.cc:23: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/12/string:45, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/ostream:38, - from /usr/include/c++/12/iostream:39, - from /build/openstructure-2.3.1/modules/gui/src/data_viewer/overlay_manager.cc:25: +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/bits/specfun.h:45, + from /usr/include/c++/12/cmath:1935, + from /usr/include/c++/12/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -25068,9 +24585,364 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 93%] Linking CXX shared library ../../../stage/lib/libost_gui.so -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_gui.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG 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/usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/openstructure-2.3.1/modules/mol/alg/pymod/export_clash.cc:19: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/trajectory_analysis.hh:29, + from /build/openstructure-2.3.1/modules/mol/alg/pymod/export_trajectory_analysis.cc:22: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/bits/specfun.h:45, + from /usr/include/c++/12/cmath:1935, + from /usr/include/c++/12/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/svd_superpose.hh:27, + from /build/openstructure-2.3.1/modules/mol/alg/pymod/export_svd_superpose.cc:26: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/bits/specfun.h:45, + from /usr/include/c++/12/cmath:1935, + from /usr/include/c++/12/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/openstructure-2.3.1/modules/mol/alg/pymod/export_sec_structure.cc:21: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/structure_analysis.hh:28, + from /build/openstructure-2.3.1/modules/mol/alg/pymod/export_structure_analysis.cc:22: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/bits/specfun.h:45, + from /usr/include/c++/12/cmath:1935, + from /usr/include/c++/12/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/clash_score.hh:26, + from /build/openstructure-2.3.1/modules/mol/alg/pymod/export_clash.cc:23: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/bits/specfun.h:45, + from /usr/include/c++/12/cmath:1935, + from /usr/include/c++/12/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/sec_struct.hh:25, + from /build/openstructure-2.3.1/modules/mol/alg/pymod/export_sec_structure.cc:24: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/bits/specfun.h:45, + from /usr/include/c++/12/cmath:1935, + from /usr/include/c++/12/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 93%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_membrane.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_membrane.cc.o -MF CMakeFiles/_ost_mol_alg.dir/export_membrane.cc.o.d -o CMakeFiles/_ost_mol_alg.dir/export_membrane.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/pymod/export_membrane.cc +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/openstructure-2.3.1/modules/mol/alg/pymod/export_accessibility.cc:21: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/openstructure-2.3.1/modules/mol/alg/pymod/export_contact_overlap.cc:1: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/accessibility.hh:23, + from /build/openstructure-2.3.1/modules/mol/alg/pymod/export_accessibility.cc:23: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/bits/specfun.h:45, + from /usr/include/c++/12/cmath:1935, + from /usr/include/c++/12/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/contact_overlap.hh:6, + from /build/openstructure-2.3.1/modules/mol/alg/pymod/export_contact_overlap.cc:4: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/bits/specfun.h:45, + from /usr/include/c++/12/cmath:1935, + from /usr/include/c++/12/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/contact_overlap.hh:8: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 32 | : public std::iterator{ + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 93%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_entity_to_density.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_entity_to_density.cc.o -MF CMakeFiles/_ost_mol_alg.dir/export_entity_to_density.cc.o.d -o CMakeFiles/_ost_mol_alg.dir/export_entity_to_density.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/pymod/export_entity_to_density.cc +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/openstructure-2.3.1/modules/mol/alg/pymod/export_non_standard.cc:19: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, + from /build/openstructure-2.3.1/modules/mol/alg/pymod/export_non_standard.cc:20: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/bits/specfun.h:45, + from /usr/include/c++/12/cmath:1935, + from /usr/include/c++/12/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/openstructure-2.3.1/modules/mol/alg/pymod/export_molck.cc:20: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E cmake_symlink_library ../../../stage/lib/libost_gui.so.2.3.1 ../../../stage/lib/libost_gui.so.2.3 ../../../stage/lib/libost_gui.so make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 93%] Built target ost_gui @@ -25090,6 +24962,128 @@ cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/gui/src/CMakeFiles/gosty.dir/moc_gosty.cpp.o -MF CMakeFiles/gosty.dir/moc_gosty.cpp.o.d -o CMakeFiles/gosty.dir/moc_gosty.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_gosty.cpp [ 93%] Building CXX object modules/gui/src/CMakeFiles/gosty.dir/qrc_dngr.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/gui/src/CMakeFiles/gosty.dir/qrc_dngr.cpp.o -MF CMakeFiles/gosty.dir/qrc_dngr.cpp.o.d -o CMakeFiles/gosty.dir/qrc_dngr.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/qrc_dngr.cpp +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/molck.hh:23, + from /build/openstructure-2.3.1/modules/mol/alg/pymod/export_molck.cc:25: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/12/string:45, + from /usr/include/c++/12/stdexcept:39, + from /build/openstructure-2.3.1/modules/mol/alg/pymod/export_molck.cc:19: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/openstructure-2.3.1/modules/mol/alg/pymod/export_membrane.cc:21: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/find_membrane.hh:22, + from /build/openstructure-2.3.1/modules/mol/alg/pymod/export_membrane.cc:23: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/bits/specfun.h:45, + from /usr/include/c++/12/cmath:1935, + from /usr/include/c++/12/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/openstructure-2.3.1/modules/mol/alg/pymod/export_entity_to_density.cc:23: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/entity_to_density.hh:4, + from /build/openstructure-2.3.1/modules/mol/alg/pymod/export_entity_to_density.cc:26: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/bits/specfun.h:45, + from /usr/include/c++/12/cmath:1935, + from /usr/include/c++/12/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -25118,6 +25112,14 @@ /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro CMakeFiles/gosty.dir/gosty.cc.o CMakeFiles/gosty.dir/moc_gosty.cpp.o CMakeFiles/gosty.dir/qrc_dngr.cpp.o -o ../../../stage/lib/openstructure/libexec/gosty -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib: ../../../stage/lib/libost_gui.so.2.3.1 /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so ../../../stage/lib/libost_gfx.so.2.3.1 /usr/lib/x86_64-linux-gnu/libOpenGL.so /usr/lib/x86_64-linux-gnu/libGLX.so /usr/lib/x86_64-linux-gnu/libGLU.so ../../../stage/lib/libost_io.so.2.3.1 /usr/lib/x86_64-linux-gnu/libtiff.so /usr/lib/x86_64-linux-gnu/libpng.so /usr/lib/x86_64-linux-gnu/libz.so ../../../stage/lib/libost_mol_alg.so.2.3.1 ../../../stage/lib/libost_conop.so.2.3.1 ../../../stage/lib/libost_db.so.2.3.1 /usr/lib/x86_64-linux-gnu/libsqlite3.so ../../../stage/lib/libost_img_alg.so.2.3.1 ../../../stage/lib/libost_img.so.2.3.1 /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libfftw3f_threads.so /usr/lib/x86_64-linux-gnu/libboost_program_options.so /usr/lib/x86_64-linux-gnu/libboost_thread.so /usr/lib/x86_64-linux-gnu/libboost_chrono.so /usr/lib/x86_64-linux-gnu/libboost_date_time.so /usr/lib/x86_64-linux-gnu/libboost_atomic.so ../../../stage/lib/libost_seq_alg.so.2.3.1 ../../../stage/lib/libost_seq.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so ../../../stage/lib/libost_mol.so.2.3.1 ../../../stage/lib/libost_info.so.2.3.1 /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 ../../../stage/lib/libost_base.so.2.3.1 ../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_regex.so make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 94%] Built target gosty +[ 94%] Linking CXX shared module ../../../stage/lib/python3.11/dist-packages/ost/gfx/_ost_gfx.so +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/pymod/gradients.xml /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/share/openstructure/scene/gradients.xml +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_gfx.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -o ../../../stage/lib/python3.11/dist-packages/ost/gfx/_ost_gfx.so CMakeFiles/_ost_gfx.dir/wrap_gfx.cc.o CMakeFiles/_ost_gfx.dir/export_scene.cc.o CMakeFiles/_ost_gfx.dir/export_gfx_node.cc.o CMakeFiles/_ost_gfx.dir/export_symmetry_node.cc.o CMakeFiles/_ost_gfx.dir/export_gfx_obj.cc.o CMakeFiles/_ost_gfx.dir/export_entity.cc.o CMakeFiles/_ost_gfx.dir/export_surface.cc.o CMakeFiles/_ost_gfx.dir/export_primitives.cc.o CMakeFiles/_ost_gfx.dir/export_primlist.cc.o CMakeFiles/_ost_gfx.dir/export_scene_observer.cc.o CMakeFiles/_ost_gfx.dir/export_render_options.cc.o CMakeFiles/_ost_gfx.dir/export_color.cc.o CMakeFiles/_ost_gfx.dir/export_gradient.cc.o CMakeFiles/_ost_gfx.dir/export_color_ops.cc.o CMakeFiles/_ost_gfx.dir/export_glwin_base.cc.o CMakeFiles/_ost_gfx.dir/export_exporter.cc.o CMakeFiles/_ost_gfx.dir/export_bitmap.cc.o CMakeFiles/_ost_gfx.dir/export_map.cc.o -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib: ../../../stage/lib/libost_gfx.so.2.3.1 /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so ../../../stage/lib/libost_conop.so.2.3.1 ../../../stage/lib/libost_db.so.2.3.1 /usr/lib/x86_64-linux-gnu/libsqlite3.so ../../../stage/lib/libost_seq.so.2.3.1 ../../../stage/lib/libost_mol.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so ../../../stage/lib/libost_img_alg.so.2.3.1 ../../../stage/lib/libost_img.so.2.3.1 ../../../stage/lib/libost_info.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 ../../../stage/lib/libost_base.so.2.3.1 ../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libfftw3f_threads.so /usr/lib/x86_64-linux-gnu/libOpenGL.so /usr/lib/x86_64-linux-gnu/libGLX.so /usr/lib/x86_64-linux-gnu/libGLU.so /usr/lib/x86_64-linux-gnu/libpng.so /usr/lib/x86_64-linux-gnu/libz.so +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gfx/pymod/__init__.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gfx/./__init__.pyc\",\"__init__.py\",doraise=True)" +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gfx/pymod/py_gfx_obj.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gfx/./py_gfx_obj.pyc\",\"py_gfx_obj.py\",doraise=True)" +make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[ 94%] Built target _ost_gfx [ 94%] Linking CXX shared module ../../../../stage/lib/python3.11/dist-packages/ost/mol/alg/_ost_mol_alg.so cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_mol_alg.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -o ../../../../stage/lib/python3.11/dist-packages/ost/mol/alg/_ost_mol_alg.so CMakeFiles/_ost_mol_alg.dir/wrap_mol_alg.cc.o CMakeFiles/_ost_mol_alg.dir/export_svd_superpose.cc.o CMakeFiles/_ost_mol_alg.dir/export_clash.cc.o CMakeFiles/_ost_mol_alg.dir/export_trajectory_analysis.cc.o CMakeFiles/_ost_mol_alg.dir/export_structure_analysis.cc.o CMakeFiles/_ost_mol_alg.dir/export_contact_overlap.cc.o CMakeFiles/_ost_mol_alg.dir/export_accessibility.cc.o CMakeFiles/_ost_mol_alg.dir/export_sec_structure.cc.o CMakeFiles/_ost_mol_alg.dir/export_non_standard.cc.o CMakeFiles/_ost_mol_alg.dir/export_molck.cc.o CMakeFiles/_ost_mol_alg.dir/export_membrane.cc.o CMakeFiles/_ost_mol_alg.dir/export_entity_to_density.cc.o -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib: ../../../../stage/lib/libost_mol_alg.so.2.3.1 /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so /usr/lib/x86_64-linux-gnu/libboost_program_options.so /usr/lib/x86_64-linux-gnu/libboost_thread.so /usr/lib/x86_64-linux-gnu/libboost_chrono.so /usr/lib/x86_64-linux-gnu/libboost_date_time.so /usr/lib/x86_64-linux-gnu/libboost_atomic.so ../../../../stage/lib/libost_img_alg.so.2.3.1 ../../../../stage/lib/libost_img.so.2.3.1 /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libfftw3f_threads.so ../../../../stage/lib/libost_seq_alg.so.2.3.1 ../../../../stage/lib/libost_conop.so.2.3.1 ../../../../stage/lib/libost_db.so.2.3.1 ../../../../stage/lib/libost_seq.so.2.3.1 ../../../../stage/lib/libost_mol.so.2.3.1 ../../../../stage/lib/libost_info.so.2.3.1 /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../../stage/lib/libost_base.so.2.3.1 ../../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libsqlite3.so @@ -25138,9 +25140,9 @@ make -f modules/io/pymod/CMakeFiles/_ost_io.dir/build.make modules/io/pymod/CMakeFiles/_ost_io.dir/build make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 94%] Building CXX object modules/io/pymod/CMakeFiles/_ost_io.dir/wrap_io.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/pymod/CMakeFiles/_ost_io.dir/wrap_io.cc.o -MF CMakeFiles/_ost_io.dir/wrap_io.cc.o.d -o CMakeFiles/_ost_io.dir/wrap_io.cc.o -c /build/openstructure-2.3.1/modules/io/pymod/wrap_io.cc [ 94%] Building CXX object modules/io/pymod/CMakeFiles/_ost_io.dir/export_pdb_io.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/pymod/CMakeFiles/_ost_io.dir/export_pdb_io.cc.o -MF CMakeFiles/_ost_io.dir/export_pdb_io.cc.o.d -o CMakeFiles/_ost_io.dir/export_pdb_io.cc.o -c /build/openstructure-2.3.1/modules/io/pymod/export_pdb_io.cc -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/pymod/CMakeFiles/_ost_io.dir/wrap_io.cc.o -MF CMakeFiles/_ost_io.dir/wrap_io.cc.o.d -o CMakeFiles/_ost_io.dir/wrap_io.cc.o -c /build/openstructure-2.3.1/modules/io/pymod/wrap_io.cc [ 94%] Building CXX object modules/io/pymod/CMakeFiles/_ost_io.dir/export_mmcif_io.cc.o [ 96%] Building CXX object modules/io/pymod/CMakeFiles/_ost_io.dir/export_omf_io.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/pymod/CMakeFiles/_ost_io.dir/export_mmcif_io.cc.o -MF CMakeFiles/_ost_io.dir/export_mmcif_io.cc.o.d -o CMakeFiles/_ost_io.dir/export_mmcif_io.cc.o -c /build/openstructure-2.3.1/modules/io/pymod/export_mmcif_io.cc @@ -25160,7 +25162,7 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/io/pymod/export_omf_io.cc:19: + from /build/openstructure-2.3.1/modules/io/pymod/export_mmcif_io.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ @@ -25200,7 +25202,7 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/io/pymod/wrap_io.cc:20: + from /build/openstructure-2.3.1/modules/io/pymod/export_pdb_io.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ @@ -25220,7 +25222,7 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/io/pymod/export_mmcif_io.cc:19: + from /build/openstructure-2.3.1/modules/io/pymod/wrap_io.cc:20: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ @@ -25240,7 +25242,7 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/io/pymod/export_pdb_io.cc:19: + from /build/openstructure-2.3.1/modules/io/pymod/export_omf_io.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ @@ -25278,6 +25280,44 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/io_profile.hh:24, + from /build/openstructure-2.3.1/modules/io/pymod/export_mmcif_io.cc:26: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/bits/specfun.h:45, + from /usr/include/c++/12/cmath:1935, + from /usr/include/c++/12/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/mmcif_reader.hh:25, + from /build/openstructure-2.3.1/modules/io/pymod/export_mmcif_io.cc:27: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 32 | : public std::iterator{ + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/io_manager.hh:28, @@ -25303,8 +25343,8 @@ from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/omf.hh:26, - from /build/openstructure-2.3.1/modules/io/pymod/export_omf_io.cc:22: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/io_profile.hh:24, + from /build/openstructure-2.3.1/modules/io/pymod/export_pdb_io.cc:22: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -25326,15 +25366,6 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mmcif_info.hh:25, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/omf.hh:29: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 32 | : public std::iterator{ - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -25355,32 +25386,12 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/io_profile.hh:24, - from /build/openstructure-2.3.1/modules/io/pymod/export_pdb_io.cc:22: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/specfun.h:45, - from /usr/include/c++/12/cmath:1935, - from /usr/include/c++/12/math.h:36, - from /usr/include/python3.11/pyport.h:218, - from /usr/include/python3.11/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, + from /build/openstructure-2.3.1/modules/io/pymod/export_pdb_io.cc:23: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 32 | : public std::iterator{ + | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -25390,8 +25401,8 @@ from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/io_profile.hh:24, - from /build/openstructure-2.3.1/modules/io/pymod/export_mmcif_io.cc:26: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/omf.hh:26, + from /build/openstructure-2.3.1/modules/io/pymod/export_omf_io.cc:22: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -25414,17 +25425,8 @@ 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/mmcif_reader.hh:25, - from /build/openstructure-2.3.1/modules/io/pymod/export_mmcif_io.cc:27: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 32 | : public std::iterator{ - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, - from /build/openstructure-2.3.1/modules/io/pymod/export_pdb_io.cc:23: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mmcif_info.hh:25, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/omf.hh:29: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ @@ -25446,43 +25448,41 @@ make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/build.make modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/build make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/gui/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod/CMakeFiles/_ost_gui.dir/DependInfo.cmake --color= +[ 96%] Building CXX object modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_forcefield.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_mm_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_forcefield.cc.o -MF CMakeFiles/_ost_mol_mm.dir/export_forcefield.cc.o.d -o CMakeFiles/_ost_mol_mm.dir/export_forcefield.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/pymod/export_forcefield.cc +[ 96%] Building CXX object modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_settings.cc.o make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/gui/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod/CMakeFiles/_ost_gui.dir/DependInfo.cmake --color= +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_mm_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_settings.cc.o -MF CMakeFiles/_ost_mol_mm.dir/export_settings.cc.o.d -o CMakeFiles/_ost_mol_mm.dir/export_settings.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/pymod/export_settings.cc +[ 96%] Building CXX object modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_simulation.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_mm_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_simulation.cc.o -MF CMakeFiles/_ost_mol_mm.dir/export_simulation.cc.o.d -o CMakeFiles/_ost_mol_mm.dir/export_simulation.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/pymod/export_simulation.cc make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/gui/pymod/CMakeFiles/_ost_gui.dir/build.make modules/gui/pymod/CMakeFiles/_ost_gui.dir/build -[ 96%] Building CXX object modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_settings.cc.o make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 96%] Building CXX object modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_forcefield.cc.o -[ 96%] Building CXX object modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_simulation.cc.o +[ 96%] Building CXX object modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_openmm.cc.o [ 96%] Building CXX object modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_observers.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_mm_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_settings.cc.o -MF CMakeFiles/_ost_mol_mm.dir/export_settings.cc.o.d -o CMakeFiles/_ost_mol_mm.dir/export_settings.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/pymod/export_settings.cc -[ 96%] Building CXX object modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/wrap_mol_mm.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_mm_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_openmm.cc.o -MF CMakeFiles/_ost_mol_mm.dir/export_openmm.cc.o.d -o CMakeFiles/_ost_mol_mm.dir/export_openmm.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/pymod/export_openmm.cc +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_mm_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_observers.cc.o -MF CMakeFiles/_ost_mol_mm.dir/export_observers.cc.o.d -o CMakeFiles/_ost_mol_mm.dir/export_observers.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/pymod/export_observers.cc +[ 96%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/wrap_gui.cc.o [ 96%] Building CXX object modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_interaction.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_mm_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_interaction.cc.o -MF CMakeFiles/_ost_mol_mm.dir/export_interaction.cc.o.d -o CMakeFiles/_ost_mol_mm.dir/export_interaction.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/pymod/export_interaction.cc [ 97%] Building CXX object modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_ff_reader.cc.o -[ 97%] Building CXX object modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_block_modifiers.cc.o -[ 97%] Building CXX object modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_modeller.cc.o -[ 97%] Building CXX object modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_openmm.cc.o -[ 97%] Building CXX object modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_topology.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_mm_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_forcefield.cc.o -MF CMakeFiles/_ost_mol_mm.dir/export_forcefield.cc.o.d -o CMakeFiles/_ost_mol_mm.dir/export_forcefield.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/pymod/export_forcefield.cc -[ 97%] Building CXX object modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_buildingblock.cc.o -[ 97%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/wrap_gui.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_mm_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_simulation.cc.o -MF CMakeFiles/_ost_mol_mm.dir/export_simulation.cc.o.d -o CMakeFiles/_ost_mol_mm.dir/export_simulation.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/pymod/export_simulation.cc [ 97%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_alignment_view.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_mm_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_openmm.cc.o -MF CMakeFiles/_ost_mol_mm.dir/export_openmm.cc.o.d -o CMakeFiles/_ost_mol_mm.dir/export_openmm.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/pymod/export_openmm.cc cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/wrap_gui.cc.o -MF CMakeFiles/_ost_gui.dir/wrap_gui.cc.o.d -o CMakeFiles/_ost_gui.dir/wrap_gui.cc.o -c /build/openstructure-2.3.1/modules/gui/pymod/wrap_gui.cc -[ 97%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_message_widget.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_mm_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_observers.cc.o -MF CMakeFiles/_ost_mol_mm.dir/export_observers.cc.o.d -o CMakeFiles/_ost_mol_mm.dir/export_observers.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/pymod/export_observers.cc +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_mm_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_ff_reader.cc.o -MF CMakeFiles/_ost_mol_mm.dir/export_ff_reader.cc.o.d -o CMakeFiles/_ost_mol_mm.dir/export_ff_reader.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/pymod/export_ff_reader.cc cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_alignment_view.cc.o -MF CMakeFiles/_ost_gui.dir/export_alignment_view.cc.o.d -o CMakeFiles/_ost_gui.dir/export_alignment_view.cc.o -c /build/openstructure-2.3.1/modules/gui/pymod/export_alignment_view.cc +[ 97%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_message_widget.cc.o [ 97%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_gl_win.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_mm_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_ff_reader.cc.o -MF CMakeFiles/_ost_mol_mm.dir/export_ff_reader.cc.o.d -o CMakeFiles/_ost_mol_mm.dir/export_ff_reader.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/pymod/export_ff_reader.cc cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_message_widget.cc.o -MF CMakeFiles/_ost_gui.dir/export_message_widget.cc.o.d -o CMakeFiles/_ost_gui.dir/export_message_widget.cc.o -c /build/openstructure-2.3.1/modules/gui/pymod/export_message_widget.cc +[ 97%] Building CXX object modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_buildingblock.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_gl_win.cc.o -MF CMakeFiles/_ost_gui.dir/export_gl_win.cc.o.d -o CMakeFiles/_ost_gui.dir/export_gl_win.cc.o -c /build/openstructure-2.3.1/modules/gui/pymod/export_gl_win.cc -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_mm_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_interaction.cc.o -MF CMakeFiles/_ost_mol_mm.dir/export_interaction.cc.o.d -o CMakeFiles/_ost_mol_mm.dir/export_interaction.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/pymod/export_interaction.cc cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_mm_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_buildingblock.cc.o -MF CMakeFiles/_ost_mol_mm.dir/export_buildingblock.cc.o.d -o CMakeFiles/_ost_mol_mm.dir/export_buildingblock.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/pymod/export_buildingblock.cc +[ 97%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_tool.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_tool.cc.o -MF CMakeFiles/_ost_gui.dir/export_tool.cc.o.d -o CMakeFiles/_ost_gui.dir/export_tool.cc.o -c /build/openstructure-2.3.1/modules/gui/pymod/export_tool.cc +[ 97%] Building CXX object modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_block_modifiers.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_mm_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_block_modifiers.cc.o -MF CMakeFiles/_ost_mol_mm.dir/export_block_modifiers.cc.o.d -o CMakeFiles/_ost_mol_mm.dir/export_block_modifiers.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/pymod/export_block_modifiers.cc +[ 97%] Building CXX object modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_topology.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_mm_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_topology.cc.o -MF CMakeFiles/_ost_mol_mm.dir/export_topology.cc.o.d -o CMakeFiles/_ost_mol_mm.dir/export_topology.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/pymod/export_topology.cc -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_mm_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_modeller.cc.o -MF CMakeFiles/_ost_mol_mm.dir/export_modeller.cc.o.d -o CMakeFiles/_ost_mol_mm.dir/export_modeller.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/pymod/export_modeller.cc -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_mm_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/wrap_mol_mm.cc.o -MF CMakeFiles/_ost_mol_mm.dir/wrap_mol_mm.cc.o.d -o CMakeFiles/_ost_mol_mm.dir/wrap_mol_mm.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/pymod/wrap_mol_mm.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -25496,42 +25496,13 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/mol/mm/pymod/export_block_modifiers.cc:20: + from /build/openstructure-2.3.1/modules/gui/pymod/export_message_widget.cc:20: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/block_modifiers.hh:23, - from /build/openstructure-2.3.1/modules/mol/mm/pymod/export_block_modifiers.cc:21: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/specfun.h:45, - from /usr/include/c++/12/cmath:1935, - from /usr/include/c++/12/math.h:36, - from /usr/include/python3.11/pyport.h:218, - from /usr/include/python3.11/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -25545,7 +25516,7 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/mol/mm/pymod/export_observers.cc:20: + from /build/openstructure-2.3.1/modules/gui/pymod/export_gl_win.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ @@ -25572,36 +25543,6 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/io_profile.hh:24, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/observer.hh:26, - from /build/openstructure-2.3.1/modules/mol/mm/pymod/export_observers.cc:22: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/specfun.h:45, - from /usr/include/c++/12/cmath:1935, - from /usr/include/c++/12/math.h:36, - from /usr/include/python3.11/pyport.h:218, - from /usr/include/python3.11/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -25615,7 +25556,7 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/gui/pymod/export_gl_win.cc:19: + from /build/openstructure-2.3.1/modules/mol/mm/pymod/export_block_modifiers.cc:20: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ @@ -25635,7 +25576,7 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/mol/mm/pymod/export_settings.cc:20: + from /build/openstructure-2.3.1/modules/gui/pymod/wrap_gui.cc:20: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ @@ -25655,7 +25596,7 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/mol/mm/pymod/export_forcefield.cc:20: + from /build/openstructure-2.3.1/modules/mol/mm/pymod/export_openmm.cc:20: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ @@ -25675,7 +25616,7 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/mol/mm/pymod/export_openmm.cc:20: + from /build/openstructure-2.3.1/modules/mol/mm/pymod/export_ff_reader.cc:20: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ @@ -25695,7 +25636,7 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/gui/pymod/wrap_gui.cc:20: + from /build/openstructure-2.3.1/modules/mol/mm/pymod/export_settings.cc:20: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ @@ -25715,7 +25656,7 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/mol/mm/pymod/export_topology.cc:20: + from /build/openstructure-2.3.1/modules/gui/pymod/export_tool.cc:20: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ @@ -25735,23 +25676,13 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/mol/mm/pymod/export_buildingblock.cc:21: + from /build/openstructure-2.3.1/modules/mol/mm/pymod/export_topology.cc:20: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/modeller.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/observer.hh:33: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 32 | : public std::iterator{ - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -25765,42 +25696,13 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/mol/mm/pymod/wrap_mol_mm.cc:20: + from /build/openstructure-2.3.1/modules/mol/mm/pymod/export_forcefield.cc:20: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/interaction.hh:34, - from /build/openstructure-2.3.1/modules/mol/mm/pymod/export_interaction.cc:23: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/specfun.h:45, - from /usr/include/c++/12/cmath:1935, - from /usr/include/c++/12/math.h:36, - from /usr/include/python3.11/pyport.h:218, - from /usr/include/python3.11/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -25814,13 +25716,10 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/mol/mm/pymod/export_ff_reader.cc:20: + from /build/openstructure-2.3.1/modules/mol/mm/pymod/export_observers.cc:20: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -25834,13 +25733,16 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/mol/mm/pymod/export_simulation.cc:20: + from /build/openstructure-2.3.1/modules/mol/mm/pymod/export_buildingblock.cc:21: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -25854,13 +25756,10 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/mol/mm/pymod/export_modeller.cc:20: + from /build/openstructure-2.3.1/modules/gui/pymod/export_alignment_view.cc:20: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -25874,21 +25773,53 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/gui/pymod/export_message_widget.cc:20: + from /build/openstructure-2.3.1/modules/mol/mm/pymod/export_simulation.cc:20: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/settings.hh:31, - from /build/openstructure-2.3.1/modules/mol/mm/pymod/export_settings.cc:21: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/block_modifiers.hh:23, + from /build/openstructure-2.3.1/modules/mol/mm/pymod/export_block_modifiers.cc:21: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/bits/specfun.h:45, + from /usr/include/c++/12/cmath:1935, + from /usr/include/c++/12/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/interaction.hh:34, + from /build/openstructure-2.3.1/modules/mol/mm/pymod/export_interaction.cc:23: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -25919,7 +25850,8 @@ from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/interaction.hh:34, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/buildingblock.hh:29, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/forcefield.hh:31, - from /build/openstructure-2.3.1/modules/mol/mm/pymod/export_forcefield.cc:22: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/ff_reader.hh:32, + from /build/openstructure-2.3.1/modules/mol/mm/pymod/export_ff_reader.cc:21: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -25941,16 +25873,14 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 97%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_tool.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_tool.cc.o -MF CMakeFiles/_ost_gui.dir/export_tool.cc.o.d -o CMakeFiles/_ost_gui.dir/export_tool.cc.o -c /build/openstructure-2.3.1/modules/gui/pymod/export_tool.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/topology.hh:31, - from /build/openstructure-2.3.1/modules/mol/mm/pymod/export_topology.cc:21: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/settings.hh:31, + from /build/openstructure-2.3.1/modules/mol/mm/pymod/export_settings.cc:21: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -25972,15 +25902,16 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 97%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_py_shell.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_py_shell.cc.o -MF CMakeFiles/_ost_gui.dir/export_py_shell.cc.o.d -o CMakeFiles/_ost_gui.dir/export_py_shell.cc.o -c /build/openstructure-2.3.1/modules/gui/pymod/export_py_shell.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/interaction.hh:34, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/buildingblock.hh:29, - from /build/openstructure-2.3.1/modules/mol/mm/pymod/export_buildingblock.cc:22: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/topology.hh:31, + from /build/openstructure-2.3.1/modules/mol/mm/pymod/export_topology.cc:21: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -26002,34 +25933,15 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/gui/pymod/export_alignment_view.cc:20: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/block_modifiers.hh:23, - from /build/openstructure-2.3.1/modules/mol/mm/pymod/export_modeller.cc:21: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/interaction.hh:34, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/buildingblock.hh:29, + from /build/openstructure-2.3.1/modules/mol/mm/pymod/export_buildingblock.cc:22: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -26056,10 +25968,11 @@ from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/simulation.hh:26, - from /build/openstructure-2.3.1/modules/mol/mm/pymod/export_simulation.cc:21: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_viewer.hh:28, + from /build/openstructure-2.3.1/modules/gui/pymod/export_alignment_view.cc:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -26086,12 +25999,10 @@ from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/interaction.hh:34, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/buildingblock.hh:29, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/forcefield.hh:31, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/ff_reader.hh:32, - from /build/openstructure-2.3.1/modules/mol/mm/pymod/export_ff_reader.cc:21: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/simulation.hh:26, + from /build/openstructure-2.3.1/modules/mol/mm/pymod/export_simulation.cc:21: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -26113,24 +26024,52 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool.hh:30, + from /build/openstructure-2.3.1/modules/gui/pymod/export_tool.cc:25: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:37:22: warning: 'Qt::MidButton' is deprecated: MidButton is deprecated. Use MiddleButton instead [-Wdeprecated-declarations] + 37 | MiddleButton=Qt::MidButton + | ^~~~~~~~~ +In file included from /usr/include/x86_64-linux-gnu/qt5/QtCore/qpoint.h:43, + from /usr/include/x86_64-linux-gnu/qt5/QtCore/QPoint:1, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:24: +/usr/include/x86_64-linux-gnu/qt5/QtCore/qnamespace.h:132:9: note: declared here + 132 | MidButton Q_DECL_ENUMERATOR_DEPRECATED_X("MidButton is deprecated. Use MiddleButton instead") = MiddleButton, + | ^~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/modeller.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/topology_creator.hh:37, - from /build/openstructure-2.3.1/modules/mol/mm/pymod/export_topology.cc:22: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/modeller.hh:28, - from /build/openstructure-2.3.1/modules/mol/mm/pymod/export_modeller.cc:22: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 32 | : public std::iterator{ - | ^~~~~~~~ +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/io_profile.hh:24, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/observer.hh:26, + from /build/openstructure-2.3.1/modules/mol/mm/pymod/export_observers.cc:22: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/bits/specfun.h:45, + from /usr/include/c++/12/cmath:1935, + from /usr/include/c++/12/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -26139,11 +26078,11 @@ from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_viewer.hh:28, - from /build/openstructure-2.3.1/modules/gui/pymod/export_alignment_view.cc:24: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/interaction.hh:34, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/buildingblock.hh:29, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/forcefield.hh:31, + from /build/openstructure-2.3.1/modules/mol/mm/pymod/export_forcefield.cc:22: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -26165,18 +26104,19 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 97%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_gosty.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_gosty.cc.o -MF CMakeFiles/_ost_gui.dir/export_gosty.cc.o.d -o CMakeFiles/_ost_gui.dir/export_gosty.cc.o -c /build/openstructure-2.3.1/modules/gui/pymod/export_gosty.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/modeller.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/topology_creator.hh:37, + from /build/openstructure-2.3.1/modules/mol/mm/pymod/export_topology.cc:22: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 97%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_py_shell.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_py_shell.cc.o -MF CMakeFiles/_ost_gui.dir/export_py_shell.cc.o.d -o CMakeFiles/_ost_gui.dir/export_py_shell.cc.o -c /build/openstructure-2.3.1/modules/gui/pymod/export_py_shell.cc -[ 97%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_gosty.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_gosty.cc.o -MF CMakeFiles/_ost_gui.dir/export_gosty.cc.o.d -o CMakeFiles/_ost_gui.dir/export_gosty.cc.o -c /build/openstructure-2.3.1/modules/gui/pymod/export_gosty.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/modeller.hh:28, @@ -26188,14 +26128,24 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/modeller.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/observer.hh:33: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 32 | : public std::iterator{ + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ [ 98%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_scene_win.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_scene_win.cc.o -MF CMakeFiles/_ost_gui.dir/export_scene_win.cc.o.d -o CMakeFiles/_ost_gui.dir/export_scene_win.cc.o -c /build/openstructure-2.3.1/modules/gui/pymod/export_scene_win.cc [ 98%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_sequence_viewer.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_sequence_viewer.cc.o -MF CMakeFiles/_ost_gui.dir/export_sequence_viewer.cc.o.d -o CMakeFiles/_ost_gui.dir/export_sequence_viewer.cc.o -c /build/openstructure-2.3.1/modules/gui/pymod/export_sequence_viewer.cc -[ 98%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_perspective.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_perspective.cc.o -MF CMakeFiles/_ost_gui.dir/export_perspective.cc.o.d -o CMakeFiles/_ost_gui.dir/export_perspective.cc.o -c /build/openstructure-2.3.1/modules/gui/pymod/export_perspective.cc -[ 98%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_sip_handler.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_sip_handler.cc.o -MF CMakeFiles/_ost_gui.dir/export_sip_handler.cc.o.d -o CMakeFiles/_ost_gui.dir/export_sip_handler.cc.o -c /build/openstructure-2.3.1/modules/gui/pymod/export_sip_handler.cc +[ 98%] Building CXX object modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_modeller.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_mm_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_modeller.cc.o -MF CMakeFiles/_ost_mol_mm.dir/export_modeller.cc.o.d -o CMakeFiles/_ost_mol_mm.dir/export_modeller.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/pymod/export_modeller.cc +[ 98%] Building CXX object modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/wrap_mol_mm.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_mm_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/wrap_mol_mm.cc.o -MF CMakeFiles/_ost_mol_mm.dir/wrap_mol_mm.cc.o.d -o CMakeFiles/_ost_mol_mm.dir/wrap_mol_mm.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/pymod/wrap_mol_mm.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -26216,8 +26166,8 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 98%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_scene_selection.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_scene_selection.cc.o -MF CMakeFiles/_ost_gui.dir/export_scene_selection.cc.o.d -o CMakeFiles/_ost_gui.dir/export_scene_selection.cc.o -c /build/openstructure-2.3.1/modules/gui/pymod/export_scene_selection.cc +[ 98%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_perspective.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_perspective.cc.o -MF CMakeFiles/_ost_gui.dir/export_perspective.cc.o.d -o CMakeFiles/_ost_gui.dir/export_perspective.cc.o -c /build/openstructure-2.3.1/modules/gui/pymod/export_perspective.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -26231,17 +26181,17 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/gui/pymod/export_tool.cc:20: + from /build/openstructure-2.3.1/modules/gui/pymod/export_gosty.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 98%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_main_area.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_main_area.cc.o -MF CMakeFiles/_ost_gui.dir/export_main_area.cc.o.d -o CMakeFiles/_ost_gui.dir/export_main_area.cc.o -c /build/openstructure-2.3.1/modules/gui/pymod/export_main_area.cc -[ 98%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_panels.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_panels.cc.o -MF CMakeFiles/_ost_gui.dir/export_panels.cc.o.d -o CMakeFiles/_ost_gui.dir/export_panels.cc.o -c /build/openstructure-2.3.1/modules/gui/pymod/export_panels.cc +[ 98%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_sip_handler.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_sip_handler.cc.o -MF CMakeFiles/_ost_gui.dir/export_sip_handler.cc.o.d -o CMakeFiles/_ost_gui.dir/export_sip_handler.cc.o -c /build/openstructure-2.3.1/modules/gui/pymod/export_sip_handler.cc +[ 98%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_scene_selection.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_scene_selection.cc.o -MF CMakeFiles/_ost_gui.dir/export_scene_selection.cc.o.d -o CMakeFiles/_ost_gui.dir/export_scene_selection.cc.o -c /build/openstructure-2.3.1/modules/gui/pymod/export_scene_selection.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -26255,28 +26205,45 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/gui/pymod/export_gosty.cc:19: + from /build/openstructure-2.3.1/modules/gui/pymod/export_scene_win.cc:20: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 98%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_menu_bar.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_menu_bar.cc.o -MF CMakeFiles/_ost_gui.dir/export_menu_bar.cc.o.d -o CMakeFiles/_ost_gui.dir/export_menu_bar.cc.o -c /build/openstructure-2.3.1/modules/gui/pymod/export_menu_bar.cc -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool.hh:30, - from /build/openstructure-2.3.1/modules/gui/pymod/export_tool.cc:25: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:37:22: warning: 'Qt::MidButton' is deprecated: MidButton is deprecated. Use MiddleButton instead [-Wdeprecated-declarations] - 37 | MiddleButton=Qt::MidButton - | ^~~~~~~~~ -In file included from /usr/include/x86_64-linux-gnu/qt5/QtCore/qpoint.h:43, - from /usr/include/x86_64-linux-gnu/qt5/QtCore/QPoint:1, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:24: -/usr/include/x86_64-linux-gnu/qt5/QtCore/qnamespace.h:132:9: note: declared here - 132 | MidButton Q_DECL_ENUMERATOR_DEPRECATED_X("MidButton is deprecated. Use MiddleButton instead") = MiddleButton, - | ^~~~~~~~~ -[ 98%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_file_loader.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_file_loader.cc.o -MF CMakeFiles/_ost_gui.dir/export_file_loader.cc.o.d -o CMakeFiles/_ost_gui.dir/export_file_loader.cc.o -c /build/openstructure-2.3.1/modules/gui/pymod/export_file_loader.cc +[ 98%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_main_area.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_main_area.cc.o -MF CMakeFiles/_ost_gui.dir/export_main_area.cc.o.d -o CMakeFiles/_ost_gui.dir/export_main_area.cc.o -c /build/openstructure-2.3.1/modules/gui/pymod/export_main_area.cc +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/scene_win.hh:23, + from /build/openstructure-2.3.1/modules/gui/pymod/export_scene_win.cc:22: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/bits/specfun.h:45, + from /usr/include/c++/12/cmath:1935, + from /usr/include/c++/12/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -26290,15 +26257,13 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/gui/pymod/export_scene_win.cc:20: + from /build/openstructure-2.3.1/modules/gui/pymod/export_sequence_viewer.cc:20: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 98%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_file_viewer.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_file_viewer.cc.o -MF CMakeFiles/_ost_gui.dir/export_file_viewer.cc.o.d -o CMakeFiles/_ost_gui.dir/export_file_viewer.cc.o -c /build/openstructure-2.3.1/modules/gui/pymod/export_file_viewer.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -26329,8 +26294,8 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 98%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_widget.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_widget.cc.o -MF CMakeFiles/_ost_gui.dir/export_widget.cc.o.d -o CMakeFiles/_ost_gui.dir/export_widget.cc.o -c /build/openstructure-2.3.1/modules/gui/pymod/export_widget.cc +[ 98%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_panels.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_panels.cc.o -MF CMakeFiles/_ost_gui.dir/export_panels.cc.o.d -o CMakeFiles/_ost_gui.dir/export_panels.cc.o -c /build/openstructure-2.3.1/modules/gui/pymod/export_panels.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool.hh:30, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool_options_win.hh:27, from /build/openstructure-2.3.1/modules/gui/pymod/export_gosty.cc:30: @@ -26351,6 +26316,37 @@ /usr/include/x86_64-linux-gnu/qt5/QtCore/qnamespace.h:132:9: note: declared here 132 | MidButton Q_DECL_ENUMERATOR_DEPRECATED_X("MidButton is deprecated. Use MiddleButton instead") = MiddleButton, | ^~~~~~~~~ +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_viewer.hh:28, + from /build/openstructure-2.3.1/modules/gui/pymod/export_sequence_viewer.cc:24: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/bits/specfun.h:45, + from /usr/include/c++/12/cmath:1935, + from /usr/include/c++/12/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_viewer.hh:28, @@ -26361,15 +26357,68 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 32 | : public std::iterator{ + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/openstructure-2.3.1/modules/mol/mm/pymod/export_modeller.cc:20: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/openstructure-2.3.1/modules/mol/mm/pymod/wrap_mol_mm.cc:20: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 98%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_menu_bar.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_menu_bar.cc.o -MF CMakeFiles/_ost_gui.dir/export_menu_bar.cc.o.d -o CMakeFiles/_ost_gui.dir/export_menu_bar.cc.o -c /build/openstructure-2.3.1/modules/gui/pymod/export_menu_bar.cc +[ 98%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_file_loader.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_file_loader.cc.o -MF CMakeFiles/_ost_gui.dir/export_file_loader.cc.o.d -o CMakeFiles/_ost_gui.dir/export_file_loader.cc.o -c /build/openstructure-2.3.1/modules/gui/pymod/export_file_loader.cc +[ 98%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_file_viewer.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_file_viewer.cc.o -MF CMakeFiles/_ost_gui.dir/export_file_viewer.cc.o.d -o CMakeFiles/_ost_gui.dir/export_file_viewer.cc.o -c /build/openstructure-2.3.1/modules/gui/pymod/export_file_viewer.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/scene_win.hh:23, - from /build/openstructure-2.3.1/modules/gui/pymod/export_scene_win.cc:22: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/block_modifiers.hh:23, + from /build/openstructure-2.3.1/modules/mol/mm/pymod/export_modeller.cc:21: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -26404,13 +26453,35 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/gui/pymod/export_perspective.cc:19: + from /build/openstructure-2.3.1/modules/gui/pymod/export_sip_handler.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/data_viewer.hh:37, + from /build/openstructure-2.3.1/modules/gui/pymod/data_viewer_proxy.hh:41, + from /build/openstructure-2.3.1/modules/gui/pymod/export_gosty.cc:38: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main_window.hh:46:55: warning: 'constexpr QFlags::QFlags(Zero) [with Enum = Qt::WindowType; Zero = int QFlags::Private::*]' is deprecated: Use default constructor instead [-Wdeprecated-declarations] + 46 | MainWindow(QWidget* parent=0, Qt::WindowFlags flags=0); + | ^ +In file included from /usr/include/x86_64-linux-gnu/qt5/QtCore/qglobal.h:1305, + from /usr/include/x86_64-linux-gnu/qt5/QtCore/qchar.h:43, + from /usr/include/x86_64-linux-gnu/qt5/QtCore/qstring.h:49: +/usr/include/x86_64-linux-gnu/qt5/QtCore/qflags.h:123:80: note: declared here + 123 | QT_DEPRECATED_X("Use default constructor instead") Q_DECL_CONSTEXPR inline QFlags(Zero) noexcept : i(0) {} + | ^~~~~~ +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/modeller.hh:28, + from /build/openstructure-2.3.1/modules/mol/mm/pymod/export_modeller.cc:22: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 32 | : public std::iterator{ + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -26424,7 +26495,7 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/gui/pymod/export_sip_handler.cc:19: + from /build/openstructure-2.3.1/modules/gui/pymod/export_perspective.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ @@ -26444,7 +26515,7 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/gui/pymod/export_scene_selection.cc:19: + from /build/openstructure-2.3.1/modules/gui/pymod/export_main_area.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ @@ -26464,25 +26535,13 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/gui/pymod/export_sequence_viewer.cc:20: + from /build/openstructure-2.3.1/modules/gui/pymod/export_scene_selection.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/data_viewer.hh:37, - from /build/openstructure-2.3.1/modules/gui/pymod/data_viewer_proxy.hh:41, - from /build/openstructure-2.3.1/modules/gui/pymod/export_gosty.cc:38: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main_window.hh:46:55: warning: 'constexpr QFlags::QFlags(Zero) [with Enum = Qt::WindowType; Zero = int QFlags::Private::*]' is deprecated: Use default constructor instead [-Wdeprecated-declarations] - 46 | MainWindow(QWidget* parent=0, Qt::WindowFlags flags=0); - | ^ -In file included from /usr/include/x86_64-linux-gnu/qt5/QtCore/qglobal.h:1305, - from /usr/include/x86_64-linux-gnu/qt5/QtCore/qchar.h:43, - from /usr/include/x86_64-linux-gnu/qt5/QtCore/qstring.h:49: -/usr/include/x86_64-linux-gnu/qt5/QtCore/qflags.h:123:80: note: declared here - 123 | QT_DEPRECATED_X("Use default constructor instead") Q_DECL_CONSTEXPR inline QFlags(Zero) noexcept : i(0) {} - | ^~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -26496,13 +26555,15 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/gui/pymod/export_main_area.cc:19: + from /build/openstructure-2.3.1/modules/gui/pymod/export_panels.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 98%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_widget.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_widget.cc.o -MF CMakeFiles/_ost_gui.dir/export_widget.cc.o.d -o CMakeFiles/_ost_gui.dir/export_widget.cc.o -c /build/openstructure-2.3.1/modules/gui/pymod/export_widget.cc [100%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_gl_canvas.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_gl_canvas.cc.o -MF CMakeFiles/_ost_gui.dir/export_gl_canvas.cc.o.d -o CMakeFiles/_ost_gui.dir/export_gl_canvas.cc.o -c /build/openstructure-2.3.1/modules/gui/pymod/export_gl_canvas.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, @@ -26510,45 +26571,6 @@ from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_viewer.hh:28, - from /build/openstructure-2.3.1/modules/gui/pymod/export_sequence_viewer.cc:24: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/specfun.h:45, - from /usr/include/c++/12/cmath:1935, - from /usr/include/c++/12/math.h:36, - from /usr/include/python3.11/pyport.h:218, - from /usr/include/python3.11/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 32 | : public std::iterator{ - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_selection.hh:23, @@ -26574,6 +26596,8 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[100%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/data_viewer_proxy.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/data_viewer_proxy.cc.o -MF CMakeFiles/_ost_gui.dir/data_viewer_proxy.cc.o.d -o CMakeFiles/_ost_gui.dir/data_viewer_proxy.cc.o -c /build/openstructure-2.3.1/modules/gui/pymod/data_viewer_proxy.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -26594,6 +26618,10 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +[100%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_data_viewer.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_data_viewer.cc.o -MF CMakeFiles/_ost_gui.dir/export_data_viewer.cc.o.d -o CMakeFiles/_ost_gui.dir/export_data_viewer.cc.o -c /build/openstructure-2.3.1/modules/gui/pymod/export_data_viewer.cc +[100%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_overlay.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_overlay.cc.o -MF CMakeFiles/_ost_gui.dir/export_overlay.cc.o.d -o CMakeFiles/_ost_gui.dir/export_overlay.cc.o -c /build/openstructure-2.3.1/modules/gui/pymod/export_overlay.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -26607,13 +26635,15 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/gui/pymod/export_panels.cc:19: + from /build/openstructure-2.3.1/modules/gui/pymod/export_file_viewer.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +[100%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_overlay_manager.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_overlay_manager.cc.o -MF CMakeFiles/_ost_gui.dir/export_overlay_manager.cc.o.d -o CMakeFiles/_ost_gui.dir/export_overlay_manager.cc.o -c /build/openstructure-2.3.1/modules/gui/pymod/export_overlay_manager.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -26634,8 +26664,6 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[100%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/data_viewer_proxy.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/data_viewer_proxy.cc.o -MF CMakeFiles/_ost_gui.dir/data_viewer_proxy.cc.o.d -o CMakeFiles/_ost_gui.dir/data_viewer_proxy.cc.o -c /build/openstructure-2.3.1/modules/gui/pymod/data_viewer_proxy.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -26664,6 +26692,15 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/file_loader.hh:30: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 32 | : public std::iterator{ + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -26684,15 +26721,6 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/file_loader.hh:30: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 32 | : public std::iterator{ - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -26706,19 +26734,13 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/gui/pymod/export_file_viewer.cc:19: + from /build/openstructure-2.3.1/modules/gui/pymod/export_gl_canvas.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[100%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_data_viewer.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_data_viewer.cc.o -MF CMakeFiles/_ost_gui.dir/export_data_viewer.cc.o.d -o CMakeFiles/_ost_gui.dir/export_data_viewer.cc.o -c /build/openstructure-2.3.1/modules/gui/pymod/export_data_viewer.cc -[100%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_overlay.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_overlay.cc.o -MF CMakeFiles/_ost_gui.dir/export_overlay.cc.o.d -o CMakeFiles/_ost_gui.dir/export_overlay.cc.o -c /build/openstructure-2.3.1/modules/gui/pymod/export_overlay.cc -[100%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_overlay_manager.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_overlay_manager.cc.o -MF CMakeFiles/_ost_gui.dir/export_overlay_manager.cc.o.d -o CMakeFiles/_ost_gui.dir/export_overlay_manager.cc.o -c /build/openstructure-2.3.1/modules/gui/pymod/export_overlay_manager.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -26732,7 +26754,9 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/gui/pymod/export_gl_canvas.cc:19: + from /build/openstructure-2.3.1/modules/gui/pymod/sip_handler.hh:22, + from /build/openstructure-2.3.1/modules/gui/pymod/data_viewer_proxy.hh:30, + from /build/openstructure-2.3.1/modules/gui/pymod/data_viewer_proxy.cc:26: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ @@ -26764,9 +26788,27 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/gui/pymod/sip_handler.hh:22, - from /build/openstructure-2.3.1/modules/gui/pymod/data_viewer_proxy.hh:30, - from /build/openstructure-2.3.1/modules/gui/pymod/data_viewer_proxy.cc:26: + from /build/openstructure-2.3.1/modules/gui/pymod/export_overlay_manager.cc:16: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/openstructure-2.3.1/modules/gui/pymod/export_overlay.cc:26: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ @@ -26798,9 +26840,7 @@ from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/data_viewer.hh:33, - from /build/openstructure-2.3.1/modules/gui/pymod/export_data_viewer.cc:27: + from /build/openstructure-2.3.1/modules/gui/pymod/data_viewer_proxy.hh:35: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -26822,52 +26862,14 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/gui/pymod/export_overlay.cc:26: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/openstructure-2.3.1/modules/gui/pymod/export_overlay_manager.cc:16: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/openstructure-2.3.1/modules/gui/pymod/data_viewer_proxy.hh:35: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/data_viewer.hh:33, + from /build/openstructure-2.3.1/modules/gui/pymod/export_data_viewer.cc:27: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -26889,19 +26891,6 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/data_viewer.hh:37: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main_window.hh:46:55: warning: 'constexpr QFlags::QFlags(Zero) [with Enum = Qt::WindowType; Zero = int QFlags::Private::*]' is deprecated: Use default constructor instead [-Wdeprecated-declarations] - 46 | MainWindow(QWidget* parent=0, Qt::WindowFlags flags=0); - | ^ -In file included from /usr/include/x86_64-linux-gnu/qt5/QtCore/qglobal.h:1305, - from /usr/include/x86_64-linux-gnu/qt5/QtGui/qtguiglobal.h:43, - from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/qtwidgetsglobal.h:43, - from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/qmainwindow.h:43, - from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/QMainWindow:1, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main_window.hh:35: -/usr/include/x86_64-linux-gnu/qt5/QtCore/qflags.h:123:80: note: declared here - 123 | QT_DEPRECATED_X("Use default constructor instead") Q_DECL_CONSTEXPR inline QFlags(Zero) noexcept : i(0) {} - | ^~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/data_viewer.hh:37, from /build/openstructure-2.3.1/modules/gui/pymod/data_viewer_proxy.hh:41: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main_window.hh:46:55: warning: 'constexpr QFlags::QFlags(Zero) [with Enum = Qt::WindowType; Zero = int QFlags::Private::*]' is deprecated: Use default constructor instead [-Wdeprecated-declarations] @@ -26945,6 +26934,26 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/data_viewer.hh:37: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main_window.hh:46:55: warning: 'constexpr QFlags::QFlags(Zero) [with Enum = Qt::WindowType; Zero = int QFlags::Private::*]' is deprecated: Use default constructor instead [-Wdeprecated-declarations] + 46 | MainWindow(QWidget* parent=0, Qt::WindowFlags flags=0); + | ^ +In file included from /usr/include/x86_64-linux-gnu/qt5/QtCore/qglobal.h:1305, + from /usr/include/x86_64-linux-gnu/qt5/QtGui/qtguiglobal.h:43, + from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/qtwidgetsglobal.h:43, + from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/qmainwindow.h:43, + from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/QMainWindow:1, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main_window.hh:35: +/usr/include/x86_64-linux-gnu/qt5/QtCore/qflags.h:123:80: note: declared here + 123 | QT_DEPRECATED_X("Use default constructor instead") Q_DECL_CONSTEXPR inline QFlags(Zero) noexcept : i(0) {} + | ^~~~~~ +[100%] Linking CXX shared module ../../../../stage/lib/python3.11/dist-packages/ost/mol/mm/_ost_mol_mm.so +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_mol_mm.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -o ../../../../stage/lib/python3.11/dist-packages/ost/mol/mm/_ost_mol_mm.so CMakeFiles/_ost_mol_mm.dir/export_forcefield.cc.o CMakeFiles/_ost_mol_mm.dir/export_settings.cc.o CMakeFiles/_ost_mol_mm.dir/export_simulation.cc.o CMakeFiles/_ost_mol_mm.dir/export_openmm.cc.o CMakeFiles/_ost_mol_mm.dir/export_observers.cc.o CMakeFiles/_ost_mol_mm.dir/export_ff_reader.cc.o CMakeFiles/_ost_mol_mm.dir/export_interaction.cc.o CMakeFiles/_ost_mol_mm.dir/export_buildingblock.cc.o CMakeFiles/_ost_mol_mm.dir/export_block_modifiers.cc.o CMakeFiles/_ost_mol_mm.dir/export_topology.cc.o CMakeFiles/_ost_mol_mm.dir/export_modeller.cc.o CMakeFiles/_ost_mol_mm.dir/wrap_mol_mm.cc.o -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib: ../../../../stage/lib/libost_mol_mm.so.2.3.1 /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so ../../../../stage/lib/libost_io.so.2.3.1 ../../../../stage/lib/libost_mol_alg.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_program_options.so ../../../../stage/lib/libost_conop.so.2.3.1 ../../../../stage/lib/libost_db.so.2.3.1 /usr/lib/x86_64-linux-gnu/libsqlite3.so /usr/lib/x86_64-linux-gnu/libboost_thread.so /usr/lib/x86_64-linux-gnu/libboost_chrono.so /usr/lib/x86_64-linux-gnu/libboost_date_time.so /usr/lib/x86_64-linux-gnu/libboost_atomic.so ../../../../stage/lib/libost_seq_alg.so.2.3.1 ../../../../stage/lib/libost_seq.so.2.3.1 ../../../../stage/lib/libost_mol.so.2.3.1 ../../../../stage/lib/libost_img_alg.so.2.3.1 ../../../../stage/lib/libost_img.so.2.3.1 ../../../../stage/lib/libost_info.so.2.3.1 ../../../../stage/lib/libost_base.so.2.3.1 ../../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libfftw3f_threads.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libtiff.so /usr/lib/x86_64-linux-gnu/libpng.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libOpenMM.so +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/mol/mm/pymod/__init__.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/mm/./__init__.pyc\",\"__init__.py\",doraise=True)" +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/mol/mm/pymod/antechamber.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/mm/./antechamber.pyc\",\"antechamber.py\",doraise=True)" +make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[100%] Built target _ost_mol_mm [100%] Linking CXX shared module ../../../stage/lib/python3.11/dist-packages/ost/gui/_ost_gui.so cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/presets.xml /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/share/openstructure/scene/presets.xml cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/icons/color_icon.png /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/share/openstructure/scene/icons/color_icon.png @@ -26953,9 +26962,6 @@ cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/icons/tool_icon.png /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/share/openstructure/scene/icons/tool_icon.png cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_gui.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -o ../../../stage/lib/python3.11/dist-packages/ost/gui/_ost_gui.so CMakeFiles/_ost_gui.dir/wrap_gui.cc.o CMakeFiles/_ost_gui.dir/export_alignment_view.cc.o CMakeFiles/_ost_gui.dir/export_message_widget.cc.o CMakeFiles/_ost_gui.dir/export_gl_win.cc.o CMakeFiles/_ost_gui.dir/export_tool.cc.o CMakeFiles/_ost_gui.dir/export_py_shell.cc.o CMakeFiles/_ost_gui.dir/export_gosty.cc.o CMakeFiles/_ost_gui.dir/export_scene_win.cc.o CMakeFiles/_ost_gui.dir/export_sequence_viewer.cc.o CMakeFiles/_ost_gui.dir/export_perspective.cc.o CMakeFiles/_ost_gui.dir/export_sip_handler.cc.o CMakeFiles/_ost_gui.dir/export_scene_selection.cc.o CMakeFiles/_ost_gui.dir/export_main_area.cc.o CMakeFiles/_ost_gui.dir/export_panels.cc.o CMakeFiles/_ost_gui.dir/export_menu_bar.cc.o CMakeFiles/_ost_gui.dir/export_file_loader.cc.o CMakeFiles/_ost_gui.dir/export_file_viewer.cc.o CMakeFiles/_ost_gui.dir/export_widget.cc.o CMakeFiles/_ost_gui.dir/export_gl_canvas.cc.o CMakeFiles/_ost_gui.dir/data_viewer_proxy.cc.o CMakeFiles/_ost_gui.dir/export_data_viewer.cc.o CMakeFiles/_ost_gui.dir/export_overlay.cc.o CMakeFiles/_ost_gui.dir/export_overlay_manager.cc.o -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib: ../../../stage/lib/libost_gui.so.2.3.1 /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so ../../../stage/lib/libost_gfx.so.2.3.1 /usr/lib/x86_64-linux-gnu/libOpenGL.so /usr/lib/x86_64-linux-gnu/libGLX.so /usr/lib/x86_64-linux-gnu/libGLU.so ../../../stage/lib/libost_io.so.2.3.1 /usr/lib/x86_64-linux-gnu/libtiff.so /usr/lib/x86_64-linux-gnu/libpng.so /usr/lib/x86_64-linux-gnu/libz.so ../../../stage/lib/libost_mol_alg.so.2.3.1 ../../../stage/lib/libost_conop.so.2.3.1 ../../../stage/lib/libost_db.so.2.3.1 /usr/lib/x86_64-linux-gnu/libsqlite3.so ../../../stage/lib/libost_img_alg.so.2.3.1 ../../../stage/lib/libost_img.so.2.3.1 /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libfftw3f_threads.so /usr/lib/x86_64-linux-gnu/libboost_program_options.so /usr/lib/x86_64-linux-gnu/libboost_thread.so /usr/lib/x86_64-linux-gnu/libboost_chrono.so /usr/lib/x86_64-linux-gnu/libboost_date_time.so /usr/lib/x86_64-linux-gnu/libboost_atomic.so ../../../stage/lib/libost_seq_alg.so.2.3.1 ../../../stage/lib/libost_seq.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so ../../../stage/lib/libost_mol.so.2.3.1 ../../../stage/lib/libost_info.so.2.3.1 /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 ../../../stage/lib/libost_base.so.2.3.1 ../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -[100%] Linking CXX shared module ../../../../stage/lib/python3.11/dist-packages/ost/mol/mm/_ost_mol_mm.so -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_mol_mm.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -o ../../../../stage/lib/python3.11/dist-packages/ost/mol/mm/_ost_mol_mm.so CMakeFiles/_ost_mol_mm.dir/export_forcefield.cc.o CMakeFiles/_ost_mol_mm.dir/export_settings.cc.o CMakeFiles/_ost_mol_mm.dir/export_simulation.cc.o CMakeFiles/_ost_mol_mm.dir/export_openmm.cc.o CMakeFiles/_ost_mol_mm.dir/export_observers.cc.o CMakeFiles/_ost_mol_mm.dir/export_ff_reader.cc.o CMakeFiles/_ost_mol_mm.dir/export_interaction.cc.o CMakeFiles/_ost_mol_mm.dir/export_buildingblock.cc.o CMakeFiles/_ost_mol_mm.dir/export_block_modifiers.cc.o CMakeFiles/_ost_mol_mm.dir/export_topology.cc.o CMakeFiles/_ost_mol_mm.dir/export_modeller.cc.o CMakeFiles/_ost_mol_mm.dir/wrap_mol_mm.cc.o -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib: ../../../../stage/lib/libost_mol_mm.so.2.3.1 /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so ../../../../stage/lib/libost_io.so.2.3.1 ../../../../stage/lib/libost_mol_alg.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_program_options.so ../../../../stage/lib/libost_conop.so.2.3.1 ../../../../stage/lib/libost_db.so.2.3.1 /usr/lib/x86_64-linux-gnu/libsqlite3.so /usr/lib/x86_64-linux-gnu/libboost_thread.so /usr/lib/x86_64-linux-gnu/libboost_chrono.so /usr/lib/x86_64-linux-gnu/libboost_date_time.so /usr/lib/x86_64-linux-gnu/libboost_atomic.so ../../../../stage/lib/libost_seq_alg.so.2.3.1 ../../../../stage/lib/libost_seq.so.2.3.1 ../../../../stage/lib/libost_mol.so.2.3.1 ../../../../stage/lib/libost_img_alg.so.2.3.1 ../../../../stage/lib/libost_img.so.2.3.1 ../../../../stage/lib/libost_info.so.2.3.1 ../../../../stage/lib/libost_base.so.2.3.1 ../../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libfftw3f_threads.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libtiff.so /usr/lib/x86_64-linux-gnu/libpng.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libOpenMM.so cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/scene/__init__.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/__init__.pyc\",\"__init__.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/scene/color_options_widget.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/color_options_widget.pyc\",\"color_options_widget.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/scene/color_select_widget.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/color_select_widget.pyc\",\"color_select_widget.py\",doraise=True)" @@ -26965,12 +26971,8 @@ cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/scene/gradient_editor_widget.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/gradient_editor_widget.pyc\",\"gradient_editor_widget.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/scene/gradient_info_handler.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/gradient_info_handler.pyc\",\"gradient_info_handler.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/scene/gradient_list_model.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/gradient_list_model.pyc\",\"gradient_list_model.py\",doraise=True)" -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/mol/mm/pymod/__init__.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/mm/./__init__.pyc\",\"__init__.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/scene/gradient_preset_widget.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/gradient_preset_widget.pyc\",\"gradient_preset_widget.py\",doraise=True)" -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/mol/mm/pymod/antechamber.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/mm/./antechamber.pyc\",\"antechamber.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/scene/hsc_widget.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/hsc_widget.pyc\",\"hsc_widget.py\",doraise=True)" -make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[100%] Built target _ost_mol_mm cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/scene/immutable_gradient_info_handler.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/immutable_gradient_info_handler.pyc\",\"immutable_gradient_info_handler.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/scene/immutable_preset_info_handler.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/immutable_preset_info_handler.pyc\",\"immutable_preset_info_handler.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/scene/init_inspector.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/init_inspector.pyc\",\"init_inspector.py\",doraise=True)" @@ -27031,7 +27033,7 @@ /usr/bin/cmake -E cmake_progress_start /build/openstructure-2.3.1/obj-x86_64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' dh_auto_test - cd obj-x86_64-linux-gnu && make -j16 check ARGS\+=--verbose ARGS\+=-j16 + cd obj-x86_64-linux-gnu && make -j15 check ARGS\+=--verbose ARGS\+=-j15 make[1]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/openstructure-2.3.1 -B/build/openstructure-2.3.1/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 check @@ -27050,1027 +27052,1045 @@ make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/scripts /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/scripts /build/openstructure-2.3.1/obj-x86_64-linux-gnu/scripts/CMakeFiles/subst_ost_config.dir/DependInfo.cmake --color= make -f scripts/CMakeFiles/subst_ost.dir/build.make scripts/CMakeFiles/subst_ost.dir/depend -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/scripts /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/scripts /build/openstructure-2.3.1/obj-x86_64-linux-gnu/scripts/CMakeFiles/subst_ost.dir/DependInfo.cmake --color= -make -f scripts/CMakeFiles/subst_ost_startup.py.dir/build.make scripts/CMakeFiles/subst_ost_startup.py.dir/build -make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -DINPUT_FILE=/build/openstructure-2.3.1/scripts/ost_startup.py.in -DOUT_FILE=ost_startup.py -DBUILD_TYPE=Release -DPython_EXECUTABLE=/usr/bin/python3 -DPython_VERSION=3.11.2 -DLIBDIR=lib -DLIBEXEC_PATH=lib/openstructure/libexec -DPYTHON_MODULE_PATH=python3.11/dist-packages/ -P /build/openstructure-2.3.1/cmake_support/substitute.cmake make -f scripts/CMakeFiles/subst_dng.dir/build.make scripts/CMakeFiles/subst_dng.dir/depend -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/scripts /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/scripts /build/openstructure-2.3.1/obj-x86_64-linux-gnu/scripts/CMakeFiles/subst_dng.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +make -f scripts/CMakeFiles/subst_ost_startup.py.dir/build.make scripts/CMakeFiles/subst_ost_startup.py.dir/build +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -DINPUT_FILE=/build/openstructure-2.3.1/scripts/ost_startup.py.in -DOUT_FILE=ost_startup.py -DBUILD_TYPE=Release -DPython_EXECUTABLE=/usr/bin/python3 -DPython_VERSION=3.11.2 -DLIBDIR=lib -DLIBEXEC_PATH=lib/openstructure/libexec -DPYTHON_MODULE_PATH=python3.11/dist-packages/ -P /build/openstructure-2.3.1/cmake_support/substitute.cmake make -f modules/base/src/CMakeFiles/create_stage.dir/build.make modules/base/src/CMakeFiles/create_stage.dir/build +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E make_directory /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib +make -f scripts/CMakeFiles/subst_ost_config.dir/build.make scripts/CMakeFiles/subst_ost_config.dir/build make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f scripts/CMakeFiles/subst_ost.dir/build.make scripts/CMakeFiles/subst_ost.dir/build -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -DINPUT_FILE=/build/openstructure-2.3.1/scripts/ost_config.in -DOUT_FILE=ost_config -DBUILD_TYPE=Release -DPython_EXECUTABLE=/usr/bin/python3 -DPython_VERSION=3.11.2 -DLIBDIR=lib -DLIBEXEC_PATH=lib/openstructure/libexec -DPYTHON_MODULE_PATH=python3.11/dist-packages/ -P /build/openstructure-2.3.1/cmake_support/substitute.cmake make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -DINPUT_FILE=/build/openstructure-2.3.1/scripts/ost.in -DOUT_FILE=ost -DBUILD_TYPE=Release -DPython_EXECUTABLE=/usr/bin/python3 -DPython_VERSION=3.11.2 -DLIBDIR=lib -DLIBEXEC_PATH=lib/openstructure/libexec -DPYTHON_MODULE_PATH=python3.11/dist-packages/ -P /build/openstructure-2.3.1/cmake_support/substitute.cmake -make -f scripts/CMakeFiles/subst_ost_config.dir/build.make scripts/CMakeFiles/subst_ost_config.dir/build make -f scripts/CMakeFiles/subst_dng.dir/build.make scripts/CMakeFiles/subst_dng.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -DINPUT_FILE=/build/openstructure-2.3.1/scripts/ost_config.in -DOUT_FILE=ost_config -DBUILD_TYPE=Release -DPython_EXECUTABLE=/usr/bin/python3 -DPython_VERSION=3.11.2 -DLIBDIR=lib -DLIBEXEC_PATH=lib/openstructure/libexec -DPYTHON_MODULE_PATH=python3.11/dist-packages/ -P /build/openstructure-2.3.1/cmake_support/substitute.cmake -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E make_directory /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/bin -make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -DINPUT_FILE=/build/openstructure-2.3.1/scripts/dng.in -DOUT_FILE=dng -DBUILD_TYPE=Release -DPython_EXECUTABLE=/usr/bin/python3 -DPython_VERSION=3.11.2 -DLIBDIR=lib -DLIBEXEC_PATH=lib/openstructure/libexec -DPYTHON_MODULE_PATH=python3.11/dist-packages/ -P /build/openstructure-2.3.1/cmake_support/substitute.cmake make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E make_directory /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/bin make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E make_directory /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/openstructure/libexec make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 0%] Built target subst_ost_startup.py make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E make_directory /build/openstructure-2.3.1/obj-x86_64-linux-gnu/tests +[ 0%] Built target subst_ost_startup.py +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E make_directory /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/openstructure/libexec +[ 0%] Built target subst_ost_config [ 0%] Built target subst_ost [ 0%] Built target subst_dng +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E make_directory /build/openstructure-2.3.1/obj-x86_64-linux-gnu/tests make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 0%] Built target subst_ost_config [ 0%] Built target create_stage make -f modules/seq/alg/src/CMakeFiles/ost_seq_alg_headers.dir/build.make modules/seq/alg/src/CMakeFiles/ost_seq_alg_headers.dir/depend -make -f modules/geom/src/CMakeFiles/ost_geom_headers.dir/build.make modules/geom/src/CMakeFiles/ost_geom_headers.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/seq/alg/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src/CMakeFiles/ost_seq_alg_headers.dir/DependInfo.cmake --color= -make -f modules/config/CMakeFiles/ost_config_headers.dir/build.make modules/config/CMakeFiles/ost_config_headers.dir/depend +make -f modules/geom/src/CMakeFiles/ost_geom_headers.dir/build.make modules/geom/src/CMakeFiles/ost_geom_headers.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/geom/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src/CMakeFiles/ost_geom_headers.dir/DependInfo.cmake --color= +make -f modules/config/CMakeFiles/ost_config_headers.dir/build.make modules/config/CMakeFiles/ost_config_headers.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/config /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/config /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/config/CMakeFiles/ost_config_headers.dir/DependInfo.cmake --color= make -f modules/base/src/CMakeFiles/ost_base_headers.dir/build.make modules/base/src/CMakeFiles/ost_base_headers.dir/depend +make -f modules/info/src/CMakeFiles/ost_info_headers.dir/build.make modules/info/src/CMakeFiles/ost_info_headers.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/base/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src/CMakeFiles/ost_base_headers.dir/DependInfo.cmake --color= -make -f modules/info/src/CMakeFiles/ost_info_headers.dir/build.make modules/info/src/CMakeFiles/ost_info_headers.dir/depend +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/info/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src/CMakeFiles/ost_info_headers.dir/DependInfo.cmake --color= -make -f modules/mol/base/src/CMakeFiles/ost_mol_headers.dir/build.make modules/mol/base/src/CMakeFiles/ost_mol_headers.dir/depend -make -f modules/seq/base/src/CMakeFiles/ost_seq_headers.dir/build.make modules/seq/base/src/CMakeFiles/ost_seq_headers.dir/depend -make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/base/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src/CMakeFiles/ost_mol_headers.dir/DependInfo.cmake --color= -make -f modules/conop/src/CMakeFiles/ost_conop_headers.dir/build.make modules/conop/src/CMakeFiles/ost_conop_headers.dir/depend -make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/seq/base/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src/CMakeFiles/ost_seq_headers.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/seq/alg/src/CMakeFiles/ost_seq_alg_headers.dir/build.make modules/seq/alg/src/CMakeFiles/ost_seq_alg_headers.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/conop/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src/CMakeFiles/ost_conop_headers.dir/DependInfo.cmake --color= -make -f modules/db/src/CMakeFiles/ost_db_headers.dir/build.make modules/db/src/CMakeFiles/ost_db_headers.dir/depend -make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./alignment_opts.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./alignment_opts.hh +make -f modules/mol/base/src/CMakeFiles/ost_mol_headers.dir/build.make modules/mol/base/src/CMakeFiles/ost_mol_headers.dir/depend +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/base/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src/CMakeFiles/ost_mol_headers.dir/DependInfo.cmake --color= +make -f modules/base/src/CMakeFiles/ost_base_headers.dir/build.make modules/base/src/CMakeFiles/ost_base_headers.dir/build make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/geom/src/CMakeFiles/ost_geom_headers.dir/build.make modules/geom/src/CMakeFiles/ost_geom_headers.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/db/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/src/CMakeFiles/ost_db_headers.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/export_helper/generic_property_def.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/export_helper/generic_property_def.hh make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/export_helper/vector.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/export_helper/vector.hh -make -f modules/info/src/CMakeFiles/ost_info_headers.dir/build.make modules/info/src/CMakeFiles/ost_info_headers.dir/build -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./info.hh make -f modules/config/CMakeFiles/ost_config_headers.dir/build.make modules/config/CMakeFiles/ost_config_headers.dir/build -make -f modules/mol/base/src/CMakeFiles/ost_mol_headers.dir/build.make modules/mol/base/src/CMakeFiles/ost_mol_headers.dir/build +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/config && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/config/./base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./base.hh +make -f modules/info/src/CMakeFiles/ost_info_headers.dir/build.make modules/info/src/CMakeFiles/ost_info_headers.dir/build +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./clip_alignment.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./clip_alignment.hh make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/pointer_iterator.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh -make -f modules/gfx/src/CMakeFiles/ost_gfx_headers.dir/build.make modules/gfx/src/CMakeFiles/ost_gfx_headers.dir/depend -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/gfx/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src/CMakeFiles/ost_gfx_headers.dir/DependInfo.cmake --color= -make -f modules/base/src/CMakeFiles/ost_base_headers.dir/build.make modules/base/src/CMakeFiles/ost_base_headers.dir/build +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./info.hh +make -f modules/seq/base/src/CMakeFiles/ost_seq_headers.dir/build.make modules/seq/base/src/CMakeFiles/ost_seq_headers.dir/depend make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/seq/base/src/CMakeFiles/ost_seq_headers.dir/build.make modules/seq/base/src/CMakeFiles/ost_seq_headers.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/export_helper/generic_property_def.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/export_helper/generic_property_def.hh -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./clip_alignment.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./clip_alignment.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info_error.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./info_error.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/seq/base/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src/CMakeFiles/ost_seq_headers.dir/DependInfo.cmake --color= +make -f modules/mol/base/src/CMakeFiles/ost_mol_headers.dir/build.make modules/mol/base/src/CMakeFiles/ost_mol_headers.dir/build +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/export_helper/pair_to_tuple_conv.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/export_helper/pair_to_tuple_conv.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./conservation.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./conservation.hh make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/impl/sequence_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_impl.hh -make -f modules/conop/src/CMakeFiles/ost_conop_headers.dir/build.make modules/conop/src/CMakeFiles/ost_conop_headers.dir/build +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/pointer_iterator.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh +make -f modules/conop/src/CMakeFiles/ost_conop_headers.dir/build.make modules/conop/src/CMakeFiles/ost_conop_headers.dir/depend cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./def.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./def.hh -make -f modules/db/src/CMakeFiles/ost_db_headers.dir/build.make modules/db/src/CMakeFiles/ost_db_headers.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./conop.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/./conop.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/conop/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src/CMakeFiles/ost_conop_headers.dir/DependInfo.cmake --color= +make -f modules/db/src/CMakeFiles/ost_db_headers.dir/build.make modules/db/src/CMakeFiles/ost_db_headers.dir/depend +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/config && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/config/./config.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./config.hh +make -f modules/gfx/src/CMakeFiles/ost_gfx_headers.dir/build.make modules/gfx/src/CMakeFiles/ost_gfx_headers.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/db/src/./sqlite_wrap.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/db/./sqlite_wrap.hh -make -f modules/img/base/src/CMakeFiles/ost_img_headers.dir/build.make modules/img/base/src/CMakeFiles/ost_img_headers.dir/depend +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/db/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/src/CMakeFiles/ost_db_headers.dir/DependInfo.cmake --color= +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/atom_group.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/atom_group.hh make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/img/base/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src/CMakeFiles/ost_img_headers.dir/DependInfo.cmake --color= +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/gfx/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src/CMakeFiles/ost_gfx_headers.dir/DependInfo.cmake --color= +make -f modules/img/base/src/CMakeFiles/ost_img_headers.dir/build.make modules/img/base/src/CMakeFiles/ost_img_headers.dir/depend +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info_error.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./info_error.hh make -f modules/img/alg/src/CMakeFiles/ost_img_alg_headers.dir/build.make modules/img/alg/src/CMakeFiles/ost_img_alg_headers.dir/depend -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/config && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/config/./config.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./config.hh make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/img/alg/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src/CMakeFiles/ost_img_alg_headers.dir/DependInfo.cmake --color= make -f modules/gui/src/CMakeFiles/ost_gui_headers.dir/build.make modules/gui/src/CMakeFiles/ost_gui_headers.dir/depend -make -f modules/io/src/CMakeFiles/ost_io_headers.dir/build.make modules/io/src/CMakeFiles/ost_io_headers.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/gui/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/CMakeFiles/ost_gui_headers.dir/DependInfo.cmake --color= -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./info_impl.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/img/base/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src/CMakeFiles/ost_img_headers.dir/DependInfo.cmake --color= +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./contact_prediction_score.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./contact_prediction_score.hh +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/export_helper/pair_to_tuple_conv.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/export_helper/pair_to_tuple_conv.hh -make -f modules/gfx/src/CMakeFiles/ost_gfx_headers.dir/build.make modules/gfx/src/CMakeFiles/ost_gfx_headers.dir/build -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/atom_group.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/atom_group.hh -make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/io/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src/CMakeFiles/ost_io_headers.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/map_iso_gen.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/map_iso_gen.hh -make -f modules/mol/alg/src/CMakeFiles/ost_mol_alg_headers.dir/build.make modules/mol/alg/src/CMakeFiles/ost_mol_alg_headers.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/alg/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src/CMakeFiles/ost_mol_alg_headers.dir/DependInfo.cmake --color= -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/db/src/./sqlite_conv.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/db/./sqlite_conv.hh -make -f modules/bindings/src/CMakeFiles/ost_bindings_headers.dir/build.make modules/bindings/src/CMakeFiles/ost_bindings_headers.dir/depend +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/gui/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/CMakeFiles/ost_gui_headers.dir/DependInfo.cmake --color= cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./exc.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./exc.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./conservation.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./conservation.hh -make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/bindings/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/src/CMakeFiles/ost_bindings_headers.dir/DependInfo.cmake --color= -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./processor.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/./processor.hh -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/config && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/config/./dllexport.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./dllexport.hh -make -f modules/gui/src/CMakeFiles/ost_gui_headers.dir/build.make modules/gui/src/CMakeFiles/ost_gui_headers.dir/build -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/impl/sequence_impl_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_impl_fw.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/export_helper/vec_to_list_conv.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/export_helper/vec_to_list_conv.hh +make -f modules/seq/base/src/CMakeFiles/ost_seq_headers.dir/build.make modules/seq/base/src/CMakeFiles/ost_seq_headers.dir/build +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/config && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/config/./dllexport.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./dllexport.hh make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/tool.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/impl/sequence_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_impl.hh +make -f modules/conop/src/CMakeFiles/ost_conop_headers.dir/build.make modules/conop/src/CMakeFiles/ost_conop_headers.dir/build +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./info_impl.hh +make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./conop.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/./conop.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/io/src/CMakeFiles/ost_io_headers.dir/build.make modules/io/src/CMakeFiles/ost_io_headers.dir/build +make -f modules/io/src/CMakeFiles/ost_io_headers.dir/build.make modules/io/src/CMakeFiles/ost_io_headers.dir/depend make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/io/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src/CMakeFiles/ost_io_headers.dir/DependInfo.cmake --color= +make -f modules/db/src/CMakeFiles/ost_db_headers.dir/build.make modules/db/src/CMakeFiles/ost_db_headers.dir/build cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/atom_prop.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/atom_prop.hh -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info_impl_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./info_impl_fw.hh +make -f modules/gfx/src/CMakeFiles/ost_gfx_headers.dir/build.make modules/gfx/src/CMakeFiles/ost_gfx_headers.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/chemdict_parser.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/chemdict_parser.hh -make -f modules/img/alg/src/CMakeFiles/ost_img_alg_headers.dir/build.make modules/img/alg/src/CMakeFiles/ost_img_alg_headers.dir/build +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/db/src/./sqlite_wrap.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/db/./sqlite_wrap.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./contact_weight_matrix.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./contact_weight_matrix.hh make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./anisotropic.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./anisotropic.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/map_iso_gen_s.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/map_iso_gen_s.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/db/src/./module_config.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/db/./module_config.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/map_iso_gen.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/map_iso_gen.hh make -f modules/img/base/src/CMakeFiles/ost_img_headers.dir/build.make modules/img/base/src/CMakeFiles/ost_img_headers.dir/build -make -f modules/mol/alg/src/CMakeFiles/ost_mol_alg_headers.dir/build.make modules/mol/alg/src/CMakeFiles/ost_mol_alg_headers.dir/build +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/test_utils/compare_files.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/test_utils/compare_files.hh +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/config && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/config/./version.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./version.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./geom.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./geom.hh +make -f modules/img/alg/src/CMakeFiles/ost_img_alg_headers.dir/build.make modules/img/alg/src/CMakeFiles/ost_img_alg_headers.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/raster_image/raster_image.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/raster_image/raster_image.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./geom.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./geom.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./contact_prediction_score.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./contact_prediction_score.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/impl/sequence_impl_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_impl_fw.hh +make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./anisotropic.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./anisotropic.hh +make -f modules/gui/src/CMakeFiles/ost_gui_headers.dir/build.make modules/gui/src/CMakeFiles/ost_gui_headers.dir/build +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./processor.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/./processor.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/atom_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/atom_impl.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/config && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/config/./version.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./version.hh +make -f modules/mol/alg/src/CMakeFiles/ost_mol_alg_headers.dir/build.make modules/mol/alg/src/CMakeFiles/ost_mol_alg_headers.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./svd_superpose.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./svd_superpose.hh -make -f modules/bindings/src/CMakeFiles/ost_bindings_headers.dir/build.make modules/bindings/src/CMakeFiles/ost_bindings_headers.dir/build -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./amino_acids.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/./amino_acids.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/tool.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info_impl_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./info_impl_fw.hh +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/db/src/./sqlite_conv.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/db/./sqlite_conv.hh +make -f modules/io/src/CMakeFiles/ost_io_headers.dir/build.make modules/io/src/CMakeFiles/ost_io_headers.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/bindings/src/./wrap_tmalign.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/bindings/./wrap_tmalign.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/tool_option_group.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool_option_group.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/impl/sequence_list_impl_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_impl_fw.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/map_iso_gen_s.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/map_iso_gen_s.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/test_utils/compare_files.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/test_utils/compare_files.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info_handle.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./info_handle.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/alg/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src/CMakeFiles/ost_mol_alg_headers.dir/DependInfo.cmake --color= +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./distance_map.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./distance_map.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./generic_property.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./generic_property.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./mat.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./mat.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/map_iso_gen_s.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/map_iso_gen_s.hh +make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/chemdict_parser.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/chemdict_parser.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/star_parser.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/star_parser.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./contact_weight_matrix.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./contact_weight_matrix.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./auto_correlate.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./auto_correlate.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./amino_acids.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/./amino_acids.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/dispatch.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/dispatch.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/db/src/./linear_indexer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/db/./linear_indexer.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/impl/sequence_list_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_impl.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./module_config.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./module_config.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./generic_property.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./generic_property.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/impl/sequence_list_impl_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_impl_fw.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./auto_correlate.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./auto_correlate.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/atom_impl_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/atom_impl_fw.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info_handle.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./info_handle.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./entropy.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./entropy.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/tool_option_group.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool_option_group.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/db/src/./module_config.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/db/./module_config.hh +make -f modules/mol/alg/src/CMakeFiles/ost_mol_alg_headers.dir/build.make modules/mol/alg/src/CMakeFiles/ost_mol_alg_headers.dir/build cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./diag.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/./diag.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info_group.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./info_group.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/map_iso_spec.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/map_iso_spec.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/atom_impl_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/atom_impl_fw.hh [ 0%] Built target ost_config_headers -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/tool_options.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool_options.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/mmcif_reader.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/mmcif_reader.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./mat2.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./mat2.hh -make -f modules/mol/mm/src/CMakeFiles/ost_mol_mm_headers.dir/build.make modules/mol/mm/src/CMakeFiles/ost_mol_mm_headers.dir/depend -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/db/src/./binary_container.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/db/./binary_container.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./distance_map.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./distance_map.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/impl/sequence_list_iterator.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh -[ 0%] Built target ost_bindings_headers -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./clear.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./clear.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/tool_bar.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool_bar.hh -make -f modules/config/CMakeFiles/ost_config.dir/build.make modules/config/CMakeFiles/ost_config.dir/depend -make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/config /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/config /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/config/CMakeFiles/ost_config.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/mm/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src/CMakeFiles/ost_mol_mm_headers.dir/DependInfo.cmake --color= +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./svd_superpose.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./svd_superpose.hh +make -f modules/bindings/src/CMakeFiles/ost_bindings_headers.dir/build.make modules/bindings/src/CMakeFiles/ost_bindings_headers.dir/depend cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./integrity_error.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./integrity_error.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./sec_structure_segments.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./sec_structure_segments.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/./sequence_list.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/./sequence_list.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/map_iso_gen_s.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/map_iso_gen_s.hh +make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/bindings/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/src/CMakeFiles/ost_bindings_headers.dir/DependInfo.cmake --color= +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./mat2.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./mat2.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/chain_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/chain_impl.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info_group.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./info_group.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./global_align.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./global_align.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/impl/sequence_list_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_impl.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/db/src/./linear_indexer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/db/./linear_indexer.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/star_parser.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/star_parser.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./model_check.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/./model_check.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info_item.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./info_item.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/selection_tool.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/selection_tool.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/tool_options.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool_options.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./module_config.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./module_config.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./clear.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./clear.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/map_iso_spec.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/map_iso_spec.hh +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +make -f modules/bindings/src/CMakeFiles/ost_bindings_headers.dir/build.make modules/bindings/src/CMakeFiles/ost_bindings_headers.dir/build cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./invalid_handle.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./invalid_handle.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/chain_impl_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/chain_impl_fw.hh +make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/bindings/src/./wrap_tmalign.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/bindings/./wrap_tmalign.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./mat3.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./mat3.hh -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/config/CMakeFiles/ost_config.dir/build.make modules/config/CMakeFiles/ost_config.dir/build -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./entropy.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./entropy.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info_item.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./info_item.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./ins_del.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./ins_del.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/mmcif_reader.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/mmcif_reader.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./heuristic.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/./heuristic.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/impl/sequence_list_iterator.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_fw.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/db/src/./binary_container.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/db/./binary_container.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/tool_bar.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool_bar.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./clip_min_max.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./clip_min_max.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./sec_structure_segments.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./sec_structure_segments.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./ptr_observer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./ptr_observer.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./mat4.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./mat4.hh +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/connector_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/connector_impl.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./compound.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/./compound.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./local_align.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./local_align.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./info_fw.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/selection_tool.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/selection_tool.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/mmcif_info.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/mmcif_info.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./conjugate.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./conjugate.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_base.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./log.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./log.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/./sequence_list.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/./sequence_list.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/db/src/./extract_data_helper.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/db/./extract_data_helper.hh +[ 0%] Built target ost_bindings_headers +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./local_dist_diff_test.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./local_dist_diff_test.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./merge_pairwise_alignments.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./merge_pairwise_alignments.hh +make -f modules/mol/mm/src/CMakeFiles/ost_mol_mm_headers.dir/build.make modules/mol/mm/src/CMakeFiles/ost_mol_mm_headers.dir/depend +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./compound_lib.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/./compound_lib.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/map_octree.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/map_octree.hh make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'modules/config/CMakeFiles/ost_config.dir/build'. -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_fw.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/mm/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src/CMakeFiles/ost_mol_mm_headers.dir/DependInfo.cmake --color= +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/connector_impl_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/connector_impl_fw.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_base_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_base_fw.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./module_config.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./module_config.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/io_profile.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/io_profile.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./convolute.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./convolute.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./log_sink.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./log_sink.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./vec.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./vec.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/measure_tool.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/measure_tool.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/db/src/./extract_data_helper.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/db/./extract_data_helper.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/./sequence_handle.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/./sequence_handle.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./module_config.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./module_config.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/octree_isocont.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/octree_isocont.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/dcd_io.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/dcd_io.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/dihedral.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/dihedral.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_def.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info_path.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./info_path.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./module_config.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/./module_config.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./distance_test_common.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./distance_test_common.hh +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/mol/mm/src/CMakeFiles/ost_mol_mm_headers.dir/build.make modules/mol/mm/src/CMakeFiles/ost_mol_mm_headers.dir/build -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./local_dist_diff_test.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./local_dist_diff_test.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./profile.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./profile.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./correlate.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./correlate.hh make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./forcefield.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./forcefield.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./mat4.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./mat4.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/measure_tool.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/measure_tool.hh -[ 0%] Built target ost_config -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./heuristic.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/./heuristic.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/chain_impl_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/chain_impl_fw.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/./alignment_handle.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/./alignment_handle.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_base.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./ptr_observer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./ptr_observer.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./info_fw.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./vec.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./vec.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./conjugate.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./conjugate.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./global_align.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./global_align.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/tool_option.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool_option.hh -[ 0%] Built target ost_db_headers -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./distance_test_common.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./distance_test_common.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./compound.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/./compound.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./ff_reader.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./ff_reader.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/connector_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/connector_impl.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/io_profile.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/io_profile.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/./module_config.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/./module_config.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./module_config.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./module_config.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./ins_del.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./ins_del.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./vec2.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./vec2.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./compound_lib.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/./compound_lib.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_base_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_base_fw.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/./sequence_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/./sequence_op.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./log.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./log.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./convolute.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./convolute.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./buildingblock.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./buildingblock.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info_path.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./info_path.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./vec3.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./vec3.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/connector_impl_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/connector_impl_fw.hh +[ 0%] Built target ost_db_headers +make -f modules/config/CMakeFiles/ost_config.dir/build.make modules/config/CMakeFiles/ost_config.dir/depend +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./rule_based.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/./rule_based.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/entity_io_crd_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/entity_io_crd_handler.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/cartoon_renderer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/cartoon_renderer.hh +make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/config /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/config /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/config/CMakeFiles/ost_config.dir/DependInfo.cmake --color= +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/./alignment_handle.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/./alignment_handle.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./pair_subst_weight_matrix.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./pair_subst_weight_matrix.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./distance_rmsd_test.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./distance_rmsd_test.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./minimal_compound_lib.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/./minimal_compound_lib.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info_set.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./info_set.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/tool_manager.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool_manager.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/dcd_io.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/dcd_io.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./local_align.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./local_align.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/./aligned_region.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/./aligned_region.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./module_config.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/./module_config.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_def.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./log_sink.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./log_sink.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/tool_options_widget.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool_options_widget.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/dihedral.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/dihedral.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./vec4.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./vec4.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_factory.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_factory.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./block_modifiers.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./block_modifiers.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/./aligned_column.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/./aligned_column.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info_set.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./info_set.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./merge_pairwise_alignments.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./merge_pairwise_alignments.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/manipulator.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/manipulator.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/entity_io_crd_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/entity_io_crd_handler.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./superpose_frames.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./superpose_frames.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./rule_based.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/./rule_based.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./correlate.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./correlate.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_frequency_domain.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_frequency_domain.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./profile.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./profile.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/./aligned_column_iterator.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/./aligned_column_iterator.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./gromacs_block_modifiers.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./gromacs_block_modifiers.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./module_config.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./module_config.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./vecmat_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./vecmat_op.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info_visitor.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./info_visitor.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./minimal_compound_lib.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/./minimal_compound_lib.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./cross_correlate.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./cross_correlate.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./ff_reader.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./ff_reader.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./vec3.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./vec3.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/entity_io_pqr_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/entity_io_pqr_handler.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/./invalid_sequence.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/./invalid_sequence.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_half_frequency_domain.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_half_frequency_domain.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./filter_clashes.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./filter_clashes.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/entity_impl_fw.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./heuristic_block_modifiers.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./heuristic_block_modifiers.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/tool_options_win.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool_options_win.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/map_octree.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/map_octree.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./pair_subst_weight_matrix.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./pair_subst_weight_matrix.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./compound_lib_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/./compound_lib_base.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./dyn_cast.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./dyn_cast.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./vecmat2_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./vecmat2_op.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/custom_renderer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/custom_renderer.hh +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/./module_config.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/./module_config.hh +make -f modules/config/CMakeFiles/ost_config.dir/build.make modules/config/CMakeFiles/ost_config.dir/build +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info_visitor.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./info_visitor.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./semiglobal_align.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./semiglobal_align.hh +make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +make[4]: Nothing to be done for 'modules/config/CMakeFiles/ost_config.dir/build'. +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./superpose_frames.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./superpose_frames.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./density_slice.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./density_slice.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info_verbose_visitor.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./info_verbose_visitor.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./compound_lib_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/./compound_lib_base.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./buildingblock.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./buildingblock.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/entity_impl_fw.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./ring_finder.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/./ring_finder.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/tool_options_widget.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool_options_widget.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_frequency_domain.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_frequency_domain.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/entity_io_mae_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/entity_io_mae_handler.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./construct_cbeta.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./construct_cbeta.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/./views_from_sequences.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/./views_from_sequences.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/octree_isocont.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/octree_isocont.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./vec4.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./vec4.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./stdint.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./stdint.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./interaction.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./interaction.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/mouse_event.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./ring_finder.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/./ring_finder.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./clash_score.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./clash_score.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./vecmat3_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./vecmat3_op.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/entity_io_mmcif_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/entity_io_mmcif_handler.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./semiglobal_align.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./semiglobal_align.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/fragment_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/fragment_impl.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_spatial_domain.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_spatial_domain.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/./profile_handle.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/./profile_handle.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/cpk_renderer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/cpk_renderer.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/./sequence_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/./sequence_op.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./filter_clashes.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./filter_clashes.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./block_modifiers.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./block_modifiers.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info_verbose_visitor.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./info_verbose_visitor.hh +[ 0%] Built target ost_config cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./dft.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./dft.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./item_type.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./item_type.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/map_tool.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/map_tool.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/cartoon_renderer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/cartoon_renderer.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./stdint_msc.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./stdint_msc.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/fragment_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/fragment_impl.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./settings.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./settings.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./trajectory_analysis.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./trajectory_analysis.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/entity_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/entity_io_handler.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./vecmat4_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./vecmat4_op.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./geom_info_conversion.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./geom_info_conversion.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./sequence_identity.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./sequence_identity.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/entity_io_mmcif_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/entity_io_mmcif_handler.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/manipulator.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/manipulator.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_half_frequency_domain.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_half_frequency_domain.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./vecmat_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./vecmat_op.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./stdint_msc.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./stdint_msc.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./item_type.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./item_type.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/./aligned_region.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/./aligned_region.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/debug_renderer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/debug_renderer.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./construct_cbeta.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./construct_cbeta.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./fft.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./fft.hh -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./gromacs_block_modifiers.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./gromacs_block_modifiers.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/fragment_impl_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/fragment_impl_fw.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_visitor.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_visitor.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./structure_analysis.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./structure_analysis.hh [ 0%] Built target ost_conop_headers -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/align_properties_painter.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/align_properties_painter.hh -[ 0%] Built target ost_seq_headers -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./range.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./range.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/custom_renderer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/custom_renderer.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./sequence_similarity.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./sequence_similarity.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/tool_options_win.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool_options_win.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./vecmat2_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./vecmat2_op.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/entity_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/entity_io_handler.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./geom_info_conversion.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./geom_info_conversion.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/./aligned_column.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/./aligned_column.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/simple_renderer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/simple_renderer.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/query_ast.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/query_ast.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./clash_score.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./clash_score.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./heuristic_block_modifiers.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./heuristic_block_modifiers.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./fftw_helper.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./fftw_helper.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./simulation.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./simulation.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./range.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./range.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./subst_weight_matrix.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./subst_weight_matrix.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_spatial_domain.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_spatial_domain.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/query_ast_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/query_ast_fw.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/pdb_reader.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./circular_iterator.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./circular_iterator.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./sequence_similarity.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./sequence_similarity.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_algorithm.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_algorithm.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./item_type_cast.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./item_type_cast.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./consistency_checks.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./consistency_checks.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/mouse_event.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/./aligned_column_iterator.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/./aligned_column_iterator.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./vecmat3_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./vecmat3_op.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./interaction.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./interaction.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/sline_renderer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/sline_renderer.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./fill.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./fill.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./module_config.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./module_config.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/cpk_renderer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/cpk_renderer.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/base_row.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/base_row.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/query_ast.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/query_ast.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./modeller.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./modeller.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./trajectory_analysis.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./trajectory_analysis.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./variance_map.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./variance_map.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/query_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/query_impl.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_visitor.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_visitor.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./settings.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./settings.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/./invalid_sequence.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/./invalid_sequence.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/trace_renderer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/trace_renderer.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./vecmat4_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./vecmat4_op.hh +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/map_tool.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/map_tool.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./structure_analysis.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./structure_analysis.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./units.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./units.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/query_impl_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/query_impl_fw.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./data/default_contact_weight_matrix.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./default_contact_weight_matrix.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/entity_io_pdb_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/entity_io_pdb_handler.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./subst_weight_matrix.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./subst_weight_matrix.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./filter.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./filter.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/./views_from_sequences.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/./views_from_sequences.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./simulation.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./simulation.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_algorithm.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_algorithm.hh +[ 0%] Built target ost_info_headers +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./circular_iterator.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./circular_iterator.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/line_trace_renderer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/line_trace_renderer.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./consistency_checks.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./consistency_checks.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/pdb_writer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/pdb_writer.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/align_properties_painter.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/align_properties_painter.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/residue_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/residue_impl.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./message.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./message.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./data/default_pair_subst_weight_matrix.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./default_pair_subst_weight_matrix.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./modeller.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./modeller.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./constants.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./constants.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./fourier_filters.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./fourier_filters.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/./profile_handle.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/./profile_handle.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/backbone_trace.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/backbone_trace.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_visitor_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_visitor_fw.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./units.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./units.hh -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./fill.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./fill.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/entity_io_sdf_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/entity_io_sdf_handler.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/residue_impl_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/residue_impl_fw.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./pdbize.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./pdbize.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/debug_renderer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/debug_renderer.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/pdb_writer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/pdb_writer.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/query_ast_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/query_ast_fw.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/background_painter.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/background_painter.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./hmm_pseudo_counts.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./hmm_pseudo_counts.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/base_row.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/base_row.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./platform.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./platform.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/surface_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/surface_impl.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./observer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./observer.hh +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./composite.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./composite.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/entity_detail.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/entity_detail.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./gaussian_gradient_magnitude.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./gaussian_gradient_magnitude.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/sdf_reader.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/sdf_reader.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/index.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/index.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./observer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./observer.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./variance_map.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./variance_map.hh -[ 0%] Built target ost_info_headers -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./message.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./message.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/entity_io_sdf_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/entity_io_sdf_handler.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./hmm_score.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./hmm_score.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./adjacency_bitmap.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./adjacency_bitmap.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/query_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/query_impl.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./filter.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./filter.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/type_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/type_fw.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./state_extractor.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./state_extractor.hh +[ 0%] Built target ost_seq_headers cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./composite2.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./composite2.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/simple_renderer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/simple_renderer.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/background_painter.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/background_painter.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/surface_impl_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/surface_impl_fw.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./string_ref.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./string_ref.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/entity_renderer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./gaussian.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./gaussian.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/sdf_writer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/sdf_writer.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/type_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/type_fw.hh +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./consistency_checks.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./consistency_checks.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./system_creator.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./system_creator.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/conservation_painter.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/conservation_painter.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./state_extractor.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./state_extractor.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./platform.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./platform.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./data/default_contact_weight_matrix.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./default_contact_weight_matrix.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/sdf_reader.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/sdf_reader.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./composite3.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./composite3.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/torsion_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/torsion_impl.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./pod_vector.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./pod_vector.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/save_entity.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/save_entity.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/trace_renderer_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/trace_renderer_base.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./gaussian_laplacian.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./gaussian_laplacian.hh +[ 0%] Built target ost_seq_alg_headers cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/value_holder.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/value_holder.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./fourier_filters.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./fourier_filters.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/sline_renderer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/sline_renderer.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./system_creator.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./system_creator.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./contact_overlap.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./contact_overlap.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./topology_creator.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./topology_creator.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/painter.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/painter.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./consistency_checks.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./consistency_checks.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./data/default_pair_subst_weight_matrix.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./default_pair_subst_weight_matrix.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/sdf_writer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/sdf_writer.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./string_ref.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./string_ref.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/query_impl_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/query_impl_fw.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/torsion_impl_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/torsion_impl_fw.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./composite_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./composite_op.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./topology_creator.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./topology_creator.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./algorithm.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./algorithm.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/trace_renderer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/trace_renderer.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./contact_overlap.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./contact_overlap.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/save_entity.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/save_entity.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/connect_renderer_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/connect_renderer_base.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./fixed_string.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./fixed_string.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./highest_peak_search_3d.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./highest_peak_search_3d.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/secstr_row.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/secstr_row.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/load_entity.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/load_entity.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./algorithm.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./algorithm.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./atom_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./atom_base.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./domain_find.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./domain_find.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./index.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./index.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./pod_vector.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./pod_vector.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./circle_mask.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./circle_mask.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./composite2_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./composite2_op.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./gaussian_gradient_magnitude.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./gaussian_gradient_magnitude.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/residue_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/residue_impl.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/line_trace_renderer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/line_trace_renderer.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./topology.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./topology.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./domain_find.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./domain_find.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/load_entity.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/load_entity.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/mapped_property.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/mapped_property.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./tri_matrix.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./tri_matrix.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./histogram.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./histogram.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/seq_secstr_painter.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/seq_secstr_painter.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./fixed_string.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./fixed_string.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/surface_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/surface_io_handler.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./circle_mask.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./circle_mask.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./atom_handle.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./atom_handle.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./similarity_matrix.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./similarity_matrix.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./topology.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./topology.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./line_iterator.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./line_iterator.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./composite3_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./composite3_op.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/seq_selection_painter.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/seq_selection_painter.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./atom_view.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./atom_view.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/entity_renderer_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer_fw.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/load_surface.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/load_surface.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./boost_filesystem_helper.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./boost_filesystem_helper.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./composite_mask.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./composite_mask.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./steep.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./steep.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./gaussian.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./gaussian.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/residue_impl_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/residue_impl_fw.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/backbone_trace.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/backbone_trace.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./similarity_matrix.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./similarity_matrix.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/surface_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/surface_io_handler.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/seq_selection_painter.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/seq_selection_painter.hh -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./tri_matrix.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./tri_matrix.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./local_sigma_threshold.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./local_sigma_threshold.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./aligned_cuboid.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./aligned_cuboid.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./gaussian_laplacian.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./gaussian_laplacian.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/load_surface.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/load_surface.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./data_algorithm.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./data_algorithm.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/surface_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/surface_impl.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/entity_detail.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/entity_detail.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./accessibility.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./accessibility.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./boost_filesystem_helper.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./boost_filesystem_helper.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/seq_text_painter.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/seq_text_painter.hh -[ 0%] Built target ost_mol_mm_headers -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./highest_peak_search_3d.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./highest_peak_search_3d.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/entity_renderer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./bond_handle.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./bond_handle.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/surface_io_msms_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/surface_io_msms_handler.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/surface_impl_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/surface_impl_fw.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./paged_array.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./paged_array.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/tabulated_trig.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/tabulated_trig.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./data_algorithm.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./data_algorithm.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./mask_image.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./mask_image.hh +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./vec_mat_predicates.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./vec_mat_predicates.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_delegate.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_delegate.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/pdb_str.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/pdb_str.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./data_observer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./data_observer.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./histogram.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./histogram.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_delegate.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_delegate.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./bond_table.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./bond_table.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/fast_spheres.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/fast_spheres.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./sec_struct.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./sec_struct.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./paged_array.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./paged_array.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/trace_renderer_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/trace_renderer_base.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/torsion_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/torsion_impl.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/pdb_str.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/pdb_str.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_model.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_model.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./line_iterator.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./line_iterator.hh +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[ 0%] Built target ost_mol_mm_headers cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./quat.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./quat.hh +[ 0%] Built target ost_base_headers cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./data_types.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./data_types.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/stereochemical_params_reader.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/stereochemical_params_reader.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/connect_renderer_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/connect_renderer_base.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./negate.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./negate.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_model.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_model.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./nonstandard.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./nonstandard.hh -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/torsion_impl_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/torsion_impl_fw.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_row.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_row.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./local_sigma_threshold.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./local_sigma_threshold.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./chain_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./chain_base.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/render_options/render_options.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/render_options.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/stereochemical_params_reader.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/stereochemical_params_reader.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./transform.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./transform.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/mapped_property.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/mapped_property.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./data.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./data.hh -[ 0%] Built target ost_base_headers -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./atom_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./atom_base.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_search_bar.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_search_bar.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./mask_image.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./mask_image.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./normalizer_factory.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./normalizer_factory.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./chain_handle.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./chain_handle.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./molck.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./molck.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/render_options/line_render_options.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/line_render_options.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_row.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_row.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/omf.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/omf.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/entity_renderer_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer_fw.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./point_cloud.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./point_cloud.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./debug.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./debug.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./molck.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./molck.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_table_view.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_table_view.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./atom_handle.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./atom_handle.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./norm.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./norm.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./point_cloud.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./point_cloud.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/render_options/custom_render_options.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/custom_render_options.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./find_membrane.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./find_membrane.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./module_config.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./module_config.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./negate.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./negate.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/tabulated_trig.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/tabulated_trig.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./atom_view.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./atom_view.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./chain_view.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./chain_view.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/load_map.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/load_map.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_viewer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_viewer.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./normalizer_factory.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./normalizer_factory.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_search_bar.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_search_bar.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./dllexport.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./dllexport.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./module_config.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./module_config.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./normalizer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./normalizer.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./extent_iterator.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./extent_iterator.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./entity_to_density.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./entity_to_density.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/render_options/cpk_render_options.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/cpk_render_options.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_table_view.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_table_view.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./chain_type.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./chain_type.hh +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_df3_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_df3_handler.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./norm_linear.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./norm_linear.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/render_options/simple_render_options.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/simple_render_options.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./extent_mask.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./extent_mask.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_viewer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_viewer.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./chem_class.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./chem_class.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/image_format.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/image_format.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/tick_painter.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/tick_painter.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./entity_to_density.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./entity_to_density.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./bond_handle.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./bond_handle.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./norm.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./norm.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./norm_log.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./norm_log.hh [ 0%] Built target ost_geom_headers -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_dx_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_dx_handler.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/render_options/sline_render_options.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/sline_render_options.hh make -f modules/geom/src/CMakeFiles/ost_geom.dir/build.make modules/geom/src/CMakeFiles/ost_geom.dir/depend +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./extent.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./extent.hh +[ 0%] Built target ost_mol_alg_headers make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/geom/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src/CMakeFiles/ost_geom.dir/DependInfo.cmake --color= -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/fast_spheres.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/fast_spheres.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./extent_iterator.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./extent_iterator.hh -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./bond_table.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./bond_table.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_spi_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_spi_handler.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./normalizer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./normalizer.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./extent_mask.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./extent_mask.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/title_row.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/title_row.hh -[ 0%] Built target ost_mol_alg_headers -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/render_options/render_options.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/render_options.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./norm_linear.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./norm_linear.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./extent.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./extent.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./chain_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./chain_base.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/render_options/line_render_options.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/line_render_options.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./norm_log.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./norm_log.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_situs_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_situs_handler.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/render_options/custom_render_options.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/custom_render_options.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/alignment_view_object.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/alignment_view_object.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./chain_handle.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./chain_handle.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/tick_painter.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/tick_painter.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./chem_type.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./chem_type.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_dx_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_dx_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./norm_od.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./norm_od.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/base_view_object.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/base_view_object.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_handler.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/render_options/cpk_render_options.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/cpk_render_options.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/render_options/line_trace_render_options.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/line_trace_render_options.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./image_factory.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./image_factory.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./chain_view.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./chain_view.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_mrc_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_mrc_handler.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/title_row.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/title_row.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./coord_group.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./coord_group.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/render_options/cartoon_render_options.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/cartoon_render_options.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./power_spectrum.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./power_spectrum.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_spi_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_spi_handler.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./image_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./image_fw.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./coord_source.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./coord_source.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/alignment_view_object.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/alignment_view_object.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./randomize.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./randomize.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./in_mem_coord_source.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./in_mem_coord_source.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/render_options/trace_render_options.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/trace_render_options.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_situs_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_situs_handler.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./image_handle_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./image_handle_fw.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/geom/src/CMakeFiles/ost_geom.dir/build.make modules/geom/src/CMakeFiles/ost_geom.dir/build -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./image_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./image_fw.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/render_options/simple_render_options.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/simple_render_options.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./power_spectrum.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./power_spectrum.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_view_object.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_view_object.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_dat_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_dat_handler.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/base_view_object.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/base_view_object.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./smooth_mask_image.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./smooth_mask_image.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_handler.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./image_handle.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./image_handle.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./coord_frame.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./coord_frame.hh make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'modules/geom/src/CMakeFiles/ost_geom.dir/build'. make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./image_handle_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./image_handle_fw.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./chain_type.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./chain_type.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_ipl_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_ipl_handler.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/render_options/sline_render_options.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/sline_render_options.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/main_thread_runner.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/main_thread_runner.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./randomize.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./randomize.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/color_ops/color_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/color_op.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_mrc_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_mrc_handler.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_view_object.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_view_object.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./editor_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./editor_base.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./stat.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./stat.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./image_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./image_impl.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/color_ops/by_element_color_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/by_element_color_op.hh [ 2%] Built target ost_geom make -f modules/base/src/CMakeFiles/ost_base.dir/build.make modules/base/src/CMakeFiles/ost_base.dir/depend +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_dat_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_dat_handler.hh make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/base/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src/CMakeFiles/ost_base.dir/DependInfo.cmake --color= +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./stat_accumulator.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./stat_accumulator.hh make -f modules/geom/pymod/CMakeFiles/_ost_geom.dir/build.make modules/geom/pymod/CMakeFiles/_ost_geom.dir/depend -make -f modules/geom/tests/CMakeFiles/ost_geom_tests.dir/build.make modules/geom/tests/CMakeFiles/ost_geom_tests.dir/depend +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/main_thread_runner.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/main_thread_runner.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./image_list.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./image_list.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/color_ops/by_chain_color_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/by_chain_color_op.hh make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/geom/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/pymod/CMakeFiles/_ost_geom.dir/DependInfo.cmake --color= -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_jpk_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_jpk_handler.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./image_handle.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./image_handle.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./chem_class.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./chem_class.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/output_redirector.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/output_redirector.hh +make -f modules/geom/tests/CMakeFiles/ost_geom_tests.dir/build.make modules/geom/tests/CMakeFiles/ost_geom_tests.dir/depend +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./editor_type_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./editor_type_fw.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_ipl_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_ipl_handler.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./stat_min_max.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./stat_min_max.hh make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/geom/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/tests/CMakeFiles/ost_geom_tests.dir/DependInfo.cmake --color= -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./smooth_mask_image.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./smooth_mask_image.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/render_options/line_trace_render_options.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/line_trace_render_options.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./chem_type.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./chem_type.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_nanoscope_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_nanoscope_handler.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./stat.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./stat.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/output_redirector.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/output_redirector.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./image_state_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./image_state_fw.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./mol.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./mol.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_jpk_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_jpk_handler.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/color_ops/uniform_color_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/uniform_color_op.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./threshold.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./threshold.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/completer_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/completer_base.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/render_options/cartoon_render_options.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/cartoon_render_options.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./coord_group.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./coord_group.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_png_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_png_handler.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./image_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./image_impl.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./stat_accumulator.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./stat_accumulator.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/dir_model.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/dir_model.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./entity_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_base.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./image_state.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./image_state.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/geom/tests/CMakeFiles/ost_geom_tests.dir/build.make modules/geom/tests/CMakeFiles/ost_geom_tests.dir/build +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_dm3_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_dm3_handler.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./coord_source.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./coord_source.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/gutter.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/gutter.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./image_list.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./image_list.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_tiff_handler.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./stat_min_max.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./stat_min_max.hh +make -f modules/base/src/CMakeFiles/ost_base.dir/build.make modules/base/src/CMakeFiles/ost_base.dir/build +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/dir_model.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/dir_model.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_nanoscope_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_nanoscope_handler.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./entity_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_base.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/color_ops/gradient_color_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/gradient_color_op.hh +make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +make[4]: Nothing to be done for 'modules/base/src/CMakeFiles/ost_base.dir/build'. +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./image.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./image.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_png_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_png_handler.hh [ 2%] Building CXX object modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_composite3.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/render_options/trace_render_options.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/trace_render_options.hh +[ 2%] Building CXX object modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_mat2.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/tests && /usr/bin/c++ -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_composite3.cc.o -MF CMakeFiles/ost_geom_tests.dir/test_composite3.cc.o.d -o CMakeFiles/ost_geom_tests.dir/test_composite3.cc.o -c /build/openstructure-2.3.1/modules/geom/tests/test_composite3.cc -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./in_mem_coord_source.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./in_mem_coord_source.hh -[ 2%] Building CXX object modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_composite2.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/gutter.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/gutter.hh [ 2%] Building CXX object modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_mat3.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./threshold.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./threshold.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/tests && /usr/bin/c++ -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_composite2.cc.o -MF CMakeFiles/ost_geom_tests.dir/test_composite2.cc.o.d -o CMakeFiles/ost_geom_tests.dir/test_composite2.cc.o -c /build/openstructure-2.3.1/modules/geom/tests/test_composite2.cc -[ 2%] Building CXX object modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_mat2.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./entity_handle.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_handle.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/tests && /usr/bin/c++ -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_mat2.cc.o -MF CMakeFiles/ost_geom_tests.dir/test_mat2.cc.o.d -o CMakeFiles/ost_geom_tests.dir/test_mat2.cc.o -c /build/openstructure-2.3.1/modules/geom/tests/test_mat2.cc -[ 2%] Building CXX object modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_op3.cc.o -[ 2%] Building CXX object modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_op2.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/tests && /usr/bin/c++ -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_mat3.cc.o -MF CMakeFiles/ost_geom_tests.dir/test_mat3.cc.o.d -o CMakeFiles/ost_geom_tests.dir/test_mat3.cc.o -c /build/openstructure-2.3.1/modules/geom/tests/test_mat3.cc -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/path_completer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/path_completer.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/tests && /usr/bin/c++ -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_op3.cc.o -MF CMakeFiles/ost_geom_tests.dir/test_op3.cc.o.d -o CMakeFiles/ost_geom_tests.dir/test_op3.cc.o -c /build/openstructure-2.3.1/modules/geom/tests/test_op3.cc -[ 2%] Building CXX object modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_mat4.cc.o -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/tiff_util.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/tiff_util.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/color_ops/color_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/color_op.hh -make -f modules/base/src/CMakeFiles/ost_base.dir/build.make modules/base/src/CMakeFiles/ost_base.dir/build -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/tests && /usr/bin/c++ -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_mat4.cc.o -MF CMakeFiles/ost_geom_tests.dir/test_mat4.cc.o.d -o CMakeFiles/ost_geom_tests.dir/test_mat4.cc.o -c /build/openstructure-2.3.1/modules/geom/tests/test_mat4.cc cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./transcendentals.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./transcendentals.hh -make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'modules/base/src/CMakeFiles/ost_base.dir/build'. -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/tests && /usr/bin/c++ -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_op2.cc.o -MF CMakeFiles/ost_geom_tests.dir/test_op2.cc.o.d -o CMakeFiles/ost_geom_tests.dir/test_op2.cc.o -c /build/openstructure-2.3.1/modules/geom/tests/test_op2.cc -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./coord_frame.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./coord_frame.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/jpk_util.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/jpk_util.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/color_ops/by_element_color_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/by_element_color_op.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/python_context_parser.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_context_parser.hh [ 3%] Built target ost_base +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/color_ops/entity_view_color_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/entity_view_color_op.hh make -f modules/info/src/CMakeFiles/ost_info.dir/build.make modules/info/src/CMakeFiles/ost_info.dir/depend -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./transform.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./transform.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/tests && /usr/bin/c++ -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_mat3.cc.o -MF CMakeFiles/ost_geom_tests.dir/test_mat3.cc.o.d -o CMakeFiles/ost_geom_tests.dir/test_mat3.cc.o -c /build/openstructure-2.3.1/modules/geom/tests/test_mat3.cc make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/info/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src/CMakeFiles/ost_info.dir/DependInfo.cmake --color= -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/seq/sequence_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./editor_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./editor_base.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/python_completer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_completer.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./entity_observer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_observer.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./inverted_mask.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./inverted_mask.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./transform.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./transform.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/path_completer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/path_completer.hh +[ 3%] Building CXX object modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_composite2.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/color_ops/basic_gradient_color_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/basic_gradient_color_op.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_dm3_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_dm3_handler.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/tests && /usr/bin/c++ -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_composite2.cc.o -MF CMakeFiles/ost_geom_tests.dir/test_composite2.cc.o.d -o CMakeFiles/ost_geom_tests.dir/test_composite2.cc.o -c /build/openstructure-2.3.1/modules/geom/tests/test_composite2.cc +[ 3%] Building CXX object modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_mat4.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./map.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./map.hh +[ 3%] Building CXX object modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_op2.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./transform_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./transform_fw.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/color_ops/by_chain_color_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/by_chain_color_op.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/python_context_parser.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_context_parser.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/tests && /usr/bin/c++ -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_mat4.cc.o -MF CMakeFiles/ost_geom_tests.dir/test_mat4.cc.o.d -o CMakeFiles/ost_geom_tests.dir/test_mat4.cc.o -c /build/openstructure-2.3.1/modules/geom/tests/test_mat4.cc +[ 3%] Building CXX object modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_op3.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./entity_observer_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_observer_fw.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/color_ops/gradient_level_color_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/gradient_level_color_op.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/tests && /usr/bin/c++ -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_op2.cc.o -MF CMakeFiles/ost_geom_tests.dir/test_op2.cc.o.d -o CMakeFiles/ost_geom_tests.dir/test_op2.cc.o -c /build/openstructure-2.3.1/modules/geom/tests/test_op2.cc +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/tests && /usr/bin/c++ -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_op3.cc.o -MF CMakeFiles/ost_geom_tests.dir/test_op3.cc.o.d -o CMakeFiles/ost_geom_tests.dir/test_op3.cc.o -c /build/openstructure-2.3.1/modules/geom/tests/test_op3.cc +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_tiff_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./alg_transform.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./alg_transform.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/seq/fasta_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/fasta_io_handler.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/color_ops/uniform_color_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/uniform_color_op.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./editor_type_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./editor_type_fw.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./mask_base_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./mask_base_fw.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/python_completer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_completer.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./entity_property_mapper.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_property_mapper.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/color_ops/map_handle_color_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/map_handle_color_op.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./mask_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./mask_base.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/python_shell.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_shell.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./image_state_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./image_state_fw.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/tiff_util.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/tiff_util.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./alg_mirror.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./alg_mirror.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/python_shell_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_shell_fw.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/seq/pir_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/pir_io_handler.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/color_ops/gradient_color_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/gradient_color_op.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./mol.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./mol.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./image_state.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./image_state.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./render_pass.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./render_pass.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./entity_view.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_view.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/jpk_util.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/jpk_util.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./alg_shift.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./alg_shift.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./mask_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./mask_op.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/info/src/CMakeFiles/ost_info.dir/build.make modules/info/src/CMakeFiles/ost_info.dir/build -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/python_shell_widget.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_shell_widget.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./alg_shift.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./alg_shift.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./entity_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_base.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/seq/promod_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/promod_io_handler.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/color_ops/entity_view_color_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/entity_view_color_op.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./bitmap_io.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./bitmap_io.hh +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/seq/sequence_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./discrete_shrink.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./discrete_shrink.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./entity_visitor.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_visitor.hh +make -f modules/geom/pymod/CMakeFiles/_ost_geom.dir/build.make modules/geom/pymod/CMakeFiles/_ost_geom.dir/build +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./mask_visitor.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./mask_visitor.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./collada_exporter.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./collada_exporter.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/seq/fasta_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/fasta_io_handler.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./transformation_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./transformation_base.hh make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'modules/info/src/CMakeFiles/ost_info.dir/build'. make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./image.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./image.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/python_tokenizer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_tokenizer.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./discrete_shrink.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./discrete_shrink.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/color_ops/basic_gradient_color_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/basic_gradient_color_op.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./entity_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_base.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./entity_visitor_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_visitor_fw.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./color.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./color.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./mask.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./mask.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/python_shell_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_shell_fw.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/seq/pir_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/pir_io_handler.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./transformations.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./transformations.hh [ 4%] Built target ost_info -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./inverted_mask.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./inverted_mask.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/seq/profile_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/profile_io_handler.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/python_syntax_highlighter.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_syntax_highlighter.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./transformation_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./transformation_base.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./entity_handle.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_handle.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/color_ops/gradient_level_color_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/gradient_level_color_op.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./handle_type_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./handle_type_fw.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./entity.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./entity.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./module_config.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./module_config.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/seq/promod_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/promod_io_handler.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./ics_editor.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./ics_editor.hh [ 4%] Building CXX object modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_op4.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/tests && /usr/bin/c++ -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_op4.cc.o -MF CMakeFiles/ost_geom_tests.dir/test_op4.cc.o.d -o CMakeFiles/ost_geom_tests.dir/test_op4.cc.o -c /build/openstructure-2.3.1/modules/geom/tests/test_op4.cc -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/geom/pymod/CMakeFiles/_ost_geom.dir/build.make modules/geom/pymod/CMakeFiles/_ost_geom.dir/build -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./map.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./map.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/color_ops/map_handle_color_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/map_handle_color_op.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/seq/hhm_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/hhm_io_handler.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./entity_observer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_observer.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/text_logger.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./transformations.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./transformations.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/seq/pssm_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/pssm_io_handler.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./mask_base_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./mask_base_fw.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./render_pass.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./render_pass.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./fractional_shift.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./fractional_shift.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/seq/clustal_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/clustal_io_handler.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/python_shell_widget.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_shell_widget.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./entity_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./entity_fw.hh make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'modules/geom/pymod/CMakeFiles/_ost_geom.dir/build'. make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./entity_observer_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_observer_fw.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./mask_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./mask_base.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./bitmap_io.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./bitmap_io.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./not_connected_error.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./not_connected_error.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./normalizer_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./normalizer_fw.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./module_config.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./module_config.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./mask_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./mask_op.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/python_tokenizer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_tokenizer.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/seq/profile_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/profile_io_handler.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gl_helper.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gl_helper.hh [ 6%] Built target _ost_geom +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./property_id.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./property_id.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./polar.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./polar.hh make -f modules/base/pymod/CMakeFiles/_ost_base.dir/build.make modules/base/pymod/CMakeFiles/_ost_base.dir/depend +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./normalizer_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./normalizer_impl.hh make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/base/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/pymod/CMakeFiles/_ost_base.dir/DependInfo.cmake --color= -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/seq/load.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/load.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter_worker.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./entity_property_mapper.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_property_mapper.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./polar.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./polar.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./collada_exporter.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./collada_exporter.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./mask_visitor.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./mask_visitor.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./line_average.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./line_average.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./entity_view.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_view.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/seq/save.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/save.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./color.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./color.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/python_shell_text_document_layout.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_shell_text_document_layout.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/python_syntax_highlighter.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_syntax_highlighter.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gfx.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/seq/hhm_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/hhm_io_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./rscrosscorr.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./rscrosscorr.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./hmm_pseudo_counts.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./hmm_pseudo_counts.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./mask.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./mask.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./entity_visitor.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_visitor.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./query.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./query.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./null_data.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./null_data.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gfx_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_fw.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/seq/pssm_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/pssm_io_handler.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/text_logger.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./binary_data_sink.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./binary_data_sink.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./entity_visitor_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_visitor_fw.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./entity.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./entity.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/shell_history.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/shell_history.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./io_manager.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./io_manager.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./hmm_score.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./hmm_score.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./module_config.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./module_config.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./entity_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./entity_fw.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./query_error.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./query_error.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./observable.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./observable.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gfx_node.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_node.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./query_state.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./query_state.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/seq/clustal_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/clustal_io_handler.hh [ 6%] Built target ost_img_alg_headers make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/base/pymod/CMakeFiles/_ost_base.dir/build.make modules/base/pymod/CMakeFiles/_ost_base.dir/build -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/state_machine.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/state_machine.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./handle_type_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./handle_type_fw.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gl_helper.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gl_helper.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./binary_data_source.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./binary_data_source.hh -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gfx_node_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_node_fw.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter_worker.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./paste_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./paste_impl.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./residue_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./residue_base.hh +[ 6%] Building CXX object modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_quat.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/tests && /usr/bin/c++ -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_quat.cc.o -MF CMakeFiles/ost_geom_tests.dir/test_quat.cc.o.d -o CMakeFiles/ost_geom_tests.dir/test_quat.cc.o -c /build/openstructure-2.3.1/modules/geom/tests/test_quat.cc +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/seq/load.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/load.hh make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'modules/base/pymod/CMakeFiles/_ost_base.dir/build'. make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./normalizer_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./normalizer_fw.hh -[ 6%] Building CXX object modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_quat.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/tests && /usr/bin/c++ -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_quat.cc.o -MF CMakeFiles/ost_geom_tests.dir/test_quat.cc.o.d -o CMakeFiles/ost_geom_tests.dir/test_quat.cc.o -c /build/openstructure-2.3.1/modules/geom/tests/test_quat.cc -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/state.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/state.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./module_config.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./module_config.hh -[ 6%] Built target ost_seq_alg_headers +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gfx_node_visitor.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_node_visitor.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/python_shell_text_document_layout.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_shell_text_document_layout.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/seq/save.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/save.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./residue_handle.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./residue_handle.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gfx_object_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_object_base.hh [ 6%] Built target _ost_base -make -f modules/info/pymod/CMakeFiles/_ost_info.dir/build.make modules/info/pymod/CMakeFiles/_ost_info.dir/depend -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gfx.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/transition.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/transition.hh -make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/info/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/pymod/CMakeFiles/_ost_info.dir/DependInfo.cmake --color= -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./ics_editor.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./ics_editor.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./normalizer_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./normalizer_impl.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./container_serialization.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./container_serialization.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/transition_guard.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/transition_guard.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./not_connected_error.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./not_connected_error.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/shell_history.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/shell_history.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gfx_object.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_object.hh [ 7%] Building CXX object modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_vec2.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gfx_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_fw.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./binary_data_sink.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./binary_data_sink.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./residue_prop.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./residue_prop.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/tests && /usr/bin/c++ -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_vec2.cc.o -MF CMakeFiles/ost_geom_tests.dir/test_vec2.cc.o.d -o CMakeFiles/ost_geom_tests.dir/test_vec2.cc.o -c /build/openstructure-2.3.1/modules/geom/tests/test_vec2.cc -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./swap_util.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./swap_util.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./null_data.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./null_data.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/state_machine.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/state_machine.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./peak.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./peak.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/state.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/state.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./io_manager.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./io_manager.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./residue_view.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./residue_view.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./phase.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./phase.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gfx_object_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_object_fw.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/transition.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/transition.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./binary_data_source.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./binary_data_source.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gfx_prim.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_prim.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./physical_units.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./physical_units.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./sec_structure.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./sec_structure.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/transition_guard.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/transition_guard.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./symmetry_node.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./symmetry_node.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./module_config.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./module_config.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./pixel_sampling.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./pixel_sampling.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/panels/button_bar.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/button_bar.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./property_id.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./property_id.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gfx_node.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_node.hh -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/info/pymod/CMakeFiles/_ost_info.dir/build.make modules/info/pymod/CMakeFiles/_ost_info.dir/build +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gfx_test_object.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_test_object.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./spatial_organizer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./spatial_organizer.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./container_serialization.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./container_serialization.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./point_list.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./point_list.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/panels/drop_box.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/drop_box.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./observable.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./observable.hh -make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'modules/info/pymod/CMakeFiles/_ost_info.dir/build'. -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./io_utils.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./io_utils.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gfx_node_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_node_fw.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./query.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./query.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./glwin_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./glwin_base.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./swap_util.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./swap_util.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./surface.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./surface.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./point.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./point.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/panels/panel_bar.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/panel_bar.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./paste_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./paste_impl.hh -[ 7%] Built target _ost_info -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./query_error.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./query_error.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./io_exception.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./io_exception.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./input.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./input.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./surface_builder.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./surface_builder.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./io_utils.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./io_utils.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./polygon_mask.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./polygon_mask.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/panels/panel_manager.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/panel_manager.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gfx_node_visitor.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_node_visitor.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./peak.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./peak.hh -[ 7%] Building CXX object modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_vec3.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./query_state.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./query_state.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/tests && /usr/bin/c++ -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_vec3.cc.o -MF CMakeFiles/ost_geom_tests.dir/test_vec3.cc.o.d -o CMakeFiles/ost_geom_tests.dir/test_vec3.cc.o -c /build/openstructure-2.3.1/modules/geom/tests/test_vec3.cc -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./convert.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./convert.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gfx_object_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_object_base.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./prim_list.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./prim_list.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./builder.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./builder.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./io_exception.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./io_exception.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./progress.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./progress.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/panels/bottom_bar.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/bottom_bar.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./phase.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./phase.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./converting_streams.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./converting_streams.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./residue_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./residue_base.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./scene.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./scene.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./surface_handle.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./surface_handle.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/panels/button_box.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/button_box.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gfx_object.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_object.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./residue_handle.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./residue_handle.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./formatted_line.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./formatted_line.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./physical_units.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./physical_units.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./size.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./size.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./convert.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./convert.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./selection.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./selection.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/panels/event_button.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/event_button.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gfx_object_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_object_fw.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/chemdict_parser.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./chemdict_parser.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./residue_prop.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./residue_prop.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./pixel_sampling.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./pixel_sampling.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./converting_streams.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./converting_streams.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./surface_prop.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./surface_prop.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./spherical_mask.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./spherical_mask.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./surface.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./surface.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./util.cc /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./util.cc +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./torsion_handle.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./torsion_handle.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/panels/panel_widget_container.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/panel_widget_container.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gfx_prim.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_prim.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./point_list.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./point_list.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/star_parser.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./star_parser.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./symmetry_node.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./symmetry_node.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./residue_view.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./residue_view.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./texture.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./texture.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./formatted_line.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./formatted_line.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./util.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./util.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/panels/panel_bar_widget_holder.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/panel_bar_widget_holder.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./point.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./point.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/mmcif_reader.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./mmcif_reader.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gfx_test_object.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_test_object.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./sec_structure.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./sec_structure.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/chemdict_parser.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./chemdict_parser.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./vertex_array.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./vertex_array.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./transfer_connectivity.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./transfer_connectivity.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/panels/side_bar.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/side_bar.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/mmcif_info.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./mmcif_info.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./polygon_mask.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./polygon_mask.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./glwin_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./glwin_base.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/star_parser.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./star_parser.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./vertex_array_helper.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./vertex_array_helper.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./query_view_wrapper.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./query_view_wrapper.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./value_util.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./value_util.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/panels/splitter_panel_bar.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/splitter_panel_bar.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./spatial_organizer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./spatial_organizer.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./progress.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./progress.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/io_profile.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./io_profile.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./input.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./input.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./scene_observer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./scene_observer.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./vecmat.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./vecmat.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/panels/tabbed_panel_bar.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/tabbed_panel_bar.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./prim_list.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./prim_list.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./surface.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./surface.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./size.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./size.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./view_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./view_op.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gl_include.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gl_include.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./mask_info_convert.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./mask_info_convert.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/mmcif_reader.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./mmcif_reader.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./view_type_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./view_type_fw.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/scene_win/context_menu.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/context_menu.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/dcd_io.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./dcd_io.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./surface_builder.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./surface_builder.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./scene.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./scene.hh +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./glext_include.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./glext_include.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/mmcif_info.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./mmcif_info.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./view_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./view_op.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/scene_win/current_selection_node.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/current_selection_node.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./spherical_mask.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./spherical_mask.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/entity_io_crd_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./entity_io_crd_handler.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./builder.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./builder.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./render_mode.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./render_mode.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/io_profile.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./io_profile.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/scene_win/custom_part_node.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/custom_part_node.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./util.cc /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./util.cc -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./selection.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./selection.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/entity_io_pqr_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./entity_io_pqr_handler.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./xcs_editor.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./xcs_editor.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./material.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./material.hh +[ 7%] Built target ost_img_headers +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/dcd_io.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./dcd_io.hh +make -f modules/info/pymod/CMakeFiles/_ost_info.dir/build.make modules/info/pymod/CMakeFiles/_ost_info.dir/depend +make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/info/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/pymod/CMakeFiles/_ost_info.dir/DependInfo.cmake --color= cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/scene_win/entity_node.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/entity_node.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./surface_handle.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./surface_handle.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./util.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./util.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/entity_io_mae_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./entity_io_mae_handler.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./surface.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./surface.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./surface_prop.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./surface_prop.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/entity_io_mmcif_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./entity_io_mmcif_handler.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./value_util.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./value_util.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gradient.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gradient.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./bounding_box.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./bounding_box.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/entity_io_crd_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./entity_io_crd_handler.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gradient_manager.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gradient_manager.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/scene_win/entity_part_node.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/entity_part_node.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./torsion_handle.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./torsion_handle.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./texture.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./texture.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/entity_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./entity_io_handler.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./vecmat.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./vecmat.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./transform.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./transform.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./module_config.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./module_config.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/scene_win/gfx_scene_node.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/gfx_scene_node.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./transfer_connectivity.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./transfer_connectivity.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./vertex_array.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./vertex_array.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/pdb_reader.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./pdb_reader.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./mask_info_convert.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./mask_info_convert.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./query_view_wrapper.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./query_view_wrapper.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./module_config.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./module_config.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/entity_io_pqr_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./entity_io_pqr_handler.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./primitives.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./primitives.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/scene_win/label_node.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/label_node.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./vertex_array_helper.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./vertex_array_helper.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./povray_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./povray_fw.hh +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/entity_io_mae_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./entity_io_mae_handler.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./povray.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./povray.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/scene_win/root_node.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/root_node.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/entity_io_pdb_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./entity_io_pdb_handler.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./view_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./view_op.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./scene_observer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./scene_observer.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/pdb_writer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./pdb_writer.hh -[ 7%] Built target ost_img_headers +make -f modules/info/pymod/CMakeFiles/_ost_info.dir/build.make modules/info/pymod/CMakeFiles/_ost_info.dir/build +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./exporter.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./exporter.hh +[ 7%] Built target ost_mol_headers +make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +make[4]: Nothing to be done for 'modules/info/pymod/CMakeFiles/_ost_info.dir/build'. +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/scene_win/render_mode_node.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/render_mode_node.hh make -f modules/img/base/src/CMakeFiles/ost_img.dir/build.make modules/img/base/src/CMakeFiles/ost_img.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/img/base/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src/CMakeFiles/ost_img.dir/DependInfo.cmake --color= -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./view_type_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./view_type_fw.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gl_include.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gl_include.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/entity_io_sdf_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./entity_io_sdf_handler.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./exporter_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./exporter_fw.hh +[ 7%] Built target _ost_info +make -f modules/mol/base/src/CMakeFiles/ost_mol.dir/build.make modules/mol/base/src/CMakeFiles/ost_mol.dir/depend +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/entity_io_mmcif_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./entity_io_mmcif_handler.hh +make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/base/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src/CMakeFiles/ost_mol.dir/DependInfo.cmake --color= cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/scene_win/render_modes_node.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/render_modes_node.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./glext_include.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./glext_include.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/sdf_reader.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./sdf_reader.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./view_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./view_op.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gost_exporter.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gost_exporter.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./color_ops/map_handle_color_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./map_handle_color_op.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/scene_win/scene_node.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/scene_node.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./render_mode.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./render_mode.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/sdf_writer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./sdf_writer.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/entity_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./entity_io_handler.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./map_iso.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./map_iso.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/scene_win/scene_win.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/scene_win.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./xcs_editor.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./xcs_editor.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./material.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./material.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/pdb_reader.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./pdb_reader.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./map_slab.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./map_slab.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/scene_win/scene_win_model.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/scene_win_model.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/save_entity.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./save_entity.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./bounding_box.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./bounding_box.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/entity_io_pdb_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./entity_io_pdb_handler.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./map_iso_prop.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./map_iso_prop.hh +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/messages/message_widget.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/messages/message_widget.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gradient.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gradient.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/load_entity.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./load_entity.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/pdb_writer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./pdb_writer.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/entity_io_sdf_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./entity_io_sdf_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/messages/message_box_widget.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/messages/message_box_widget.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./transform.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./transform.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gradient_manager.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gradient_manager.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/surface_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./surface_io_handler.hh +[ 7%] Built target ost_gfx_headers +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/sdf_reader.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./sdf_reader.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/sdf_writer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./sdf_writer.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/save_entity.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./save_entity.hh +[ 7%] Building CXX object modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_vec3.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/messages/log_reader.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/messages/log_reader.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./module_config.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./module_config.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/load_surface.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./load_surface.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./module_config.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./module_config.hh -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/tests && /usr/bin/c++ -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_vec3.cc.o -MF CMakeFiles/ost_geom_tests.dir/test_vec3.cc.o.d -o CMakeFiles/ost_geom_tests.dir/test_vec3.cc.o -c /build/openstructure-2.3.1/modules/geom/tests/test_vec3.cc +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/load_entity.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./load_entity.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/argand.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/argand.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/surface_io_msms_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./surface_io_msms_handler.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./primitives.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./primitives.hh -[ 7%] Built target ost_mol_headers -make -f modules/mol/base/src/CMakeFiles/ost_mol.dir/build.make modules/mol/base/src/CMakeFiles/ost_mol.dir/depend -make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/base/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src/CMakeFiles/ost_mol.dir/DependInfo.cmake --color= -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/pdb_str.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./pdb_str.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/surface_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./surface_io_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/data_viewer.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/stereochemical_params_reader.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./stereochemical_params_reader.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./povray_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./povray_fw.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/load_surface.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./load_surface.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/data_viewer_panel.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/omf.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./omf.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./povray.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./povray.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/surface_io_msms_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./surface_io_msms_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/data_viewer_panel_base.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./seq/sequence_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./sequence_io_handler.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/pdb_str.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./pdb_str.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/draw_overlay.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/draw_overlay.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./exporter.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./exporter.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./seq/fasta_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./fasta_io_handler.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/drawing_functions.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/drawing_functions.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./exporter_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./exporter_fw.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./seq/pir_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./pir_io_handler.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/drawing_functions.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/drawing_functions.hh make -f modules/img/base/src/CMakeFiles/ost_img.dir/build.make modules/img/base/src/CMakeFiles/ost_img.dir/build +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/stereochemical_params_reader.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./stereochemical_params_reader.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/omf.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./omf.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/fft_panel.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/fft_panel.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./seq/promod_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./promod_io_handler.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gost_exporter.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gost_exporter.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./seq/sequence_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./sequence_io_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/info_panel.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/info_panel.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./seq/profile_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./profile_io_handler.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./seq/fasta_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./fasta_io_handler.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/img2qt.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/img2qt.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./seq/pir_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./pir_io_handler.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/mask_overlay.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/mask_overlay.hh make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'modules/img/base/src/CMakeFiles/ost_img.dir/build'. make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./color_ops/map_handle_color_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./map_handle_color_op.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./seq/hhm_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./hhm_io_handler.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/img2qt.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/img2qt.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./seq/promod_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./promod_io_handler.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/null_overlay.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/null_overlay.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./seq/profile_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./profile_io_handler.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/overlay.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/overlay.hh [ 10%] Built target ost_img make -f modules/img/alg/src/CMakeFiles/ost_img_alg.dir/build.make modules/img/alg/src/CMakeFiles/ost_img_alg.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/img/alg/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src/CMakeFiles/ost_img_alg.dir/DependInfo.cmake --color= -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./map_iso.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./map_iso.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/mask_overlay.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/mask_overlay.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./seq/hhm_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./hhm_io_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./seq/pssm_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./pssm_io_handler.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/null_overlay.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/null_overlay.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./map_slab.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./map_slab.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/overlay_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/overlay_base.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./seq/clustal_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./clustal_io_handler.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/overlay.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/overlay.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./map_iso_prop.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./map_iso_prop.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./seq/load.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./load.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/overlay_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/overlay_base.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/overlay_base_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/overlay_base_fw.hh -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./seq/save.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./save.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/overlay_manager.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/overlay_manager.hh -[ 10%] Built target ost_gfx_headers -make -f modules/img/base/pymod/CMakeFiles/_ost_img.dir/build.make modules/img/base/pymod/CMakeFiles/_ost_img.dir/depend -make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/img/base/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/pymod/CMakeFiles/_ost_img.dir/DependInfo.cmake --color= cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/load_map.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./load_map.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/overlay_manager_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/overlay_manager_fw.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_df3_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_df3_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/overlay_manager_gui.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/overlay_manager_gui.hh +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +make -f modules/mol/base/src/CMakeFiles/ost_mol.dir/build.make modules/mol/base/src/CMakeFiles/ost_mol.dir/build cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/image_format.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./image_format.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/overlay_manager_observer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/overlay_manager_observer.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_dx_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_dx_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/pointlist_overlay.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/pointlist_overlay.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_dx_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_dx_handler.hh +make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +make[4]: Nothing to be done for 'modules/mol/base/src/CMakeFiles/ost_mol.dir/build'. +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_spi_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_spi_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/pointlist_overlay_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/pointlist_overlay_base.hh +[ 16%] Built target ost_mol +make -f modules/img/base/pymod/CMakeFiles/_ost_img.dir/build.make modules/img/base/pymod/CMakeFiles/_ost_img.dir/depend cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_situs_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_situs_handler.hh +make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/img/base/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/pymod/CMakeFiles/_ost_img.dir/DependInfo.cmake --color= cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/strategies.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/strategies.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/strategies_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/strategies_fw.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_mrc_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_mrc_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/viewer_normalizer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/viewer_normalizer.hh -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/mol/base/src/CMakeFiles/ost_mol.dir/build.make modules/mol/base/src/CMakeFiles/ost_mol.dir/build -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_dat_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_dat_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./file_browser.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./file_browser.hh -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/img/alg/src/CMakeFiles/ost_img_alg.dir/build.make modules/img/alg/src/CMakeFiles/ost_img_alg.dir/build +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_dat_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_dat_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_ipl_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_ipl_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./file_type_dialog.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./file_type_dialog.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_jpk_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_jpk_handler.hh +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +make -f modules/img/alg/src/CMakeFiles/ost_img_alg.dir/build.make modules/img/alg/src/CMakeFiles/ost_img_alg.dir/build +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./file_viewer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./file_viewer.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_nanoscope_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_nanoscope_handler.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./gl_canvas.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./gl_canvas.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_png_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_png_handler.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_dm3_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_dm3_handler.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./gl_win.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./gl_win.hh +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +make -f modules/img/base/pymod/CMakeFiles/_ost_img.dir/build.make modules/img/base/pymod/CMakeFiles/_ost_img.dir/build +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./scene_menu.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./scene_menu.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_tiff_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_tiff_handler.hh make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'modules/img/alg/src/CMakeFiles/ost_img_alg.dir/build'. make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/tiff_util.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./tiff_util.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./gosty_app.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./gosty_app.hh +[ 20%] Built target ost_img_alg +make -f modules/base/tests/CMakeFiles/ost_base_tests.dir/build.make modules/base/tests/CMakeFiles/ost_base_tests.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'modules/mol/base/src/CMakeFiles/ost_mol.dir/build'. +make[4]: Nothing to be done for 'modules/img/base/pymod/CMakeFiles/_ost_img.dir/build'. make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./file_viewer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./file_viewer.hh -[ 15%] Built target ost_img_alg +make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/base/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/tests/CMakeFiles/ost_base_tests.dir/DependInfo.cmake --color= +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/jpk_util.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./jpk_util.hh +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +make -f modules/base/tests/CMakeFiles/ost_base_tests.dir/build.make modules/base/tests/CMakeFiles/ost_base_tests.dir/build +make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./admin.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./admin.hh +[ 20%] Built target ost_io_headers make -f modules/img/base/tests/CMakeFiles/ost_img_tests.dir/build.make modules/img/base/tests/CMakeFiles/ost_img_tests.dir/depend -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_nanoscope_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_nanoscope_handler.hh -[ 20%] Built target ost_mol +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./module_config.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./module_config.hh +[ 20%] Building CXX object modules/base/tests/CMakeFiles/ost_base_tests.dir/test_generic_property.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/tests/CMakeFiles/ost_base_tests.dir/test_generic_property.cc.o -MF CMakeFiles/ost_base_tests.dir/test_generic_property.cc.o.d -o CMakeFiles/ost_base_tests.dir/test_generic_property.cc.o -c /build/openstructure-2.3.1/modules/base/tests/test_generic_property.cc +[ 21%] Built target _ost_img make -f modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/build.make modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/img/base/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/tests/CMakeFiles/ost_img_tests.dir/DependInfo.cmake --color= -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./gl_canvas.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./gl_canvas.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./main.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./main.hh make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/img/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/DependInfo.cmake --color= -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_png_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_png_handler.hh -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/img/base/pymod/CMakeFiles/_ost_img.dir/build.make modules/img/base/pymod/CMakeFiles/_ost_img.dir/build make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/img/base/tests/CMakeFiles/ost_img_tests.dir/build.make modules/img/base/tests/CMakeFiles/ost_img_tests.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./gl_win.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./gl_win.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_dm3_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_dm3_handler.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./main_area.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./main_area.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/build.make modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'modules/img/base/pymod/CMakeFiles/_ost_img.dir/build'. -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 21%] Building CXX object modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_data.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./perspective.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./perspective.hh +[ 23%] Building CXX object modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_data.cc.o +[ 23%] Building CXX object modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_clear.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_data.cc.o -MF CMakeFiles/ost_img_tests.dir/test_data.cc.o.d -o CMakeFiles/ost_img_tests.dir/test_data.cc.o -c /build/openstructure-2.3.1/modules/img/base/tests/test_data.cc -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_tiff_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_tiff_handler.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./scene_menu.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./scene_menu.hh -[ 21%] Building CXX object modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_clear.cc.o -[ 23%] Built target _ost_img +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./scene_selection.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./scene_selection.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_clear.cc.o -MF CMakeFiles/ost_img_alg_tests.dir/test_clear.cc.o.d -o CMakeFiles/ost_img_alg_tests.dir/test_clear.cc.o -c /build/openstructure-2.3.1/modules/img/alg/tests/test_clear.cc +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./main_window.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./main_window.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./dock_widget.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./dock_widget.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./dock_widget.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./dock_widget.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./thin_splitter.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./thin_splitter.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./widget.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./widget.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./widget_geom_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./widget_geom_handler.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./widget_pool.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./widget_pool.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./widget_registry.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./widget_registry.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./widget_state_saver.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./widget_state_saver.hh +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./file_loader.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./file_loader.hh +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[ 23%] Built target ost_gui_headers make -f modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/build.make modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/depend -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/tiff_util.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./tiff_util.hh make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/base/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/DependInfo.cmake --color= -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./gosty_app.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./gosty_app.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/jpk_util.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./jpk_util.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./admin.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./admin.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/build.make modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/build -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./module_config.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./module_config.hh -[ 23%] Built target ost_io_headers -make -f modules/seq/base/src/CMakeFiles/ost_seq.dir/build.make modules/seq/base/src/CMakeFiles/ost_seq.dir/depend [ 23%] Building CXX object modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_atom_groups.cc.o -make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/seq/base/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src/CMakeFiles/ost_seq.dir/DependInfo.cmake --color= cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_atom_groups.cc.o -MF CMakeFiles/ost_mol_tests.dir/test_atom_groups.cc.o.d -o CMakeFiles/ost_mol_tests.dir/test_atom_groups.cc.o -c /build/openstructure-2.3.1/modules/mol/base/tests/test_atom_groups.cc -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./main.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./main.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./main_area.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./main_area.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./perspective.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./perspective.hh In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/modules/geom/tests/test_mat2.cc:20: + from /build/openstructure-2.3.1/modules/geom/tests/test_op4.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -28088,11 +28108,10 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./scene_selection.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./scene_selection.hh In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/modules/geom/tests/test_composite2.cc:21: + from /build/openstructure-2.3.1/modules/geom/tests/test_quat.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -28110,17 +28129,10 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./main_window.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./main_window.hh -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/seq/base/src/CMakeFiles/ost_seq.dir/build.make modules/seq/base/src/CMakeFiles/ost_seq.dir/build -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./dock_widget.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./dock_widget.hh -make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'modules/seq/base/src/CMakeFiles/ost_seq.dir/build'. -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/modules/geom/tests/test_quat.cc:20: + from /build/openstructure-2.3.1/modules/geom/tests/test_mat4.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -28141,7 +28153,7 @@ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/modules/geom/tests/test_op2.cc:20: + from /build/openstructure-2.3.1/modules/geom/tests/test_mat3.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -28153,42 +28165,16 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./dock_widget.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./dock_widget.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 24%] Built target ost_seq -make -f modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/build.make modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/depend -make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/base/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/DependInfo.cmake --color= -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./thin_splitter.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./thin_splitter.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./widget.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./widget.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./widget_geom_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./widget_geom_handler.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./widget_pool.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./widget_pool.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./widget_registry.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./widget_registry.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./widget_state_saver.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./widget_state_saver.hh -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./file_loader.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./file_loader.hh -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 24%] Built target ost_gui_headers -make -f modules/db/src/CMakeFiles/ost_db.dir/build.make modules/db/src/CMakeFiles/ost_db.dir/depend -make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/db/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/src/CMakeFiles/ost_db.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/db/src/CMakeFiles/ost_db.dir/build.make modules/db/src/CMakeFiles/ost_db.dir/build -make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'modules/db/src/CMakeFiles/ost_db.dir/build'. -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 24%] Built target ost_db -make -f modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/build.make modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/depend -make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/img/alg/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/DependInfo.cmake --color= In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/modules/geom/tests/test_op4.cc:20: + from /build/openstructure-2.3.1/modules/geom/tests/test_mat2.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -28209,7 +28195,7 @@ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/modules/geom/tests/test_mat3.cc:20: + from /build/openstructure-2.3.1/modules/geom/tests/test_composite2.cc:21: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -28227,19 +28213,27 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/build.make modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/build -make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/build'. -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 25%] Built target _ost_img_alg In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/modules/geom/tests/test_mat4.cc:20: + from /build/openstructure-2.3.1/modules/geom/tests/test_composite3.cc:21: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/openstructure-2.3.1/modules/geom/tests/test_op3.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/bits/specfun.h:45, + from /usr/include/c++/12/cmath:1935, + from /build/openstructure-2.3.1/modules/geom/tests/test_composite3.cc:20: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec2.hh:22, @@ -28254,59 +28248,16 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -make -f modules/base/tests/CMakeFiles/ost_base_tests.dir/build.make modules/base/tests/CMakeFiles/ost_base_tests.dir/depend -make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/base/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/tests/CMakeFiles/ost_base_tests.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/build.make modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/build -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/modules/geom/tests/test_composite3.cc:21: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/specfun.h:45, - from /usr/include/c++/12/cmath:1935, - from /build/openstructure-2.3.1/modules/geom/tests/test_composite3.cc:20: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/base/tests/CMakeFiles/ost_base_tests.dir/build.make modules/base/tests/CMakeFiles/ost_base_tests.dir/build -make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 25%] Building CXX object modules/base/tests/CMakeFiles/ost_base_tests.dir/test_generic_property.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/tests/CMakeFiles/ost_base_tests.dir/test_generic_property.cc.o -MF CMakeFiles/ost_base_tests.dir/test_generic_property.cc.o.d -o CMakeFiles/ost_base_tests.dir/test_generic_property.cc.o -c /build/openstructure-2.3.1/modules/base/tests/test_generic_property.cc -make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/build'. -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 27%] Built target _ost_mol -make -f modules/bindings/src/CMakeFiles/ost_bindings.dir/build.make modules/bindings/src/CMakeFiles/ost_bindings.dir/depend -make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/bindings/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/src/CMakeFiles/ost_bindings.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/bindings/src/CMakeFiles/ost_bindings.dir/build.make modules/bindings/src/CMakeFiles/ost_bindings.dir/build -make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'modules/bindings/src/CMakeFiles/ost_bindings.dir/build'. -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 27%] Built target ost_bindings -make -f modules/seq/base/tests/CMakeFiles/ost_seq_tests.dir/build.make modules/seq/base/tests/CMakeFiles/ost_seq_tests.dir/depend -make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/seq/base/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/tests/CMakeFiles/ost_seq_tests.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/seq/base/tests/CMakeFiles/ost_seq_tests.dir/build.make modules/seq/base/tests/CMakeFiles/ost_seq_tests.dir/build -make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/modules/geom/tests/test_op3.cc:20: + from /build/openstructure-2.3.1/modules/geom/tests/test_vec3.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -28324,12 +28275,10 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 27%] Building CXX object modules/seq/base/tests/CMakeFiles/ost_seq_tests.dir/test_sequence.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/seq/base/tests/CMakeFiles/ost_seq_tests.dir/test_sequence.cc.o -MF CMakeFiles/ost_seq_tests.dir/test_sequence.cc.o.d -o CMakeFiles/ost_seq_tests.dir/test_sequence.cc.o -c /build/openstructure-2.3.1/modules/seq/base/tests/test_sequence.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/modules/geom/tests/test_vec2.cc:20: + from /build/openstructure-2.3.1/modules/geom/tests/test_op2.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -28350,7 +28299,7 @@ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/modules/geom/tests/test_vec3.cc:20: + from /build/openstructure-2.3.1/modules/geom/tests/test_vec2.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -28368,8 +28317,6 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 27%] Building CXX object modules/base/tests/CMakeFiles/ost_base_tests.dir/test_string_ref.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/tests/CMakeFiles/ost_base_tests.dir/test_string_ref.cc.o -MF CMakeFiles/ost_base_tests.dir/test_string_ref.cc.o.d -o CMakeFiles/ost_base_tests.dir/test_string_ref.cc.o -c /build/openstructure-2.3.1/modules/base/tests/test_string_ref.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -28403,43 +28350,11 @@ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, - from /build/openstructure-2.3.1/modules/img/alg/tests/test_clear.cc:29: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/12/string:45, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/ostream:38, - from /usr/include/c++/12/iostream:39, - from /build/openstructure-2.3.1/modules/img/alg/tests/test_clear.cc:25: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -[ 27%] Building CXX object modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_transform.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/tests && /usr/bin/c++ -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_transform.cc.o -MF CMakeFiles/ost_geom_tests.dir/test_transform.cc.o.d -o CMakeFiles/ost_geom_tests.dir/test_transform.cc.o -c /build/openstructure-2.3.1/modules/geom/tests/test_transform.cc -[ 27%] Building CXX object modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_vec4.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/tests && /usr/bin/c++ -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_vec4.cc.o -MF CMakeFiles/ost_geom_tests.dir/test_vec4.cc.o.d -o CMakeFiles/ost_geom_tests.dir/test_vec4.cc.o -c /build/openstructure-2.3.1/modules/geom/tests/test_vec4.cc -[ 27%] Building CXX object modules/geom/tests/CMakeFiles/ost_geom_tests.dir/tests.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/tests && /usr/bin/c++ -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT modules/geom/tests/CMakeFiles/ost_geom_tests.dir/tests.cc.o -MF CMakeFiles/ost_geom_tests.dir/tests.cc.o.d -o CMakeFiles/ost_geom_tests.dir/tests.cc.o -c /build/openstructure-2.3.1/modules/geom/tests/tests.cc -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, - from /build/openstructure-2.3.1/modules/base/tests/test_generic_property.cc:23: + from /build/openstructure-2.3.1/modules/mol/base/tests/test_atom_groups.cc:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -28452,7 +28367,7 @@ from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, - from /build/openstructure-2.3.1/modules/base/tests/test_generic_property.cc:21: + from /build/openstructure-2.3.1/modules/mol/base/tests/test_atom_groups.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -28465,24 +28380,20 @@ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, - from /build/openstructure-2.3.1/modules/mol/base/tests/test_atom_groups.cc:24: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, + from /build/openstructure-2.3.1/modules/img/alg/tests/test_clear.cc:29: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, - from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, - from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, - from /usr/include/boost/test/detail/global_typedef.hpp:15, - from /usr/include/boost/test/tree/observer.hpp:17, - from /usr/include/boost/test/unit_test_log.hpp:18, - from /usr/include/boost/test/tools/old/impl.hpp:19, - from /usr/include/boost/test/test_tools.hpp:46, - from /usr/include/boost/test/unit_test.hpp:18, - from /build/openstructure-2.3.1/modules/mol/base/tests/test_atom_groups.cc:23: + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/ostream:38, + from /usr/include/c++/12/iostream:39, + from /build/openstructure-2.3.1/modules/img/alg/tests/test_clear.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -28499,7 +28410,7 @@ from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, - from /build/openstructure-2.3.1/modules/seq/base/tests/test_sequence.cc:22: + from /build/openstructure-2.3.1/modules/base/tests/test_generic_property.cc:23: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -28512,7 +28423,7 @@ from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, - from /build/openstructure-2.3.1/modules/seq/base/tests/test_sequence.cc:20: + from /build/openstructure-2.3.1/modules/base/tests/test_generic_property.cc:21: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -28522,23 +28433,23 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 27%] Building CXX object modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_chain.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_chain.cc.o -MF CMakeFiles/ost_mol_tests.dir/test_chain.cc.o.d -o CMakeFiles/ost_mol_tests.dir/test_chain.cc.o -c /build/openstructure-2.3.1/modules/mol/base/tests/test_chain.cc -[ 27%] Building CXX object modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_conn.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_conn.cc.o -MF CMakeFiles/ost_mol_tests.dir/test_conn.cc.o.d -o CMakeFiles/ost_mol_tests.dir/test_conn.cc.o -c /build/openstructure-2.3.1/modules/mol/base/tests/test_conn.cc -[ 27%] Building CXX object modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_extent.cc.o +[ 23%] Building CXX object modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_extent.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_extent.cc.o -MF CMakeFiles/ost_img_tests.dir/test_extent.cc.o.d -o CMakeFiles/ost_img_tests.dir/test_extent.cc.o -c /build/openstructure-2.3.1/modules/img/base/tests/test_extent.cc -[ 27%] Building CXX object modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_coord_group.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_coord_group.cc.o -MF CMakeFiles/ost_mol_tests.dir/test_coord_group.cc.o.d -o CMakeFiles/ost_mol_tests.dir/test_coord_group.cc.o -c /build/openstructure-2.3.1/modules/mol/base/tests/test_coord_group.cc -[ 27%] Building CXX object modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_builder.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_builder.cc.o -MF CMakeFiles/ost_mol_tests.dir/test_builder.cc.o.d -o CMakeFiles/ost_mol_tests.dir/test_builder.cc.o -c /build/openstructure-2.3.1/modules/mol/base/tests/test_builder.cc -[ 27%] Building CXX object modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_delete.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_delete.cc.o -MF CMakeFiles/ost_mol_tests.dir/test_delete.cc.o.d -o CMakeFiles/ost_mol_tests.dir/test_delete.cc.o -c /build/openstructure-2.3.1/modules/mol/base/tests/test_delete.cc -[ 27%] Building CXX object modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_entity.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_entity.cc.o -MF CMakeFiles/ost_mol_tests.dir/test_entity.cc.o.d -o CMakeFiles/ost_mol_tests.dir/test_entity.cc.o -c /build/openstructure-2.3.1/modules/mol/base/tests/test_entity.cc -[ 27%] Building CXX object modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_conj.cc.o +[ 23%] Building CXX object modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_vec4.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/tests && /usr/bin/c++ -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_vec4.cc.o -MF CMakeFiles/ost_geom_tests.dir/test_vec4.cc.o.d -o CMakeFiles/ost_geom_tests.dir/test_vec4.cc.o -c /build/openstructure-2.3.1/modules/geom/tests/test_vec4.cc +[ 23%] Building CXX object modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_transform.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/tests && /usr/bin/c++ -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_transform.cc.o -MF CMakeFiles/ost_geom_tests.dir/test_transform.cc.o.d -o CMakeFiles/ost_geom_tests.dir/test_transform.cc.o -c /build/openstructure-2.3.1/modules/geom/tests/test_transform.cc +[ 23%] Building CXX object modules/geom/tests/CMakeFiles/ost_geom_tests.dir/tests.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/tests && /usr/bin/c++ -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT modules/geom/tests/CMakeFiles/ost_geom_tests.dir/tests.cc.o -MF CMakeFiles/ost_geom_tests.dir/tests.cc.o.d -o CMakeFiles/ost_geom_tests.dir/tests.cc.o -c /build/openstructure-2.3.1/modules/geom/tests/tests.cc +[ 23%] Building CXX object modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_image.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_image.cc.o -MF CMakeFiles/ost_img_tests.dir/test_image.cc.o.d -o CMakeFiles/ost_img_tests.dir/test_image.cc.o -c /build/openstructure-2.3.1/modules/img/base/tests/test_image.cc +[ 23%] Building CXX object modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_conj.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_conj.cc.o -MF CMakeFiles/ost_img_alg_tests.dir/test_conj.cc.o.d -o CMakeFiles/ost_img_alg_tests.dir/test_conj.cc.o -c /build/openstructure-2.3.1/modules/img/alg/tests/test_conj.cc -[ 27%] Building CXX object modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_convolute.cc.o +[ 23%] Building CXX object modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_image_state.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_image_state.cc.o -MF CMakeFiles/ost_img_tests.dir/test_image_state.cc.o.d -o CMakeFiles/ost_img_tests.dir/test_image_state.cc.o -c /build/openstructure-2.3.1/modules/img/base/tests/test_image_state.cc +[ 23%] Building CXX object modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_chain.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_chain.cc.o -MF CMakeFiles/ost_mol_tests.dir/test_chain.cc.o.d -o CMakeFiles/ost_mol_tests.dir/test_chain.cc.o -c /build/openstructure-2.3.1/modules/mol/base/tests/test_chain.cc +[ 23%] Building CXX object modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_convolute.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_convolute.cc.o -MF CMakeFiles/ost_img_alg_tests.dir/test_convolute.cc.o.d -o CMakeFiles/ost_img_alg_tests.dir/test_convolute.cc.o -c /build/openstructure-2.3.1/modules/img/alg/tests/test_convolute.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, @@ -28561,6 +28472,40 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 23%] Building CXX object modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_conn.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_conn.cc.o -MF CMakeFiles/ost_mol_tests.dir/test_conn.cc.o.d -o CMakeFiles/ost_mol_tests.dir/test_conn.cc.o -c /build/openstructure-2.3.1/modules/mol/base/tests/test_conn.cc +[ 23%] Building CXX object modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_coord_group.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_coord_group.cc.o -MF CMakeFiles/ost_mol_tests.dir/test_coord_group.cc.o.d -o CMakeFiles/ost_mol_tests.dir/test_coord_group.cc.o -c /build/openstructure-2.3.1/modules/mol/base/tests/test_coord_group.cc +[ 23%] Building CXX object modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_builder.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_builder.cc.o -MF CMakeFiles/ost_mol_tests.dir/test_builder.cc.o.d -o CMakeFiles/ost_mol_tests.dir/test_builder.cc.o -c /build/openstructure-2.3.1/modules/mol/base/tests/test_builder.cc +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/extent.hh:34, + from /build/openstructure-2.3.1/modules/img/base/tests/test_extent.cc:29: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/12/string:45, + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/ostream:38, + from /usr/include/c++/12/iostream:39, + from /build/openstructure-2.3.1/modules/img/base/tests/test_extent.cc:25: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 23%] Building CXX object modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_delete.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_delete.cc.o -MF CMakeFiles/ost_mol_tests.dir/test_delete.cc.o.d -o CMakeFiles/ost_mol_tests.dir/test_delete.cc.o -c /build/openstructure-2.3.1/modules/mol/base/tests/test_delete.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -28592,8 +28537,8 @@ from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/extent.hh:34, - from /build/openstructure-2.3.1/modules/img/base/tests/test_extent.cc:29: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, + from /build/openstructure-2.3.1/modules/img/base/tests/test_image.cc:29: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -28603,7 +28548,7 @@ from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, - from /build/openstructure-2.3.1/modules/img/base/tests/test_extent.cc:25: + from /build/openstructure-2.3.1/modules/img/base/tests/test_image.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -28616,24 +28561,20 @@ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, - from /build/openstructure-2.3.1/modules/mol/base/tests/test_chain.cc:25: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, + from /build/openstructure-2.3.1/modules/img/alg/tests/test_conj.cc:29: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, - from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, - from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, - from /usr/include/boost/test/detail/global_typedef.hpp:15, - from /usr/include/boost/test/tree/observer.hpp:17, - from /usr/include/boost/test/unit_test_log.hpp:18, - from /usr/include/boost/test/tools/old/impl.hpp:19, - from /usr/include/boost/test/test_tools.hpp:46, - from /usr/include/boost/test/unit_test.hpp:18, - from /build/openstructure-2.3.1/modules/mol/base/tests/test_chain.cc:23: + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/ostream:38, + from /usr/include/c++/12/iostream:39, + from /build/openstructure-2.3.1/modules/img/alg/tests/test_conj.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -28643,27 +28584,27 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 23%] Building CXX object modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_entity.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_entity.cc.o -MF CMakeFiles/ost_mol_tests.dir/test_entity.cc.o.d -o CMakeFiles/ost_mol_tests.dir/test_entity.cc.o -c /build/openstructure-2.3.1/modules/mol/base/tests/test_entity.cc +[ 23%] Building CXX object modules/base/tests/CMakeFiles/ost_base_tests.dir/test_string_ref.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/tests/CMakeFiles/ost_base_tests.dir/test_string_ref.cc.o -MF CMakeFiles/ost_base_tests.dir/test_string_ref.cc.o.d -o CMakeFiles/ost_base_tests.dir/test_string_ref.cc.o -c /build/openstructure-2.3.1/modules/base/tests/test_string_ref.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, - from /build/openstructure-2.3.1/modules/mol/base/tests/test_coord_group.cc:25: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/extent.hh:34, + from /build/openstructure-2.3.1/modules/img/base/tests/test_image_state.cc:32: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, - from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, - from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, - from /usr/include/boost/test/detail/global_typedef.hpp:15, - from /usr/include/boost/test/tree/observer.hpp:17, - from /usr/include/boost/test/unit_test_log.hpp:18, - from /usr/include/boost/test/tools/old/impl.hpp:19, - from /usr/include/boost/test/test_tools.hpp:46, - from /usr/include/boost/test/unit_test.hpp:18, - from /build/openstructure-2.3.1/modules/mol/base/tests/test_coord_group.cc:23: + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/istream:38, + from /usr/include/c++/12/sstream:38, + from /build/openstructure-2.3.1/modules/img/base/tests/test_image_state.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -28678,22 +28619,18 @@ from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, - from /build/openstructure-2.3.1/modules/mol/base/tests/test_conn.cc:24: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/builder.hh:26, + from /build/openstructure-2.3.1/modules/mol/base/tests/test_builder.cc:22: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/12/string:45, - from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, - from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, - from /usr/include/boost/test/detail/global_typedef.hpp:15, - from /usr/include/boost/test/tree/observer.hpp:17, - from /usr/include/boost/test/unit_test_log.hpp:18, - from /usr/include/boost/test/tools/old/impl.hpp:19, - from /usr/include/boost/test/test_tools.hpp:46, - from /usr/include/boost/test/unit_test.hpp:18, - from /build/openstructure-2.3.1/modules/mol/base/tests/test_conn.cc:23: +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/bits/specfun.h:45, + from /usr/include/c++/12/cmath:1935, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/builder.hh:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -28708,18 +28645,22 @@ from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/builder.hh:26, - from /build/openstructure-2.3.1/modules/mol/base/tests/test_builder.cc:22: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, + from /build/openstructure-2.3.1/modules/mol/base/tests/test_conn.cc:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/specfun.h:45, - from /usr/include/c++/12/cmath:1935, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/builder.hh:23: +In file included from /usr/include/c++/12/string:45, + from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, + from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, + from /usr/include/boost/test/detail/global_typedef.hpp:15, + from /usr/include/boost/test/tree/observer.hpp:17, + from /usr/include/boost/test/unit_test_log.hpp:18, + from /usr/include/boost/test/tools/old/impl.hpp:19, + from /usr/include/boost/test/test_tools.hpp:46, + from /usr/include/boost/test/unit_test.hpp:18, + from /build/openstructure-2.3.1/modules/mol/base/tests/test_conn.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -28729,11 +28670,16 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 23%] Building CXX object modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_discrete_shrink.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_discrete_shrink.cc.o -MF CMakeFiles/ost_img_alg_tests.dir/test_discrete_shrink.cc.o.d -o CMakeFiles/ost_img_alg_tests.dir/test_discrete_shrink.cc.o -c /build/openstructure-2.3.1/modules/img/alg/tests/test_discrete_shrink.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec_mat_predicates.hh:28, - from /build/openstructure-2.3.1/modules/mol/base/tests/test_entity.cc:25: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, + from /build/openstructure-2.3.1/modules/mol/base/tests/test_coord_group.cc:25: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -28746,7 +28692,7 @@ from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, - from /build/openstructure-2.3.1/modules/mol/base/tests/test_entity.cc:24: + from /build/openstructure-2.3.1/modules/mol/base/tests/test_coord_group.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -28762,7 +28708,7 @@ from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, - from /build/openstructure-2.3.1/modules/img/alg/tests/test_conj.cc:29: + from /build/openstructure-2.3.1/modules/img/alg/tests/test_convolute.cc:29: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -28772,7 +28718,7 @@ from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, - from /build/openstructure-2.3.1/modules/img/alg/tests/test_conj.cc:25: + from /build/openstructure-2.3.1/modules/img/alg/tests/test_convolute.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -28785,20 +28731,24 @@ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, - from /build/openstructure-2.3.1/modules/img/alg/tests/test_convolute.cc:29: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, + from /build/openstructure-2.3.1/modules/mol/base/tests/test_delete.cc:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/ostream:38, - from /usr/include/c++/12/iostream:39, - from /build/openstructure-2.3.1/modules/img/alg/tests/test_convolute.cc:25: + from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, + from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, + from /usr/include/boost/test/detail/global_typedef.hpp:15, + from /usr/include/boost/test/tree/observer.hpp:17, + from /usr/include/boost/test/unit_test_log.hpp:18, + from /usr/include/boost/test/tools/old/impl.hpp:19, + from /usr/include/boost/test/test_tools.hpp:46, + from /usr/include/boost/test/unit_test.hpp:18, + from /build/openstructure-2.3.1/modules/mol/base/tests/test_delete.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -28815,7 +28765,7 @@ from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, - from /build/openstructure-2.3.1/modules/mol/base/tests/test_delete.cc:24: + from /build/openstructure-2.3.1/modules/mol/base/tests/test_chain.cc:25: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -28828,7 +28778,7 @@ from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, - from /build/openstructure-2.3.1/modules/mol/base/tests/test_delete.cc:23: + from /build/openstructure-2.3.1/modules/mol/base/tests/test_chain.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -28838,87 +28788,85 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 27%] Building CXX object modules/base/tests/CMakeFiles/ost_base_tests.dir/test_pod_vector.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/tests/CMakeFiles/ost_base_tests.dir/test_pod_vector.cc.o -MF CMakeFiles/ost_base_tests.dir/test_pod_vector.cc.o.d -o CMakeFiles/ost_base_tests.dir/test_pod_vector.cc.o -c /build/openstructure-2.3.1/modules/base/tests/test_pod_vector.cc -[ 27%] Building CXX object modules/base/tests/CMakeFiles/ost_base_tests.dir/tests.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/tests/CMakeFiles/ost_base_tests.dir/tests.cc.o -MF CMakeFiles/ost_base_tests.dir/tests.cc.o.d -o CMakeFiles/ost_base_tests.dir/tests.cc.o -c /build/openstructure-2.3.1/modules/base/tests/tests.cc -[ 28%] Building CXX object modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_ics.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_ics.cc.o -MF CMakeFiles/ost_mol_tests.dir/test_ics.cc.o.d -o CMakeFiles/ost_mol_tests.dir/test_ics.cc.o -c /build/openstructure-2.3.1/modules/mol/base/tests/test_ics.cc -[ 28%] Building CXX object modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_image.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_image.cc.o -MF CMakeFiles/ost_img_tests.dir/test_image.cc.o.d -o CMakeFiles/ost_img_tests.dir/test_image.cc.o -c /build/openstructure-2.3.1/modules/img/base/tests/test_image.cc -[ 28%] Building CXX object modules/seq/base/tests/CMakeFiles/ost_seq_tests.dir/test_aligned_column.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/seq/base/tests/CMakeFiles/ost_seq_tests.dir/test_aligned_column.cc.o -MF CMakeFiles/ost_seq_tests.dir/test_aligned_column.cc.o.d -o CMakeFiles/ost_seq_tests.dir/test_aligned_column.cc.o -c /build/openstructure-2.3.1/modules/seq/base/tests/test_aligned_column.cc -[ 28%] Building CXX object modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_discrete_shrink.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_discrete_shrink.cc.o -MF CMakeFiles/ost_img_alg_tests.dir/test_discrete_shrink.cc.o.d -o CMakeFiles/ost_img_alg_tests.dir/test_discrete_shrink.cc.o -c /build/openstructure-2.3.1/modules/img/alg/tests/test_discrete_shrink.cc -[ 28%] Linking CXX executable ../../../tests/ost_geom_tests +[ 23%] Building CXX object modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_fft.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_fft.cc.o -MF CMakeFiles/ost_img_alg_tests.dir/test_fft.cc.o.d -o CMakeFiles/ost_img_alg_tests.dir/test_fft.cc.o -c /build/openstructure-2.3.1/modules/img/alg/tests/test_fft.cc +[ 23%] Building CXX object modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_image_state_visitor.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_image_state_visitor.cc.o -MF CMakeFiles/ost_img_tests.dir/test_image_state_visitor.cc.o.d -o CMakeFiles/ost_img_tests.dir/test_image_state_visitor.cc.o -c /build/openstructure-2.3.1/modules/img/base/tests/test_image_state_visitor.cc +[ 23%] Building CXX object modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_fill.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_fill.cc.o -MF CMakeFiles/ost_img_alg_tests.dir/test_fill.cc.o.d -o CMakeFiles/ost_img_alg_tests.dir/test_fill.cc.o -c /build/openstructure-2.3.1/modules/img/alg/tests/test_fill.cc +[ 23%] Linking CXX executable ../../../tests/ost_geom_tests cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_geom_tests.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro CMakeFiles/ost_geom_tests.dir/test_composite3.cc.o CMakeFiles/ost_geom_tests.dir/test_composite2.cc.o CMakeFiles/ost_geom_tests.dir/test_mat2.cc.o CMakeFiles/ost_geom_tests.dir/test_mat3.cc.o CMakeFiles/ost_geom_tests.dir/test_mat4.cc.o CMakeFiles/ost_geom_tests.dir/test_op2.cc.o CMakeFiles/ost_geom_tests.dir/test_op3.cc.o CMakeFiles/ost_geom_tests.dir/test_op4.cc.o CMakeFiles/ost_geom_tests.dir/test_quat.cc.o CMakeFiles/ost_geom_tests.dir/test_vec2.cc.o CMakeFiles/ost_geom_tests.dir/test_vec3.cc.o CMakeFiles/ost_geom_tests.dir/test_vec4.cc.o CMakeFiles/ost_geom_tests.dir/test_transform.cc.o CMakeFiles/ost_geom_tests.dir/tests.cc.o -o ../../../tests/ost_geom_tests -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib /usr/lib/x86_64-linux-gnu/libboost_unit_test_framework.so ../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so -[ 28%] Building CXX object modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_query.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_query.cc.o -MF CMakeFiles/ost_mol_tests.dir/test_query.cc.o.d -o CMakeFiles/ost_mol_tests.dir/test_query.cc.o -c /build/openstructure-2.3.1/modules/mol/base/tests/test_query.cc -[ 28%] Building CXX object modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_fft.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_fft.cc.o -MF CMakeFiles/ost_img_alg_tests.dir/test_fft.cc.o.d -o CMakeFiles/ost_img_alg_tests.dir/test_fft.cc.o -c /build/openstructure-2.3.1/modules/img/alg/tests/test_fft.cc -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 28%] Built target ost_geom_tests -make -f modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/build.make modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/depend -make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/seq/alg/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/build.make modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/build +[ 23%] Built target ost_geom_tests +make -f modules/seq/base/src/CMakeFiles/ost_seq.dir/build.make modules/seq/base/src/CMakeFiles/ost_seq.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/build'. +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/seq/base/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src/CMakeFiles/ost_seq.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 29%] Built target ost_seq_alg -make -f modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/build.make modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/depend +make -f modules/seq/base/src/CMakeFiles/ost_seq.dir/build.make modules/seq/base/src/CMakeFiles/ost_seq.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/seq/base/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/DependInfo.cmake --color= +make[4]: Nothing to be done for 'modules/seq/base/src/CMakeFiles/ost_seq.dir/build'. make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/build.make modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/build +[ 24%] Built target ost_seq +make -f modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/build.make modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/build'. +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/base/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 30%] Built target _ost_seq -make -f modules/conop/src/CMakeFiles/ost_conop.dir/build.make modules/conop/src/CMakeFiles/ost_conop.dir/depend +make -f modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/build.make modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/conop/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src/CMakeFiles/ost_conop.dir/DependInfo.cmake --color= -[ 30%] Building CXX object modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_fill.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_fill.cc.o -MF CMakeFiles/ost_img_alg_tests.dir/test_fill.cc.o.d -o CMakeFiles/ost_img_alg_tests.dir/test_fill.cc.o -c /build/openstructure-2.3.1/modules/img/alg/tests/test_fill.cc +make[4]: Nothing to be done for 'modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/build'. make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/conop/src/CMakeFiles/ost_conop.dir/build.make modules/conop/src/CMakeFiles/ost_conop.dir/build +[ 26%] Built target _ost_mol +make -f modules/db/src/CMakeFiles/ost_db.dir/build.make modules/db/src/CMakeFiles/ost_db.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'modules/conop/src/CMakeFiles/ost_conop.dir/build'. +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/db/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/src/CMakeFiles/ost_db.dir/DependInfo.cmake --color= +[ 26%] Building CXX object modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_filter.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_filter.cc.o -MF CMakeFiles/ost_img_alg_tests.dir/test_filter.cc.o.d -o CMakeFiles/ost_img_alg_tests.dir/test_filter.cc.o -c /build/openstructure-2.3.1/modules/img/alg/tests/test_filter.cc make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 31%] Built target ost_conop -make -f modules/db/pymod/CMakeFiles/_ost_db.dir/build.make modules/db/pymod/CMakeFiles/_ost_db.dir/depend +make -f modules/db/src/CMakeFiles/ost_db.dir/build.make modules/db/src/CMakeFiles/ost_db.dir/build +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec_mat_predicates.hh:28, + from /build/openstructure-2.3.1/modules/mol/base/tests/test_entity.cc:25: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/12/string:45, + from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, + from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, + from /usr/include/boost/test/detail/global_typedef.hpp:15, + from /usr/include/boost/test/tree/observer.hpp:17, + from /usr/include/boost/test/unit_test_log.hpp:18, + from /usr/include/boost/test/tools/old/impl.hpp:19, + from /usr/include/boost/test/test_tools.hpp:46, + from /usr/include/boost/test/unit_test.hpp:18, + from /build/openstructure-2.3.1/modules/mol/base/tests/test_entity.cc:24: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/db/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/pymod/CMakeFiles/_ost_db.dir/DependInfo.cmake --color= +make[4]: Nothing to be done for 'modules/db/src/CMakeFiles/ost_db.dir/build'. make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/db/pymod/CMakeFiles/_ost_db.dir/build.make modules/db/pymod/CMakeFiles/_ost_db.dir/build +[ 26%] Built target ost_db +make -f modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/build.make modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'modules/db/pymod/CMakeFiles/_ost_db.dir/build'. +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/img/alg/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 31%] Built target _ost_db -make -f modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/build.make modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/depend +make -f modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/build.make modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/alg/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/DependInfo.cmake --color= -[ 31%] Building CXX object modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_image_state.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_image_state.cc.o -MF CMakeFiles/ost_img_tests.dir/test_image_state.cc.o.d -o CMakeFiles/ost_img_tests.dir/test_image_state.cc.o -c /build/openstructure-2.3.1/modules/img/base/tests/test_image_state.cc +make[4]: Nothing to be done for 'modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/build'. make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/build.make modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/build -[ 31%] Building CXX object modules/seq/base/tests/CMakeFiles/ost_seq_tests.dir/test_aligned_region.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/seq/base/tests/CMakeFiles/ost_seq_tests.dir/test_aligned_region.cc.o -MF CMakeFiles/ost_seq_tests.dir/test_aligned_region.cc.o.d -o CMakeFiles/ost_seq_tests.dir/test_aligned_region.cc.o -c /build/openstructure-2.3.1/modules/seq/base/tests/test_aligned_region.cc +[ 27%] Built target _ost_img_alg +make -f modules/bindings/src/CMakeFiles/ost_bindings.dir/build.make modules/bindings/src/CMakeFiles/ost_bindings.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/build'. -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 34%] Built target ost_mol_alg -[ 34%] Building CXX object modules/seq/base/tests/CMakeFiles/ost_seq_tests.dir/test_alignment.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/seq/base/tests/CMakeFiles/ost_seq_tests.dir/test_alignment.cc.o -MF CMakeFiles/ost_seq_tests.dir/test_alignment.cc.o.d -o CMakeFiles/ost_seq_tests.dir/test_alignment.cc.o -c /build/openstructure-2.3.1/modules/seq/base/tests/test_alignment.cc -[ 34%] Building CXX object modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_surface.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_surface.cc.o -MF CMakeFiles/ost_mol_tests.dir/test_surface.cc.o.d -o CMakeFiles/ost_mol_tests.dir/test_surface.cc.o -c /build/openstructure-2.3.1/modules/mol/base/tests/test_surface.cc -[ 34%] Building CXX object modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_residue.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_residue.cc.o -MF CMakeFiles/ost_mol_tests.dir/test_residue.cc.o.d -o CMakeFiles/ost_mol_tests.dir/test_residue.cc.o -c /build/openstructure-2.3.1/modules/mol/base/tests/test_residue.cc -[ 34%] Linking CXX executable ../../../tests/ost_base_tests -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_base_tests.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro CMakeFiles/ost_base_tests.dir/test_generic_property.cc.o CMakeFiles/ost_base_tests.dir/test_string_ref.cc.o CMakeFiles/ost_base_tests.dir/test_pod_vector.cc.o CMakeFiles/ost_base_tests.dir/tests.cc.o -o ../../../tests/ost_base_tests -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib /usr/lib/x86_64-linux-gnu/libboost_unit_test_framework.so ../../../stage/lib/libost_mol.so.2.3.1 ../../../stage/lib/libost_info.so.2.3.1 ../../../stage/lib/libost_base.so.2.3.1 ../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/bindings/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/src/CMakeFiles/ost_bindings.dir/DependInfo.cmake --color= In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -28946,43 +28894,53 @@ 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 34%] Built target ost_base_tests -make -f modules/bindings/pymod/CMakeFiles/_ost_bindings.dir/build.make modules/bindings/pymod/CMakeFiles/_ost_bindings.dir/depend +make -f modules/bindings/src/CMakeFiles/ost_bindings.dir/build.make modules/bindings/src/CMakeFiles/ost_bindings.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/bindings/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod/CMakeFiles/_ost_bindings.dir/DependInfo.cmake --color= +make[4]: Nothing to be done for 'modules/bindings/src/CMakeFiles/ost_bindings.dir/build'. make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/bindings/pymod/CMakeFiles/_ost_bindings.dir/build.make modules/bindings/pymod/CMakeFiles/_ost_bindings.dir/build +[ 27%] Built target ost_bindings +make -f modules/geom/tests/CMakeFiles/ost_geom_tests_run.dir/build.make modules/geom/tests/CMakeFiles/ost_geom_tests_run.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'modules/bindings/pymod/CMakeFiles/_ost_bindings.dir/build'. +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/geom/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/tests/CMakeFiles/ost_geom_tests_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 34%] Built target _ost_bindings -make -f modules/conop/tests/CMakeFiles/ost_conop_tests.dir/build.make modules/conop/tests/CMakeFiles/ost_conop_tests.dir/depend +make -f modules/geom/tests/CMakeFiles/ost_geom_tests_run.dir/build.make modules/geom/tests/CMakeFiles/ost_geom_tests_run.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/conop/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/tests/CMakeFiles/ost_conop_tests.dir/DependInfo.cmake --color= +[ 27%] running checks for module geom +cd /build/openstructure-2.3.1/modules/geom/tests && env OST_ROOT=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage /build/openstructure-2.3.1/obj-x86_64-linux-gnu/tests/ost_geom_tests +Running 25 test cases... + +*** No errors detected +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[ 27%] Built target ost_geom_tests_run +make -f modules/seq/base/tests/CMakeFiles/ost_seq_tests.dir/build.make modules/seq/base/tests/CMakeFiles/ost_seq_tests.dir/depend +make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/seq/base/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/tests/CMakeFiles/ost_seq_tests.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/conop/tests/CMakeFiles/ost_conop_tests.dir/build.make modules/conop/tests/CMakeFiles/ost_conop_tests.dir/build +make -f modules/seq/base/tests/CMakeFiles/ost_seq_tests.dir/build.make modules/seq/base/tests/CMakeFiles/ost_seq_tests.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 34%] Building CXX object modules/conop/tests/CMakeFiles/ost_conop_tests.dir/test_amino_acids.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/conop/tests/CMakeFiles/ost_conop_tests.dir/test_amino_acids.cc.o -MF CMakeFiles/ost_conop_tests.dir/test_amino_acids.cc.o.d -o CMakeFiles/ost_conop_tests.dir/test_amino_acids.cc.o -c /build/openstructure-2.3.1/modules/conop/tests/test_amino_acids.cc +[ 27%] Building CXX object modules/seq/base/tests/CMakeFiles/ost_seq_tests.dir/test_sequence.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/seq/base/tests/CMakeFiles/ost_seq_tests.dir/test_sequence.cc.o -MF CMakeFiles/ost_seq_tests.dir/test_sequence.cc.o.d -o CMakeFiles/ost_seq_tests.dir/test_sequence.cc.o -c /build/openstructure-2.3.1/modules/seq/base/tests/test_sequence.cc +[ 28%] Building CXX object modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_ics.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_ics.cc.o -MF CMakeFiles/ost_mol_tests.dir/test_ics.cc.o.d -o CMakeFiles/ost_mol_tests.dir/test_ics.cc.o -c /build/openstructure-2.3.1/modules/mol/base/tests/test_ics.cc +[ 28%] Building CXX object modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_index.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_index.cc.o -MF CMakeFiles/ost_img_tests.dir/test_index.cc.o.d -o CMakeFiles/ost_img_tests.dir/test_index.cc.o -c /build/openstructure-2.3.1/modules/img/base/tests/test_index.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/modules/mol/base/tests/test_query.cc:24: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, + from /build/openstructure-2.3.1/modules/img/alg/tests/test_fill.cc:29: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, - from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, - from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, - from /usr/include/boost/test/detail/global_typedef.hpp:15, - from /usr/include/boost/test/tree/observer.hpp:17, - from /usr/include/boost/test/unit_test_log.hpp:18, - from /usr/include/boost/test/tools/old/impl.hpp:19, - from /usr/include/boost/test/test_tools.hpp:46, - from /usr/include/boost/test/unit_test.hpp:18, - from /build/openstructure-2.3.1/modules/mol/base/tests/test_query.cc:23: + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/ostream:38, + from /usr/include/c++/12/iostream:39, + from /build/openstructure-2.3.1/modules/img/alg/tests/test_fill.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -28992,6 +28950,8 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 28%] Building CXX object modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_query.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_query.cc.o -MF CMakeFiles/ost_mol_tests.dir/test_query.cc.o.d -o CMakeFiles/ost_mol_tests.dir/test_query.cc.o -c /build/openstructure-2.3.1/modules/mol/base/tests/test_query.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -29018,14 +28978,17 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 28%] Building CXX object modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_surface.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_surface.cc.o -MF CMakeFiles/ost_mol_tests.dir/test_surface.cc.o.d -o CMakeFiles/ost_mol_tests.dir/test_surface.cc.o -c /build/openstructure-2.3.1/modules/mol/base/tests/test_surface.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, - from /build/openstructure-2.3.1/modules/seq/base/tests/test_aligned_column.cc:22: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, + from /build/openstructure-2.3.1/modules/img/base/tests/test_image_state_visitor.cc:27: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -29038,7 +29001,8 @@ from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, - from /build/openstructure-2.3.1/modules/seq/base/tests/test_aligned_column.cc:20: + from /build/openstructure-2.3.1/modules/img/base/tests/test_image_state_visitor.hh:29, + from /build/openstructure-2.3.1/modules/img/base/tests/test_image_state_visitor.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -29048,20 +29012,36 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, - from /build/openstructure-2.3.1/modules/seq/base/tests/test_aligned_column.cc:28: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 32 | : public std::iterator{ - | ^~~~~~~~ +[ 28%] Building CXX object modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_residue.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_residue.cc.o -MF CMakeFiles/ost_mol_tests.dir/test_residue.cc.o.d -o CMakeFiles/ost_mol_tests.dir/test_residue.cc.o -c /build/openstructure-2.3.1/modules/mol/base/tests/test_residue.cc +[ 28%] Building CXX object modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_histogram.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_histogram.cc.o -MF CMakeFiles/ost_img_alg_tests.dir/test_histogram.cc.o.d -o CMakeFiles/ost_img_alg_tests.dir/test_histogram.cc.o -c /build/openstructure-2.3.1/modules/img/alg/tests/test_histogram.cc +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, + from /build/openstructure-2.3.1/modules/img/alg/tests/test_filter.cc:28: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/12/string:45, + from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, + from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, + from /usr/include/boost/test/detail/global_typedef.hpp:15, + from /usr/include/boost/test/tree/observer.hpp:17, + from /usr/include/boost/test/unit_test_log.hpp:18, + from /usr/include/boost/test/tools/old/impl.hpp:19, + from /usr/include/boost/test/test_tools.hpp:46, + from /usr/include/boost/test/unit_test.hpp:18, + from /build/openstructure-2.3.1/modules/img/alg/tests/test_filter.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_region.hh:27, - from /build/openstructure-2.3.1/modules/seq/base/tests/test_aligned_column.cc:29: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_column_iterator.hh:29:43: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 29 | class AlignedColumnIterator : public std::iterator struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -29098,20 +29078,24 @@ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, - from /build/openstructure-2.3.1/modules/img/base/tests/test_image.cc:29: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, + from /build/openstructure-2.3.1/modules/seq/base/tests/test_sequence.cc:22: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/ostream:38, - from /usr/include/c++/12/iostream:39, - from /build/openstructure-2.3.1/modules/img/base/tests/test_image.cc:25: + from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, + from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, + from /usr/include/boost/test/detail/global_typedef.hpp:15, + from /usr/include/boost/test/tree/observer.hpp:17, + from /usr/include/boost/test/unit_test_log.hpp:18, + from /usr/include/boost/test/tools/old/impl.hpp:19, + from /usr/include/boost/test/test_tools.hpp:46, + from /usr/include/boost/test/unit_test.hpp:18, + from /build/openstructure-2.3.1/modules/seq/base/tests/test_sequence.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -29121,25 +29105,27 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 34%] Building CXX object modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_view.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_view.cc.o -MF CMakeFiles/ost_mol_tests.dir/test_view.cc.o.d -o CMakeFiles/ost_mol_tests.dir/test_view.cc.o -c /build/openstructure-2.3.1/modules/mol/base/tests/test_view.cc +[ 29%] Building CXX object modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_mirror.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_mirror.cc.o -MF CMakeFiles/ost_img_alg_tests.dir/test_mirror.cc.o.d -o CMakeFiles/ost_img_alg_tests.dir/test_mirror.cc.o -c /build/openstructure-2.3.1/modules/img/alg/tests/test_mirror.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, - from /build/openstructure-2.3.1/modules/img/alg/tests/test_fill.cc:29: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/openstructure-2.3.1/modules/mol/base/tests/test_query.cc:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/ostream:38, - from /usr/include/c++/12/iostream:39, - from /build/openstructure-2.3.1/modules/img/alg/tests/test_fill.cc:25: + from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, + from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, + from /usr/include/boost/test/detail/global_typedef.hpp:15, + from /usr/include/boost/test/tree/observer.hpp:17, + from /usr/include/boost/test/unit_test_log.hpp:18, + from /usr/include/boost/test/tools/old/impl.hpp:19, + from /usr/include/boost/test/test_tools.hpp:46, + from /usr/include/boost/test/unit_test.hpp:18, + from /build/openstructure-2.3.1/modules/mol/base/tests/test_query.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -29149,13 +29135,23 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 29%] Building CXX object modules/base/tests/CMakeFiles/ost_base_tests.dir/test_pod_vector.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/tests/CMakeFiles/ost_base_tests.dir/test_pod_vector.cc.o -MF CMakeFiles/ost_base_tests.dir/test_pod_vector.cc.o.d -o CMakeFiles/ost_base_tests.dir/test_pod_vector.cc.o -c /build/openstructure-2.3.1/modules/base/tests/test_pod_vector.cc +[ 29%] Building CXX object modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_point.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_point.cc.o -MF CMakeFiles/ost_img_tests.dir/test_point.cc.o.d -o CMakeFiles/ost_img_tests.dir/test_point.cc.o -c /build/openstructure-2.3.1/modules/img/base/tests/test_point.cc +[ 29%] Building CXX object modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_sampling.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_sampling.cc.o -MF CMakeFiles/ost_img_tests.dir/test_sampling.cc.o.d -o CMakeFiles/ost_img_tests.dir/test_sampling.cc.o -c /build/openstructure-2.3.1/modules/img/base/tests/test_sampling.cc +[ 29%] Building CXX object modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_domains.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_domains.cc.o -MF CMakeFiles/ost_img_tests.dir/test_domains.cc.o.d -o CMakeFiles/ost_img_tests.dir/test_domains.cc.o -c /build/openstructure-2.3.1/modules/img/base/tests/test_domains.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/extent.hh:34, - from /build/openstructure-2.3.1/modules/img/base/tests/test_image_state.cc:32: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/histogram.hh:30, + from /build/openstructure-2.3.1/modules/img/alg/tests/test_histogram.cc:29: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -29163,9 +29159,9 @@ from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/istream:38, - from /usr/include/c++/12/sstream:38, - from /build/openstructure-2.3.1/modules/img/base/tests/test_image_state.cc:25: + from /usr/include/c++/12/ostream:38, + from /usr/include/c++/12/iostream:39, + from /build/openstructure-2.3.1/modules/img/alg/tests/test_histogram.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -29182,7 +29178,7 @@ from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, - from /build/openstructure-2.3.1/modules/seq/base/tests/test_alignment.cc:23: + from /build/openstructure-2.3.1/modules/mol/base/tests/test_residue.cc:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -29195,7 +29191,7 @@ from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, - from /build/openstructure-2.3.1/modules/seq/base/tests/test_alignment.cc:20: + from /build/openstructure-2.3.1/modules/mol/base/tests/test_residue.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -29205,23 +29201,6 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, - from /build/openstructure-2.3.1/modules/seq/base/tests/test_alignment.cc:24: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 32 | : public std::iterator{ - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_region.hh:27, - from /build/openstructure-2.3.1/modules/seq/base/tests/test_alignment.cc:25: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_column_iterator.hh:29:43: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 29 | class AlignedColumnIterator : public std::iterator struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, - from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, - from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, - from /usr/include/boost/test/detail/global_typedef.hpp:15, - from /usr/include/boost/test/tree/observer.hpp:17, - from /usr/include/boost/test/unit_test_log.hpp:18, - from /usr/include/boost/test/tools/old/impl.hpp:19, - from /usr/include/boost/test/test_tools.hpp:46, - from /usr/include/boost/test/unit_test.hpp:18, - from /build/openstructure-2.3.1/modules/mol/base/tests/test_residue.cc:23: + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/ostream:38, + from /usr/include/c++/12/iostream:39, + from /build/openstructure-2.3.1/modules/img/alg/tests/test_mirror.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -29285,11 +29258,9 @@ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, - from /build/openstructure-2.3.1/modules/seq/base/tests/test_aligned_region.cc:22: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, + from /build/openstructure-2.3.1/modules/img/base/tests/test_point.cc:27: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -29302,7 +29273,8 @@ from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, - from /build/openstructure-2.3.1/modules/seq/base/tests/test_aligned_region.cc:20: + from /build/openstructure-2.3.1/modules/img/base/tests/test_point.hh:29, + from /build/openstructure-2.3.1/modules/img/base/tests/test_point.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -29312,33 +29284,38 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, - from /build/openstructure-2.3.1/modules/seq/base/tests/test_aligned_region.cc:28: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 32 | : public std::iterator{ - | ^~~~~~~~ +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_spatial_domain.hh:31, + from /build/openstructure-2.3.1/modules/img/base/tests/test_domains.cc:31: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/12/string:45, + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/istream:38, + from /usr/include/c++/12/sstream:38, + from /build/openstructure-2.3.1/modules/img/base/tests/test_domains.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_region.hh:27, - from /build/openstructure-2.3.1/modules/seq/base/tests/test_aligned_region.cc:29: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_column_iterator.hh:29:43: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 29 | class AlignedColumnIterator : public std::iterator struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 34%] Building CXX object modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_histogram.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_histogram.cc.o -MF CMakeFiles/ost_img_alg_tests.dir/test_histogram.cc.o.d -o CMakeFiles/ost_img_alg_tests.dir/test_histogram.cc.o -c /build/openstructure-2.3.1/modules/img/alg/tests/test_histogram.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/amino_acids.hh:26, - from /build/openstructure-2.3.1/modules/conop/tests/test_amino_acids.cc:27: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, + from /build/openstructure-2.3.1/modules/img/base/tests/test_sampling.cc:27: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -29351,7 +29328,8 @@ from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, - from /build/openstructure-2.3.1/modules/conop/tests/test_amino_acids.cc:25: + from /build/openstructure-2.3.1/modules/img/base/tests/test_sampling.hh:29, + from /build/openstructure-2.3.1/modules/img/base/tests/test_sampling.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -29361,14 +29339,51 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/amino_acids.hh:61:42: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 61 | class AminoAcidSetIterator : public std::iterator struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/12/string:45, + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/ostream:38, + from /usr/include/c++/12/iostream:39, + from /build/openstructure-2.3.1/modules/img/alg/tests/test_negate.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 34%] Building CXX object modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_transfer_connectivity.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_transfer_connectivity.cc.o -MF CMakeFiles/ost_mol_tests.dir/test_transfer_connectivity.cc.o.d -o CMakeFiles/ost_mol_tests.dir/test_transfer_connectivity.cc.o -c /build/openstructure-2.3.1/modules/mol/base/tests/test_transfer_connectivity.cc +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 29%] Linking CXX executable ../../../tests/ost_base_tests +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_base_tests.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro CMakeFiles/ost_base_tests.dir/test_generic_property.cc.o CMakeFiles/ost_base_tests.dir/test_string_ref.cc.o CMakeFiles/ost_base_tests.dir/test_pod_vector.cc.o CMakeFiles/ost_base_tests.dir/tests.cc.o -o ../../../tests/ost_base_tests -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib /usr/lib/x86_64-linux-gnu/libboost_unit_test_framework.so ../../../stage/lib/libost_mol.so.2.3.1 ../../../stage/lib/libost_info.so.2.3.1 ../../../stage/lib/libost_base.so.2.3.1 ../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -29399,6 +29414,64 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[ 29%] Built target ost_base_tests +[ 29%] Building CXX object modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/tests.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/tests.cc.o -MF CMakeFiles/ost_mol_tests.dir/tests.cc.o.d -o CMakeFiles/ost_mol_tests.dir/tests.cc.o -c /build/openstructure-2.3.1/modules/mol/base/tests/tests.cc +[ 30%] Building CXX object modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_value_holder.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_value_holder.cc.o -MF CMakeFiles/ost_img_tests.dir/test_value_holder.cc.o.d -o CMakeFiles/ost_img_tests.dir/test_value_holder.cc.o -c /build/openstructure-2.3.1/modules/img/base/tests/test_value_holder.cc +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, + from /build/openstructure-2.3.1/modules/img/alg/tests/test_power_spectrum.cc:29: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/12/string:45, + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/ostream:38, + from /usr/include/c++/12/iostream:39, + from /build/openstructure-2.3.1/modules/img/alg/tests/test_power_spectrum.cc:25: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/builder.hh:26, + from /build/openstructure-2.3.1/modules/mol/base/tests/test_transfer_connectivity.cc:23: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/bits/specfun.h:45, + from /usr/include/c++/12/cmath:1935, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/builder.hh:23: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ In file included from /usr/include/c++/12/string:53: In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:866:17, @@ -29488,97 +29561,10 @@ /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/histogram.hh:30, - from /build/openstructure-2.3.1/modules/img/alg/tests/test_histogram.cc:29: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/12/string:45, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/ostream:38, - from /usr/include/c++/12/iostream:39, - from /build/openstructure-2.3.1/modules/img/alg/tests/test_histogram.cc:25: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -[ 34%] Building CXX object modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_image_state_visitor.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_image_state_visitor.cc.o -MF CMakeFiles/ost_img_tests.dir/test_image_state_visitor.cc.o.d -o CMakeFiles/ost_img_tests.dir/test_image_state_visitor.cc.o -c /build/openstructure-2.3.1/modules/img/base/tests/test_image_state_visitor.cc -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, - from /build/openstructure-2.3.1/modules/img/alg/tests/test_filter.cc:28: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/12/string:45, - from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, - from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, - from /usr/include/boost/test/detail/global_typedef.hpp:15, - from /usr/include/boost/test/tree/observer.hpp:17, - from /usr/include/boost/test/unit_test_log.hpp:18, - from /usr/include/boost/test/tools/old/impl.hpp:19, - from /usr/include/boost/test/test_tools.hpp:46, - from /usr/include/boost/test/unit_test.hpp:18, - from /build/openstructure-2.3.1/modules/img/alg/tests/test_filter.cc:25: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -[ 34%] Building CXX object modules/seq/base/tests/CMakeFiles/ost_seq_tests.dir/test_profile.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/seq/base/tests/CMakeFiles/ost_seq_tests.dir/test_profile.cc.o -MF CMakeFiles/ost_seq_tests.dir/test_profile.cc.o.d -o CMakeFiles/ost_seq_tests.dir/test_profile.cc.o -c /build/openstructure-2.3.1/modules/seq/base/tests/test_profile.cc -[ 35%] Building CXX object modules/seq/base/tests/CMakeFiles/ost_seq_tests.dir/tests.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/seq/base/tests/CMakeFiles/ost_seq_tests.dir/tests.cc.o -MF CMakeFiles/ost_seq_tests.dir/tests.cc.o.d -o CMakeFiles/ost_seq_tests.dir/tests.cc.o -c /build/openstructure-2.3.1/modules/seq/base/tests/tests.cc -[ 36%] Building CXX object modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_mirror.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_mirror.cc.o -MF CMakeFiles/ost_img_alg_tests.dir/test_mirror.cc.o.d -o CMakeFiles/ost_img_alg_tests.dir/test_mirror.cc.o -c /build/openstructure-2.3.1/modules/img/alg/tests/test_mirror.cc -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/builder.hh:26, - from /build/openstructure-2.3.1/modules/mol/base/tests/test_transfer_connectivity.cc:23: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/specfun.h:45, - from /usr/include/c++/12/cmath:1935, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/builder.hh:23: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ +[ 30%] Building CXX object modules/seq/base/tests/CMakeFiles/ost_seq_tests.dir/test_aligned_column.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/seq/base/tests/CMakeFiles/ost_seq_tests.dir/test_aligned_column.cc.o -MF CMakeFiles/ost_seq_tests.dir/test_aligned_column.cc.o.d -o CMakeFiles/ost_seq_tests.dir/test_aligned_column.cc.o -c /build/openstructure-2.3.1/modules/seq/base/tests/test_aligned_column.cc +[ 30%] Building CXX object modules/img/base/tests/CMakeFiles/ost_img_tests.dir/tests.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/base/tests/CMakeFiles/ost_img_tests.dir/tests.cc.o -MF CMakeFiles/ost_img_tests.dir/tests.cc.o.d -o CMakeFiles/ost_img_tests.dir/tests.cc.o -c /build/openstructure-2.3.1/modules/img/base/tests/tests.cc In file included from /usr/include/c++/12/string:53: In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:866:17, @@ -29689,8 +29675,6 @@ /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ -[ 36%] Building CXX object modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_view_op.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_view_op.cc.o -MF CMakeFiles/ost_mol_tests.dir/test_view_op.cc.o.d -o CMakeFiles/ost_mol_tests.dir/test_view_op.cc.o -c /build/openstructure-2.3.1/modules/mol/base/tests/test_view_op.cc In static member function 'static constexpr void std::char_traits::assign(char_type&, const char_type&)', inlined from 'static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:421:23, inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:867:18, @@ -29840,87 +29824,17 @@ /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ -[ 36%] Building CXX object modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_negate.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_negate.cc.o -MF CMakeFiles/ost_img_alg_tests.dir/test_negate.cc.o.d -o CMakeFiles/ost_img_alg_tests.dir/test_negate.cc.o -c /build/openstructure-2.3.1/modules/img/alg/tests/test_negate.cc -[ 36%] Building CXX object modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_index.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_index.cc.o -MF CMakeFiles/ost_img_tests.dir/test_index.cc.o.d -o CMakeFiles/ost_img_tests.dir/test_index.cc.o -c /build/openstructure-2.3.1/modules/img/base/tests/test_index.cc -[ 36%] Building CXX object modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_point.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_point.cc.o -MF CMakeFiles/ost_img_tests.dir/test_point.cc.o.d -o CMakeFiles/ost_img_tests.dir/test_point.cc.o -c /build/openstructure-2.3.1/modules/img/base/tests/test_point.cc -[ 36%] Building CXX object modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_sampling.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_sampling.cc.o -MF CMakeFiles/ost_img_tests.dir/test_sampling.cc.o.d -o CMakeFiles/ost_img_tests.dir/test_sampling.cc.o -c /build/openstructure-2.3.1/modules/img/base/tests/test_sampling.cc -[ 36%] Building CXX object modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/tests.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/tests.cc.o -MF CMakeFiles/ost_mol_tests.dir/tests.cc.o.d -o CMakeFiles/ost_mol_tests.dir/tests.cc.o -c /build/openstructure-2.3.1/modules/mol/base/tests/tests.cc -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, - from /build/openstructure-2.3.1/modules/img/base/tests/test_image_state_visitor.cc:27: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/12/string:45, - from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, - from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, - from /usr/include/boost/test/detail/global_typedef.hpp:15, - from /usr/include/boost/test/tree/observer.hpp:17, - from /usr/include/boost/test/unit_test_log.hpp:18, - from /usr/include/boost/test/tools/old/impl.hpp:19, - from /usr/include/boost/test/test_tools.hpp:46, - from /usr/include/boost/test/unit_test.hpp:18, - from /build/openstructure-2.3.1/modules/img/base/tests/test_image_state_visitor.hh:29, - from /build/openstructure-2.3.1/modules/img/base/tests/test_image_state_visitor.cc:25: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -[ 36%] Building CXX object modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_power_spectrum.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_power_spectrum.cc.o -MF CMakeFiles/ost_img_alg_tests.dir/test_power_spectrum.cc.o.d -o CMakeFiles/ost_img_alg_tests.dir/test_power_spectrum.cc.o -c /build/openstructure-2.3.1/modules/img/alg/tests/test_power_spectrum.cc -[ 36%] Building CXX object modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_shift.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_shift.cc.o -MF CMakeFiles/ost_img_alg_tests.dir/test_shift.cc.o.d -o CMakeFiles/ost_img_alg_tests.dir/test_shift.cc.o -c /build/openstructure-2.3.1/modules/img/alg/tests/test_shift.cc -[ 36%] Building CXX object modules/conop/tests/CMakeFiles/ost_conop_tests.dir/test_heuristic_conop.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/conop/tests/CMakeFiles/ost_conop_tests.dir/test_heuristic_conop.cc.o -MF CMakeFiles/ost_conop_tests.dir/test_heuristic_conop.cc.o.d -o CMakeFiles/ost_conop_tests.dir/test_heuristic_conop.cc.o -c /build/openstructure-2.3.1/modules/conop/tests/test_heuristic_conop.cc -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, - from /build/openstructure-2.3.1/modules/img/alg/tests/test_mirror.cc:29: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/12/string:45, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/ostream:38, - from /usr/include/c++/12/iostream:39, - from /build/openstructure-2.3.1/modules/img/alg/tests/test_mirror.cc:25: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ +[ 30%] Building CXX object modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_stat.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_stat.cc.o -MF CMakeFiles/ost_img_alg_tests.dir/test_stat.cc.o.d -o CMakeFiles/ost_img_alg_tests.dir/test_stat.cc.o -c /build/openstructure-2.3.1/modules/img/alg/tests/test_stat.cc +[ 30%] Building CXX object modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_transform.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_transform.cc.o -MF CMakeFiles/ost_img_alg_tests.dir/test_transform.cc.o.d -o CMakeFiles/ost_img_alg_tests.dir/test_transform.cc.o -c /build/openstructure-2.3.1/modules/img/alg/tests/test_transform.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, - from /build/openstructure-2.3.1/modules/img/alg/tests/test_negate.cc:29: + from /build/openstructure-2.3.1/modules/img/alg/tests/test_shift.cc:29: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -29930,7 +29844,7 @@ from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, - from /build/openstructure-2.3.1/modules/img/alg/tests/test_negate.cc:25: + from /build/openstructure-2.3.1/modules/img/alg/tests/test_shift.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -29940,12 +29854,8 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 36%] Building CXX object modules/conop/tests/CMakeFiles/ost_conop_tests.dir/tests.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/conop/tests/CMakeFiles/ost_conop_tests.dir/tests.cc.o -MF CMakeFiles/ost_conop_tests.dir/tests.cc.o.d -o CMakeFiles/ost_conop_tests.dir/tests.cc.o -c /build/openstructure-2.3.1/modules/conop/tests/tests.cc -[ 36%] Building CXX object modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_domains.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_domains.cc.o -MF CMakeFiles/ost_img_tests.dir/test_domains.cc.o.d -o CMakeFiles/ost_img_tests.dir/test_domains.cc.o -c /build/openstructure-2.3.1/modules/img/base/tests/test_domains.cc -[ 36%] Building CXX object modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_size.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_size.cc.o -MF CMakeFiles/ost_img_tests.dir/test_size.cc.o.d -o CMakeFiles/ost_img_tests.dir/test_size.cc.o -c /build/openstructure-2.3.1/modules/img/base/tests/test_size.cc +[ 30%] Building CXX object modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_normalizer.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_normalizer.cc.o -MF CMakeFiles/ost_img_alg_tests.dir/test_normalizer.cc.o.d -o CMakeFiles/ost_img_alg_tests.dir/test_normalizer.cc.o -c /build/openstructure-2.3.1/modules/img/alg/tests/test_normalizer.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -29976,13 +29886,23 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 30%] Building CXX object modules/seq/base/tests/CMakeFiles/ost_seq_tests.dir/test_aligned_region.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/seq/base/tests/CMakeFiles/ost_seq_tests.dir/test_aligned_region.cc.o -MF CMakeFiles/ost_seq_tests.dir/test_aligned_region.cc.o.d -o CMakeFiles/ost_seq_tests.dir/test_aligned_region.cc.o -c /build/openstructure-2.3.1/modules/seq/base/tests/test_aligned_region.cc +[ 30%] Building CXX object modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/tests.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/tests.cc.o -MF CMakeFiles/ost_img_alg_tests.dir/tests.cc.o.d -o CMakeFiles/ost_img_alg_tests.dir/tests.cc.o -c /build/openstructure-2.3.1/modules/img/alg/tests/tests.cc +[ 30%] Building CXX object modules/seq/base/tests/CMakeFiles/ost_seq_tests.dir/test_alignment.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/seq/base/tests/CMakeFiles/ost_seq_tests.dir/test_alignment.cc.o -MF CMakeFiles/ost_seq_tests.dir/test_alignment.cc.o.d -o CMakeFiles/ost_seq_tests.dir/test_alignment.cc.o -c /build/openstructure-2.3.1/modules/seq/base/tests/test_alignment.cc +[ 30%] Building CXX object modules/seq/base/tests/CMakeFiles/ost_seq_tests.dir/test_profile.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/seq/base/tests/CMakeFiles/ost_seq_tests.dir/test_profile.cc.o -MF CMakeFiles/ost_seq_tests.dir/test_profile.cc.o.d -o CMakeFiles/ost_seq_tests.dir/test_profile.cc.o -c /build/openstructure-2.3.1/modules/seq/base/tests/test_profile.cc +[ 31%] Building CXX object modules/seq/base/tests/CMakeFiles/ost_seq_tests.dir/tests.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/seq/base/tests/CMakeFiles/ost_seq_tests.dir/tests.cc.o -MF CMakeFiles/ost_seq_tests.dir/tests.cc.o.d -o CMakeFiles/ost_seq_tests.dir/tests.cc.o -c /build/openstructure-2.3.1/modules/seq/base/tests/tests.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, - from /build/openstructure-2.3.1/modules/img/alg/tests/test_power_spectrum.cc:29: + from /build/openstructure-2.3.1/modules/img/alg/tests/test_transform.cc:29: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -29992,7 +29912,7 @@ from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, - from /build/openstructure-2.3.1/modules/img/alg/tests/test_power_spectrum.cc:25: + from /build/openstructure-2.3.1/modules/img/alg/tests/test_transform.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -30002,12 +29922,17 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +make -f modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/build.make modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/depend +make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/seq/alg/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/DependInfo.cmake --color= In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/openstructure-2.3.1/modules/img/base/tests/test_point.cc:27: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, + from /build/openstructure-2.3.1/modules/seq/base/tests/test_aligned_column.cc:22: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -30020,8 +29945,7 @@ from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, - from /build/openstructure-2.3.1/modules/img/base/tests/test_point.hh:29, - from /build/openstructure-2.3.1/modules/img/base/tests/test_point.cc:25: + from /build/openstructure-2.3.1/modules/seq/base/tests/test_aligned_column.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -30031,76 +29955,105 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 36%] Building CXX object modules/conop/tests/CMakeFiles/ost_conop_tests.dir/test_rule_based_conop.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/conop/tests/CMakeFiles/ost_conop_tests.dir/test_rule_based_conop.cc.o -MF CMakeFiles/ost_conop_tests.dir/test_rule_based_conop.cc.o.d -o CMakeFiles/ost_conop_tests.dir/test_rule_based_conop.cc.o -c /build/openstructure-2.3.1/modules/conop/tests/test_rule_based_conop.cc -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, - from /build/openstructure-2.3.1/modules/img/base/tests/test_sampling.cc:27: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/12/string:45, - from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, - from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, - from /usr/include/boost/test/detail/global_typedef.hpp:15, - from /usr/include/boost/test/tree/observer.hpp:17, - from /usr/include/boost/test/unit_test_log.hpp:18, - from /usr/include/boost/test/tools/old/impl.hpp:19, - from /usr/include/boost/test/test_tools.hpp:46, - from /usr/include/boost/test/unit_test.hpp:18, - from /build/openstructure-2.3.1/modules/img/base/tests/test_sampling.hh:29, - from /build/openstructure-2.3.1/modules/img/base/tests/test_sampling.cc:25: +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +make -f modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/build.make modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/build +make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +make[4]: Nothing to be done for 'modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/build'. +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[ 32%] Built target ost_seq_alg +make -f modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/build.make modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/depend +make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/seq/base/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +make -f modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/build.make modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/build +make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +make[4]: Nothing to be done for 'modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/build'. +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, + from /build/openstructure-2.3.1/modules/seq/base/tests/test_aligned_column.cc:28: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 32 | : public std::iterator{ + | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ +[ 34%] Built target _ost_seq +make -f modules/conop/src/CMakeFiles/ost_conop.dir/build.make modules/conop/src/CMakeFiles/ost_conop.dir/depend +make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/conop/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src/CMakeFiles/ost_conop.dir/DependInfo.cmake --color= +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_region.hh:27, + from /build/openstructure-2.3.1/modules/seq/base/tests/test_aligned_column.cc:29: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_column_iterator.hh:29:43: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 29 | class AlignedColumnIterator : public std::iterator struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -30109,8 +30062,8 @@ from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, - from /build/openstructure-2.3.1/modules/conop/tests/test_heuristic_conop.cc:20: + from /usr/include/c++/12/iostream:39, + from /build/openstructure-2.3.1/modules/img/alg/tests/test_stat.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -30120,17 +30073,13 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 37%] Building CXX object modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_value_holder.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_value_holder.cc.o -MF CMakeFiles/ost_img_tests.dir/test_value_holder.cc.o.d -o CMakeFiles/ost_img_tests.dir/test_value_holder.cc.o -c /build/openstructure-2.3.1/modules/img/base/tests/test_value_holder.cc -[ 37%] Building CXX object modules/img/base/tests/CMakeFiles/ost_img_tests.dir/tests.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/base/tests/CMakeFiles/ost_img_tests.dir/tests.cc.o -MF CMakeFiles/ost_img_tests.dir/tests.cc.o.d -o CMakeFiles/ost_img_tests.dir/tests.cc.o -c /build/openstructure-2.3.1/modules/img/base/tests/tests.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, - from /build/openstructure-2.3.1/modules/img/alg/tests/test_shift.cc:29: + from /build/openstructure-2.3.1/modules/img/alg/tests/test_normalizer.cc:35: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -30140,7 +30089,7 @@ from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, - from /build/openstructure-2.3.1/modules/img/alg/tests/test_shift.cc:25: + from /build/openstructure-2.3.1/modules/img/alg/tests/test_normalizer.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -30150,46 +30099,96 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 35%] Linking CXX executable ../../../../tests/ost_img_tests +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_img_tests.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro CMakeFiles/ost_img_tests.dir/test_data.cc.o CMakeFiles/ost_img_tests.dir/test_extent.cc.o CMakeFiles/ost_img_tests.dir/test_image.cc.o CMakeFiles/ost_img_tests.dir/test_image_state.cc.o CMakeFiles/ost_img_tests.dir/test_image_state_visitor.cc.o CMakeFiles/ost_img_tests.dir/test_index.cc.o CMakeFiles/ost_img_tests.dir/test_point.cc.o CMakeFiles/ost_img_tests.dir/test_sampling.cc.o CMakeFiles/ost_img_tests.dir/test_domains.cc.o CMakeFiles/ost_img_tests.dir/test_size.cc.o CMakeFiles/ost_img_tests.dir/test_value_holder.cc.o CMakeFiles/ost_img_tests.dir/tests.cc.o -o ../../../../tests/ost_img_tests -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib /usr/lib/x86_64-linux-gnu/libboost_unit_test_framework.so ../../../../stage/lib/libost_img_alg.so.2.3.1 ../../../../stage/lib/libost_img.so.2.3.1 ../../../../stage/lib/libost_info.so.2.3.1 ../../../../stage/lib/libost_base.so.2.3.1 ../../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libfftw3f_threads.so make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/gfx/src/CMakeFiles/ost_gfx.dir/build.make modules/gfx/src/CMakeFiles/ost_gfx.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'modules/gfx/src/CMakeFiles/ost_gfx.dir/build'. make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 43%] Built target ost_gfx +[ 41%] Built target ost_gfx make -f modules/conop/pymod/CMakeFiles/_ost_conop.dir/build.make modules/conop/pymod/CMakeFiles/_ost_conop.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/conop/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/pymod/CMakeFiles/_ost_conop.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/conop/pymod/CMakeFiles/_ost_conop.dir/build.make modules/conop/pymod/CMakeFiles/_ost_conop.dir/build +[ 41%] Built target ost_img_tests +make -f modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/build.make modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/depend +make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/alg/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'modules/conop/pymod/CMakeFiles/_ost_conop.dir/build'. make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 43%] Building CXX object modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_normalizer.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_normalizer.cc.o -MF CMakeFiles/ost_img_alg_tests.dir/test_normalizer.cc.o.d -o CMakeFiles/ost_img_alg_tests.dir/test_normalizer.cc.o -c /build/openstructure-2.3.1/modules/img/alg/tests/test_normalizer.cc -[ 45%] Built target _ost_conop +[ 42%] Built target _ost_conop +make -f modules/img/base/tests/CMakeFiles/ost_img_tests_run.dir/build.make modules/img/base/tests/CMakeFiles/ost_img_tests_run.dir/depend +make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/img/base/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/tests/CMakeFiles/ost_img_tests_run.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +make -f modules/img/base/tests/CMakeFiles/ost_img_tests_run.dir/build.make modules/img/base/tests/CMakeFiles/ost_img_tests_run.dir/build +make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[ 42%] running checks for module img +cd /build/openstructure-2.3.1/modules/img/base/tests && env OST_ROOT=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage /build/openstructure-2.3.1/obj-x86_64-linux-gnu/tests/ost_img_tests +Running 44 test cases... + +*** No errors detected +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[ 42%] Built target ost_img_tests_run +[ 42%] Building CXX object modules/conop/tests/CMakeFiles/ost_conop_tests.dir/test_heuristic_conop.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/conop/tests/CMakeFiles/ost_conop_tests.dir/test_heuristic_conop.cc.o -MF CMakeFiles/ost_conop_tests.dir/test_heuristic_conop.cc.o.d -o CMakeFiles/ost_conop_tests.dir/test_heuristic_conop.cc.o -c /build/openstructure-2.3.1/modules/conop/tests/test_heuristic_conop.cc +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +make -f modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/build.make modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/build +make -f modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/build.make modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/depend +make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +make[4]: Nothing to be done for 'modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/build'. +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/gfx/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/DependInfo.cmake --color= +[ 45%] Built target ost_mol_alg make -f modules/io/src/CMakeFiles/ost_io.dir/build.make modules/io/src/CMakeFiles/ost_io.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/io/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src/CMakeFiles/ost_io.dir/DependInfo.cmake --color= -[ 45%] Linking CXX executable ../../../../tests/ost_seq_tests -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_seq_tests.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro CMakeFiles/ost_seq_tests.dir/test_sequence.cc.o CMakeFiles/ost_seq_tests.dir/test_aligned_column.cc.o CMakeFiles/ost_seq_tests.dir/test_aligned_region.cc.o CMakeFiles/ost_seq_tests.dir/test_alignment.cc.o CMakeFiles/ost_seq_tests.dir/test_profile.cc.o CMakeFiles/ost_seq_tests.dir/tests.cc.o -o ../../../../tests/ost_seq_tests -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib /usr/lib/x86_64-linux-gnu/libboost_unit_test_framework.so ../../../../stage/lib/libost_seq.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so ../../../../stage/lib/libost_mol.so.2.3.1 ../../../../stage/lib/libost_info.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../../stage/lib/libost_base.so.2.3.1 ../../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +make -f modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/build.make modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/build +make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +make[4]: Nothing to be done for 'modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/build'. +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[ 47%] Built target _ost_gfx +make -f modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/build.make modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/depend +make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/alg/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +make -f modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/build.make modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/build +make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +make[4]: Nothing to be done for 'modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/build'. +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[ 48%] Built target _ost_mol_alg +[ 48%] Building CXX object modules/conop/tests/CMakeFiles/ost_conop_tests.dir/tests.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/conop/tests/CMakeFiles/ost_conop_tests.dir/tests.cc.o -MF CMakeFiles/ost_conop_tests.dir/tests.cc.o.d -o CMakeFiles/ost_conop_tests.dir/tests.cc.o -c /build/openstructure-2.3.1/modules/conop/tests/tests.cc +[ 48%] Building CXX object modules/conop/tests/CMakeFiles/ost_conop_tests.dir/test_rule_based_conop.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/conop/tests/CMakeFiles/ost_conop_tests.dir/test_rule_based_conop.cc.o -MF CMakeFiles/ost_conop_tests.dir/test_rule_based_conop.cc.o.d -o CMakeFiles/ost_conop_tests.dir/test_rule_based_conop.cc.o -c /build/openstructure-2.3.1/modules/conop/tests/test_rule_based_conop.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_spatial_domain.hh:31, - from /build/openstructure-2.3.1/modules/img/base/tests/test_domains.cc:31: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, + from /build/openstructure-2.3.1/modules/seq/base/tests/test_aligned_region.cc:22: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/istream:38, - from /usr/include/c++/12/sstream:38, - from /build/openstructure-2.3.1/modules/img/base/tests/test_domains.cc:25: + from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, + from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, + from /usr/include/boost/test/detail/global_typedef.hpp:15, + from /usr/include/boost/test/tree/observer.hpp:17, + from /usr/include/boost/test/unit_test_log.hpp:18, + from /usr/include/boost/test/tools/old/impl.hpp:19, + from /usr/include/boost/test/test_tools.hpp:46, + from /usr/include/boost/test/unit_test.hpp:18, + from /build/openstructure-2.3.1/modules/seq/base/tests/test_aligned_region.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -30199,14 +30198,45 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -make -f modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/build.make modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/depend +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +make -f modules/io/src/CMakeFiles/ost_io.dir/build.make modules/io/src/CMakeFiles/ost_io.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/alg/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/DependInfo.cmake --color= +make[4]: Nothing to be done for 'modules/io/src/CMakeFiles/ost_io.dir/build'. +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[ 52%] Built target ost_io +make -f modules/gui/src/CMakeFiles/ost_gui.dir/build.make modules/gui/src/CMakeFiles/ost_gui.dir/depend +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, + from /build/openstructure-2.3.1/modules/seq/base/tests/test_aligned_region.cc:28: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 32 | : public std::iterator{ + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/gui/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/CMakeFiles/ost_gui.dir/DependInfo.cmake --color= +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_region.hh:27, + from /build/openstructure-2.3.1/modules/seq/base/tests/test_aligned_region.cc:29: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_column_iterator.hh:29:43: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 29 | class AlignedColumnIterator : public std::iterator struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -30219,7 +30249,7 @@ from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, - from /build/openstructure-2.3.1/modules/conop/tests/helper.cc:2: + from /build/openstructure-2.3.1/modules/seq/base/tests/test_alignment.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -30229,35 +30259,69 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +make[4]: Nothing to be done for 'modules/io/pymod/CMakeFiles/_ost_io.dir/build'. make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/build.make modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/build +[ 53%] Built target _ost_io +make -f modules/gfx/tests/CMakeFiles/ost_gfx_tests.dir/build.make modules/gfx/tests/CMakeFiles/ost_gfx_tests.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/build'. +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/gfx/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/tests/CMakeFiles/ost_gfx_tests.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 46%] Built target _ost_mol_alg -make -f modules/base/tests/CMakeFiles/ost_base_tests_run.dir/build.make modules/base/tests/CMakeFiles/ost_base_tests_run.dir/depend +make -f modules/gfx/tests/CMakeFiles/ost_gfx_tests.dir/build.make modules/gfx/tests/CMakeFiles/ost_gfx_tests.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/base/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/tests/CMakeFiles/ost_base_tests_run.dir/DependInfo.cmake --color= +[ 53%] Building CXX object modules/gfx/tests/CMakeFiles/ost_gfx_tests.dir/tests.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/gfx/tests/CMakeFiles/ost_gfx_tests.dir/tests.cc.o -MF CMakeFiles/ost_gfx_tests.dir/tests.cc.o.d -o CMakeFiles/ost_gfx_tests.dir/tests.cc.o -c /build/openstructure-2.3.1/modules/gfx/tests/tests.cc +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, + from /build/openstructure-2.3.1/modules/seq/base/tests/test_alignment.cc:24: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 32 | : public std::iterator{ + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_region.hh:27, + from /build/openstructure-2.3.1/modules/seq/base/tests/test_alignment.cc:25: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_column_iterator.hh:29:43: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 29 | class AlignedColumnIterator : public std::iterator struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -30270,7 +30334,7 @@ from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, - from /build/openstructure-2.3.1/modules/conop/tests/test_rule_based_conop.cc:22: + from /build/openstructure-2.3.1/modules/conop/tests/test_amino_acids.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -30280,55 +30344,20 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'modules/io/src/CMakeFiles/ost_io.dir/build'. -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 50%] Built target ost_io -make -f modules/seq/base/tests/CMakeFiles/ost_seq_tests_run.dir/build.make modules/seq/base/tests/CMakeFiles/ost_seq_tests_run.dir/depend -make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/seq/base/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/tests/CMakeFiles/ost_seq_tests_run.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/seq/base/tests/CMakeFiles/ost_seq_tests_run.dir/build.make modules/seq/base/tests/CMakeFiles/ost_seq_tests_run.dir/build -make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 50%] running checks for module seq -cd /build/openstructure-2.3.1/modules/seq/base/tests && env OST_ROOT=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage /build/openstructure-2.3.1/obj-x86_64-linux-gnu/tests/ost_seq_tests -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/build.make modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/build -make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/build'. -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 52%] Built target _ost_gfx -make -f modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests.dir/build.make modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests.dir/depend -Running 5 test cases... - -*** No errors detected -make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/seq/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests.dir/build.make modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests.dir/build -[ 52%] Built target ost_base_tests_run -make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/gui/src/CMakeFiles/ost_gui.dir/build.make modules/gui/src/CMakeFiles/ost_gui.dir/depend -make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/gui/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/CMakeFiles/ost_gui.dir/DependInfo.cmake --color= -[ 52%] Building CXX object modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests.dir/test_distance_analysis.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests.dir/test_distance_analysis.cc.o -MF CMakeFiles/ost_seq_alg_tests.dir/test_distance_analysis.cc.o.d -o CMakeFiles/ost_seq_alg_tests.dir/test_distance_analysis.cc.o -c /build/openstructure-2.3.1/modules/seq/alg/tests/test_distance_analysis.cc -Running 32 test cases... - -*** No errors detected -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 52%] Built target ost_seq_tests_run -make -f modules/io/pymod/CMakeFiles/_ost_io.dir/build.make modules/io/pymod/CMakeFiles/_ost_io.dir/depend -make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/io/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/pymod/CMakeFiles/_ost_io.dir/DependInfo.cmake --color= +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/amino_acids.hh:61:42: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 61 | class AminoAcidSetIterator : public std::iterator struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -30337,8 +30366,8 @@ from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, - from /usr/include/c++/12/iostream:39, - from /build/openstructure-2.3.1/modules/img/alg/tests/test_stat.cc:25: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, + from /build/openstructure-2.3.1/modules/conop/tests/test_heuristic_conop.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -30348,37 +30377,27 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/io/pymod/CMakeFiles/_ost_io.dir/build.make modules/io/pymod/CMakeFiles/_ost_io.dir/build -make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'modules/io/pymod/CMakeFiles/_ost_io.dir/build'. -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 53%] Built target _ost_io -make -f modules/gfx/tests/CMakeFiles/ost_gfx_tests.dir/build.make modules/gfx/tests/CMakeFiles/ost_gfx_tests.dir/depend -make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/gfx/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/tests/CMakeFiles/ost_gfx_tests.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/gfx/tests/CMakeFiles/ost_gfx_tests.dir/build.make modules/gfx/tests/CMakeFiles/ost_gfx_tests.dir/build -make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 53%] Building CXX object modules/gfx/tests/CMakeFiles/ost_gfx_tests.dir/tests.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/gfx/tests/CMakeFiles/ost_gfx_tests.dir/tests.cc.o -MF CMakeFiles/ost_gfx_tests.dir/tests.cc.o.d -o CMakeFiles/ost_gfx_tests.dir/tests.cc.o -c /build/openstructure-2.3.1/modules/gfx/tests/tests.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, - from /build/openstructure-2.3.1/modules/img/alg/tests/test_transform.cc:29: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, + from /build/openstructure-2.3.1/modules/conop/tests/test_rule_based_conop.cc:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/ostream:38, - from /usr/include/c++/12/iostream:39, - from /build/openstructure-2.3.1/modules/img/alg/tests/test_transform.cc:25: + from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, + from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, + from /usr/include/boost/test/detail/global_typedef.hpp:15, + from /usr/include/boost/test/tree/observer.hpp:17, + from /usr/include/boost/test/unit_test_log.hpp:18, + from /usr/include/boost/test/tools/old/impl.hpp:19, + from /usr/include/boost/test/test_tools.hpp:46, + from /usr/include/boost/test/unit_test.hpp:18, + from /build/openstructure-2.3.1/modules/conop/tests/test_rule_based_conop.cc:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -30388,25 +30407,21 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 54%] Building CXX object modules/gfx/tests/CMakeFiles/ost_gfx_tests.dir/test_gfx_node.cc.o +[ 89%] Building CXX object modules/gfx/tests/CMakeFiles/ost_gfx_tests.dir/test_gfx_node.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/gfx/tests/CMakeFiles/ost_gfx_tests.dir/test_gfx_node.cc.o -MF CMakeFiles/ost_gfx_tests.dir/test_gfx_node.cc.o.d -o CMakeFiles/ost_gfx_tests.dir/test_gfx_node.cc.o -c /build/openstructure-2.3.1/modules/gfx/tests/test_gfx_node.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, - from /build/openstructure-2.3.1/modules/img/alg/tests/test_normalizer.cc:35: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/svd_superpose.hh:27, + from /build/openstructure-2.3.1/modules/mol/alg/tests/test_superposition.cc:23: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/12/string:45, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/ostream:38, - from /usr/include/c++/12/iostream:39, - from /build/openstructure-2.3.1/modules/img/alg/tests/test_normalizer.cc:25: +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/bits/specfun.h:45, + from /usr/include/c++/12/cmath:1935, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/svd_superpose.hh:26: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -30416,40 +30431,33 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 54%] Building CXX object modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/tests.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/tests.cc.o -MF CMakeFiles/ost_img_alg_tests.dir/tests.cc.o.d -o CMakeFiles/ost_img_alg_tests.dir/tests.cc.o -c /build/openstructure-2.3.1/modules/img/alg/tests/tests.cc -[ 54%] Building CXX object modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests.dir/test_merge_pairwise_alignments.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests.dir/test_merge_pairwise_alignments.cc.o -MF CMakeFiles/ost_seq_alg_tests.dir/test_merge_pairwise_alignments.cc.o.d -o CMakeFiles/ost_seq_alg_tests.dir/test_merge_pairwise_alignments.cc.o -c /build/openstructure-2.3.1/modules/seq/alg/tests/test_merge_pairwise_alignments.cc -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/gui/src/CMakeFiles/ost_gui.dir/build.make modules/gui/src/CMakeFiles/ost_gui.dir/build -[ 54%] Building CXX object modules/gfx/tests/CMakeFiles/ost_gfx_tests.dir/test_color.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/gfx/tests/CMakeFiles/ost_gfx_tests.dir/test_color.cc.o -MF CMakeFiles/ost_gfx_tests.dir/test_color.cc.o.d -o CMakeFiles/ost_gfx_tests.dir/test_color.cc.o -c /build/openstructure-2.3.1/modules/gfx/tests/test_color.cc -make -f modules/io/tests/CMakeFiles/ost_io_tests.dir/build.make modules/io/tests/CMakeFiles/ost_io_tests.dir/depend -make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'modules/gui/src/CMakeFiles/ost_gui.dir/build'. -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/io/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/tests/CMakeFiles/ost_io_tests.dir/DependInfo.cmake --color= -[ 87%] Built target ost_gui -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/io/tests/CMakeFiles/ost_io_tests.dir/build.make modules/io/tests/CMakeFiles/ost_io_tests.dir/build -make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 89%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/test_clustal.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/io/tests/CMakeFiles/ost_io_tests.dir/test_clustal.cc.o -MF CMakeFiles/ost_io_tests.dir/test_clustal.cc.o.d -o CMakeFiles/ost_io_tests.dir/test_clustal.cc.o -c /build/openstructure-2.3.1/modules/io/tests/test_clustal.cc -[ 90%] Building CXX object modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests.dir/test_sequence_identity.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests.dir/test_sequence_identity.cc.o -MF CMakeFiles/ost_seq_alg_tests.dir/test_sequence_identity.cc.o.d -o CMakeFiles/ost_seq_alg_tests.dir/test_sequence_identity.cc.o -c /build/openstructure-2.3.1/modules/seq/alg/tests/test_sequence_identity.cc -[ 90%] Building CXX object modules/gfx/tests/CMakeFiles/ost_gfx_tests.dir/test_map_octree.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/gfx/tests/CMakeFiles/ost_gfx_tests.dir/test_map_octree.cc.o -MF CMakeFiles/ost_gfx_tests.dir/test_map_octree.cc.o.d -o CMakeFiles/ost_gfx_tests.dir/test_map_octree.cc.o -c /build/openstructure-2.3.1/modules/gfx/tests/test_map_octree.cc -[ 90%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/test_io_pdb.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/io/tests/CMakeFiles/ost_io_tests.dir/test_io_pdb.cc.o -MF CMakeFiles/ost_io_tests.dir/test_io_pdb.cc.o.d -o CMakeFiles/ost_io_tests.dir/test_io_pdb.cc.o -c /build/openstructure-2.3.1/modules/io/tests/test_io_pdb.cc -[ 90%] Linking CXX executable ../../../../tests/ost_img_tests -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_img_tests.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro CMakeFiles/ost_img_tests.dir/test_data.cc.o CMakeFiles/ost_img_tests.dir/test_extent.cc.o CMakeFiles/ost_img_tests.dir/test_image.cc.o CMakeFiles/ost_img_tests.dir/test_image_state.cc.o CMakeFiles/ost_img_tests.dir/test_image_state_visitor.cc.o CMakeFiles/ost_img_tests.dir/test_index.cc.o CMakeFiles/ost_img_tests.dir/test_point.cc.o CMakeFiles/ost_img_tests.dir/test_sampling.cc.o CMakeFiles/ost_img_tests.dir/test_domains.cc.o CMakeFiles/ost_img_tests.dir/test_size.cc.o CMakeFiles/ost_img_tests.dir/test_value_holder.cc.o CMakeFiles/ost_img_tests.dir/tests.cc.o -o ../../../../tests/ost_img_tests -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib /usr/lib/x86_64-linux-gnu/libboost_unit_test_framework.so ../../../../stage/lib/libost_img_alg.so.2.3.1 ../../../../stage/lib/libost_img.so.2.3.1 ../../../../stage/lib/libost_info.so.2.3.1 ../../../../stage/lib/libost_base.so.2.3.1 ../../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libfftw3f_threads.so +[ 89%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/test_io_crd.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/io/tests/CMakeFiles/ost_io_tests.dir/test_io_crd.cc.o -MF CMakeFiles/ost_io_tests.dir/test_io_crd.cc.o.d -o CMakeFiles/ost_io_tests.dir/test_io_crd.cc.o -c /build/openstructure-2.3.1/modules/io/tests/test_io_crd.cc +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/clustal_io_handler.hh:25, + from /build/openstructure-2.3.1/modules/io/tests/test_clustal.cc:27: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 32 | : public std::iterator{ + | ^~~~~~~~ +In file included from /usr/include/c++/12/string:45, + from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, + from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, + from /usr/include/boost/test/detail/global_typedef.hpp:15, + from /usr/include/boost/test/tree/observer.hpp:17, + from /usr/include/boost/test/unit_test_log.hpp:18, + from /usr/include/boost/test/tools/old/impl.hpp:19, + from /usr/include/boost/test/test_tools.hpp:46, + from /usr/include/boost/test/unit_test.hpp:18, + from /build/openstructure-2.3.1/modules/io/tests/test_clustal.cc:25: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/xcs_editor.hh:26, - from /build/openstructure-2.3.1/modules/seq/alg/tests/test_distance_analysis.cc:28: + from /build/openstructure-2.3.1/modules/conop/tests/helper.cc:3: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -30462,7 +30470,7 @@ from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, - from /build/openstructure-2.3.1/modules/seq/alg/tests/test_distance_analysis.cc:25: + from /build/openstructure-2.3.1/modules/conop/tests/helper.cc:2: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -30472,24 +30480,6 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/clip_alignment.hh:27, - from /build/openstructure-2.3.1/modules/seq/alg/tests/test_distance_analysis.cc:30: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 32 | : public std::iterator{ - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -make -f modules/mol/alg/tests/CMakeFiles/ost_mol_alg_tests.dir/build.make modules/mol/alg/tests/CMakeFiles/ost_mol_alg_tests.dir/depend -make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/tests/CMakeFiles/ost_mol_alg_tests.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/mol/alg/tests/CMakeFiles/ost_mol_alg_tests.dir/build.make modules/mol/alg/tests/CMakeFiles/ost_mol_alg_tests.dir/build -make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 90%] Building CXX object modules/mol/alg/tests/CMakeFiles/ost_mol_alg_tests.dir/test_superposition.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/alg/tests/CMakeFiles/ost_mol_alg_tests.dir/test_superposition.cc.o -MF CMakeFiles/ost_mol_alg_tests.dir/test_superposition.cc.o.d -o CMakeFiles/ost_mol_alg_tests.dir/test_superposition.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/tests/test_superposition.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -30497,9 +30487,28 @@ from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/merge_pairwise_alignments.hh:22, - from /build/openstructure-2.3.1/modules/seq/alg/tests/test_merge_pairwise_alignments.cc:26: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 89%] Building CXX object modules/mol/alg/tests/CMakeFiles/ost_mol_alg_tests.dir/tests.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/alg/tests/CMakeFiles/ost_mol_alg_tests.dir/tests.cc.o -MF CMakeFiles/ost_mol_alg_tests.dir/tests.cc.o.d -o CMakeFiles/ost_mol_alg_tests.dir/tests.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/tests/tests.cc +[ 89%] Linking CXX executable ../../../../tests/ost_img_alg_tests +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_img_alg_tests.dir/link.txt --verbose=1 +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec_mat_predicates.hh:28, + from /build/openstructure-2.3.1/modules/io/tests/test_io_pdb.cc:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -30512,7 +30521,7 @@ from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, - from /build/openstructure-2.3.1/modules/seq/alg/tests/test_merge_pairwise_alignments.cc:24: + from /build/openstructure-2.3.1/modules/io/tests/test_io_pdb.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -30522,52 +30531,102 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 32 | : public std::iterator{ - | ^~~~~~~~ +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro CMakeFiles/ost_img_alg_tests.dir/test_clear.cc.o CMakeFiles/ost_img_alg_tests.dir/test_conj.cc.o CMakeFiles/ost_img_alg_tests.dir/test_convolute.cc.o CMakeFiles/ost_img_alg_tests.dir/test_discrete_shrink.cc.o CMakeFiles/ost_img_alg_tests.dir/test_fft.cc.o CMakeFiles/ost_img_alg_tests.dir/test_fill.cc.o CMakeFiles/ost_img_alg_tests.dir/test_filter.cc.o CMakeFiles/ost_img_alg_tests.dir/test_histogram.cc.o CMakeFiles/ost_img_alg_tests.dir/test_mirror.cc.o CMakeFiles/ost_img_alg_tests.dir/test_negate.cc.o CMakeFiles/ost_img_alg_tests.dir/test_power_spectrum.cc.o CMakeFiles/ost_img_alg_tests.dir/test_shift.cc.o CMakeFiles/ost_img_alg_tests.dir/test_stat.cc.o CMakeFiles/ost_img_alg_tests.dir/test_transform.cc.o CMakeFiles/ost_img_alg_tests.dir/test_normalizer.cc.o CMakeFiles/ost_img_alg_tests.dir/tests.cc.o -o ../../../../tests/ost_img_alg_tests -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib /usr/lib/x86_64-linux-gnu/libboost_unit_test_framework.so ../../../../stage/lib/libost_img_alg.so.2.3.1 /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libfftw3f_threads.so ../../../../stage/lib/libost_img.so.2.3.1 ../../../../stage/lib/libost_info.so.2.3.1 ../../../../stage/lib/libost_base.so.2.3.1 ../../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, + from /build/openstructure-2.3.1/modules/gfx/tests/test_gfx_node.cc:24: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/vector:60, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_node.hh:26, + from /build/openstructure-2.3.1/modules/gfx/tests/test_gfx_node.cc:23: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 90%] Built target ost_img_tests +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[ 89%] Built target ost_img_alg_tests make -f modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/build.make modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/mm/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/build.make modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/build +make -f modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests.dir/build.make modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests.dir/depend +make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/seq/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/build'. make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 91%] Built target ost_mol_mm +[ 90%] Built target ost_mol_mm make -f modules/gui/pymod/CMakeFiles/_ost_gui.dir/build.make modules/gui/pymod/CMakeFiles/_ost_gui.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/gui/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod/CMakeFiles/_ost_gui.dir/DependInfo.cmake --color= -[ 91%] Building CXX object modules/mol/alg/tests/CMakeFiles/ost_mol_alg_tests.dir/tests.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/alg/tests/CMakeFiles/ost_mol_alg_tests.dir/tests.cc.o -MF CMakeFiles/ost_mol_alg_tests.dir/tests.cc.o.d -o CMakeFiles/ost_mol_alg_tests.dir/tests.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/tests/tests.cc +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +make -f modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests.dir/build.make modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests.dir/build +make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[ 90%] Building CXX object modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests.dir/test_distance_analysis.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests.dir/test_distance_analysis.cc.o -MF CMakeFiles/ost_seq_alg_tests.dir/test_distance_analysis.cc.o.d -o CMakeFiles/ost_seq_alg_tests.dir/test_distance_analysis.cc.o -c /build/openstructure-2.3.1/modules/seq/alg/tests/test_distance_analysis.cc make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/gui/pymod/CMakeFiles/_ost_gui.dir/build.make modules/gui/pymod/CMakeFiles/_ost_gui.dir/build +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, + from /build/openstructure-2.3.1/modules/io/tests/test_io_pdb.cc:33: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 32 | : public std::iterator{ + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'modules/gui/pymod/CMakeFiles/_ost_gui.dir/build'. make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 93%] Built target _ost_gui -make -f modules/img/base/tests/CMakeFiles/ost_img_tests_run.dir/build.make modules/img/base/tests/CMakeFiles/ost_img_tests_run.dir/depend +[ 92%] Built target _ost_gui +make -f modules/img/alg/tests/CMakeFiles/ost_img_alg_tests_run.dir/build.make modules/img/alg/tests/CMakeFiles/ost_img_alg_tests_run.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/img/base/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/tests/CMakeFiles/ost_img_tests_run.dir/DependInfo.cmake --color= +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/img/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/tests/CMakeFiles/ost_img_alg_tests_run.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +make -f modules/img/alg/tests/CMakeFiles/ost_img_alg_tests_run.dir/build.make modules/img/alg/tests/CMakeFiles/ost_img_alg_tests_run.dir/build +make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[ 92%] running checks for module img_alg +cd /build/openstructure-2.3.1/modules/img/alg/tests && env OST_ROOT=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage /build/openstructure-2.3.1/obj-x86_64-linux-gnu/tests/ost_img_alg_tests +Running 25 test cases... + +*** No errors detected +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[ 92%] Built target ost_img_alg_tests_run +[ 92%] Building CXX object modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests.dir/test_merge_pairwise_alignments.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests.dir/test_merge_pairwise_alignments.cc.o -MF CMakeFiles/ost_seq_alg_tests.dir/test_merge_pairwise_alignments.cc.o.d -o CMakeFiles/ost_seq_alg_tests.dir/test_merge_pairwise_alignments.cc.o -c /build/openstructure-2.3.1/modules/seq/alg/tests/test_merge_pairwise_alignments.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, - from /build/openstructure-2.3.1/modules/gfx/tests/test_gfx_node.cc:24: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, + from /build/openstructure-2.3.1/modules/io/tests/test_io_crd.cc:23: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/vector:60, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_node.hh:26, - from /build/openstructure-2.3.1/modules/gfx/tests/test_gfx_node.cc:23: +In file included from /usr/include/c++/12/string:45, + from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, + from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, + from /usr/include/boost/test/detail/global_typedef.hpp:15, + from /usr/include/boost/test/tree/observer.hpp:17, + from /usr/include/boost/test/unit_test_log.hpp:18, + from /usr/include/boost/test/tools/old/impl.hpp:19, + from /usr/include/boost/test/test_tools.hpp:46, + from /usr/include/boost/test/unit_test.hpp:18, + from /build/openstructure-2.3.1/modules/io/tests/test_io_crd.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -30577,33 +30636,43 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 92%] Building CXX object modules/mol/alg/tests/CMakeFiles/ost_mol_alg_tests.dir/test_consistency_checks.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/alg/tests/CMakeFiles/ost_mol_alg_tests.dir/test_consistency_checks.cc.o -MF CMakeFiles/ost_mol_alg_tests.dir/test_consistency_checks.cc.o.d -o CMakeFiles/ost_mol_alg_tests.dir/test_consistency_checks.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/tests/test_consistency_checks.cc +[ 92%] Building CXX object modules/mol/alg/tests/CMakeFiles/ost_mol_alg_tests.dir/test_partial_sec_struct_assignment.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/alg/tests/CMakeFiles/ost_mol_alg_tests.dir/test_partial_sec_struct_assignment.cc.o -MF CMakeFiles/ost_mol_alg_tests.dir/test_partial_sec_struct_assignment.cc.o.d -o CMakeFiles/ost_mol_alg_tests.dir/test_partial_sec_struct_assignment.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/tests/test_partial_sec_struct_assignment.cc +[ 92%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/test_io_dcd.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/io/tests/CMakeFiles/ost_io_tests.dir/test_io_dcd.cc.o -MF CMakeFiles/ost_io_tests.dir/test_io_dcd.cc.o.d -o CMakeFiles/ost_io_tests.dir/test_io_dcd.cc.o -c /build/openstructure-2.3.1/modules/io/tests/test_io_dcd.cc +[ 92%] Linking CXX executable ../../../../tests/ost_seq_tests +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_seq_tests.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro CMakeFiles/ost_seq_tests.dir/test_sequence.cc.o CMakeFiles/ost_seq_tests.dir/test_aligned_column.cc.o CMakeFiles/ost_seq_tests.dir/test_aligned_region.cc.o CMakeFiles/ost_seq_tests.dir/test_alignment.cc.o CMakeFiles/ost_seq_tests.dir/test_profile.cc.o CMakeFiles/ost_seq_tests.dir/tests.cc.o -o ../../../../tests/ost_seq_tests -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib /usr/lib/x86_64-linux-gnu/libboost_unit_test_framework.so ../../../../stage/lib/libost_seq.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so ../../../../stage/lib/libost_mol.so.2.3.1 ../../../../stage/lib/libost_info.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../../stage/lib/libost_base.so.2.3.1 ../../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/img/base/tests/CMakeFiles/ost_img_tests_run.dir/build.make modules/img/base/tests/CMakeFiles/ost_img_tests_run.dir/build -make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 93%] running checks for module img -cd /build/openstructure-2.3.1/modules/img/base/tests && env OST_ROOT=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage /build/openstructure-2.3.1/obj-x86_64-linux-gnu/tests/ost_img_tests -Running 44 test cases... - -*** No errors detected -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 93%] Built target ost_img_tests_run +[ 92%] Built target ost_seq_tests make -f modules/mol/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/build.make modules/mol/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/mm/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/mol/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/build.make modules/mol/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[ 92%] Building CXX object modules/mol/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/test_interaction.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/test_interaction.cc.o -MF CMakeFiles/ost_mol_mm_tests.dir/test_interaction.cc.o.d -o CMakeFiles/ost_mol_mm_tests.dir/test_interaction.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/tests/test_interaction.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color.hh:31, - from /build/openstructure-2.3.1/modules/gfx/tests/test_color.cc:24: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/xcs_editor.hh:26, + from /build/openstructure-2.3.1/modules/seq/alg/tests/test_distance_analysis.cc:28: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/12/iterator:61, - from /usr/include/boost/operators.hpp:98, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color.hh:28: +In file included from /usr/include/c++/12/string:45, + from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, + from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, + from /usr/include/boost/test/detail/global_typedef.hpp:15, + from /usr/include/boost/test/tree/observer.hpp:17, + from /usr/include/boost/test/unit_test_log.hpp:18, + from /usr/include/boost/test/tools/old/impl.hpp:19, + from /usr/include/boost/test/test_tools.hpp:46, + from /usr/include/boost/test/unit_test.hpp:18, + from /build/openstructure-2.3.1/modules/seq/alg/tests/test_distance_analysis.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -30613,30 +30682,18 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 93%] Building CXX object modules/mol/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/test_interaction.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/test_interaction.cc.o -MF CMakeFiles/ost_mol_mm_tests.dir/test_interaction.cc.o.d -o CMakeFiles/ost_mol_mm_tests.dir/test_interaction.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/tests/test_interaction.cc -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/svd_superpose.hh:27, - from /build/openstructure-2.3.1/modules/mol/alg/tests/test_superposition.cc:23: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/bits/specfun.h:45, - from /usr/include/c++/12/cmath:1935, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/svd_superpose.hh:26: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/clip_alignment.hh:27, + from /build/openstructure-2.3.1/modules/seq/alg/tests/test_distance_analysis.cc:30: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 32 | : public std::iterator{ + | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 92%] Building CXX object modules/mol/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/test_block.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/test_block.cc.o -MF CMakeFiles/ost_mol_mm_tests.dir/test_block.cc.o.d -o CMakeFiles/ost_mol_mm_tests.dir/test_block.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/tests/test_block.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -30645,8 +30702,8 @@ from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/sequence_identity.hh:26, - from /build/openstructure-2.3.1/modules/seq/alg/tests/test_sequence_identity.cc:25: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/merge_pairwise_alignments.hh:22, + from /build/openstructure-2.3.1/modules/seq/alg/tests/test_merge_pairwise_alignments.cc:26: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -30659,7 +30716,7 @@ from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, - from /build/openstructure-2.3.1/modules/seq/alg/tests/test_sequence_identity.cc:24: + from /build/openstructure-2.3.1/modules/seq/alg/tests/test_merge_pairwise_alignments.cc:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -30677,13 +30734,34 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/clustal_io_handler.hh:25, - from /build/openstructure-2.3.1/modules/io/tests/test_clustal.cc:27: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 32 | : public std::iterator{ - | ^~~~~~~~ +[ 92%] Building CXX object modules/mol/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/test_block_modifiers.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/test_block_modifiers.cc.o -MF CMakeFiles/ost_mol_mm_tests.dir/test_block_modifiers.cc.o.d -o CMakeFiles/ost_mol_mm_tests.dir/test_block_modifiers.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/tests/test_block_modifiers.cc +make -f modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/build.make modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/depend +make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/mm/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +make -f modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/build.make modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/build +make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +make[4]: Nothing to be done for 'modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/build'. +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[ 93%] Built target _ost_mol_mm +make -f modules/seq/base/tests/CMakeFiles/ost_seq_tests_run.dir/build.make modules/seq/base/tests/CMakeFiles/ost_seq_tests_run.dir/depend +make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/seq/base/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/tests/CMakeFiles/ost_seq_tests_run.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +make -f modules/seq/base/tests/CMakeFiles/ost_seq_tests_run.dir/build.make modules/seq/base/tests/CMakeFiles/ost_seq_tests_run.dir/build +make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, + from /build/openstructure-2.3.1/modules/mol/alg/tests/test_consistency_checks.cc:26: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, @@ -30693,24 +30771,7 @@ from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, - from /build/openstructure-2.3.1/modules/io/tests/test_clustal.cc:25: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -[ 93%] Linking CXX executable ../../../../tests/ost_img_alg_tests -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_img_alg_tests.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro CMakeFiles/ost_img_alg_tests.dir/test_clear.cc.o CMakeFiles/ost_img_alg_tests.dir/test_conj.cc.o CMakeFiles/ost_img_alg_tests.dir/test_convolute.cc.o CMakeFiles/ost_img_alg_tests.dir/test_discrete_shrink.cc.o CMakeFiles/ost_img_alg_tests.dir/test_fft.cc.o CMakeFiles/ost_img_alg_tests.dir/test_fill.cc.o CMakeFiles/ost_img_alg_tests.dir/test_filter.cc.o CMakeFiles/ost_img_alg_tests.dir/test_histogram.cc.o CMakeFiles/ost_img_alg_tests.dir/test_mirror.cc.o CMakeFiles/ost_img_alg_tests.dir/test_negate.cc.o CMakeFiles/ost_img_alg_tests.dir/test_power_spectrum.cc.o CMakeFiles/ost_img_alg_tests.dir/test_shift.cc.o CMakeFiles/ost_img_alg_tests.dir/test_stat.cc.o CMakeFiles/ost_img_alg_tests.dir/test_transform.cc.o CMakeFiles/ost_img_alg_tests.dir/test_normalizer.cc.o CMakeFiles/ost_img_alg_tests.dir/tests.cc.o -o ../../../../tests/ost_img_alg_tests -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib /usr/lib/x86_64-linux-gnu/libboost_unit_test_framework.so ../../../../stage/lib/libost_img_alg.so.2.3.1 /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libfftw3f_threads.so ../../../../stage/lib/libost_img.so.2.3.1 ../../../../stage/lib/libost_info.so.2.3.1 ../../../../stage/lib/libost_base.so.2.3.1 ../../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ + from /build/openstructure-2.3.1/modules/mol/alg/tests/test_consistency_checks.cc:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -30720,25 +30781,62 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 93%] running checks for module seq +cd /build/openstructure-2.3.1/modules/seq/base/tests && env OST_ROOT=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage /build/openstructure-2.3.1/obj-x86_64-linux-gnu/tests/ost_seq_tests +Running 32 test cases... + +*** No errors detected +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[ 93%] Built target ost_seq_tests_run +make -f scripts/CMakeFiles/ost_scripts.dir/build.make scripts/CMakeFiles/ost_scripts.dir/depend +make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/scripts /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/scripts /build/openstructure-2.3.1/obj-x86_64-linux-gnu/scripts/CMakeFiles/ost_scripts.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +make -f scripts/CMakeFiles/ost_scripts.dir/build.make scripts/CMakeFiles/ost_scripts.dir/build +make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -E copy_if_different ost_config /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/openstructure/libexec/ost_config +[ 93%] Building CXX object modules/mol/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/test_topology.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/test_topology.cc.o -MF CMakeFiles/ost_mol_mm_tests.dir/test_topology.cc.o.d -o CMakeFiles/ost_mol_mm_tests.dir/test_topology.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/tests/test_topology.cc +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -E copy_if_different ost /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/bin/ost +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -E copy_if_different dng /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/bin/dng +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -E copy_if_different ost_startup.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/ost_startup.py +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/scripts/dng_startup.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/dng_startup.py +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[ 93%] Built target ost_scripts +make -f modules/seq/alg/tests/CMakeFiles/test_aaindex.py_run.dir/build.make modules/seq/alg/tests/CMakeFiles/test_aaindex.py_run.dir/depend +make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/seq/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/tests/CMakeFiles/test_aaindex.py_run.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +make -f modules/seq/alg/tests/CMakeFiles/test_aaindex.py_run.dir/build.make modules/seq/alg/tests/CMakeFiles/test_aaindex.py_run.dir/build +make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[ 93%] running checks test_aaindex.py +cd /build/openstructure-2.3.1/modules/seq/alg/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/seq/alg/tests/test_aaindex.py" +. +---------------------------------------------------------------------- +Ran 1 test in 0.615s + +OK +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[ 93%] Built target test_aaindex.py_run +make -f modules/base/tests/CMakeFiles/test_stutil.py_run.dir/build.make modules/base/tests/CMakeFiles/test_stutil.py_run.dir/depend +make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/base/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/tests/CMakeFiles/test_stutil.py_run.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +make -f modules/base/tests/CMakeFiles/test_stutil.py_run.dir/build.make modules/base/tests/CMakeFiles/test_stutil.py_run.dir/build +make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[ 93%] running checks test_stutil.py +cd /build/openstructure-2.3.1/modules/base/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/base/tests/test_stutil.py" In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_handle.hh:38, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/map_octree.hh:22, - from /build/openstructure-2.3.1/modules/gfx/tests/test_map_octree.cc:24: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/sec_struct.hh:25, + from /build/openstructure-2.3.1/modules/mol/alg/tests/test_partial_sec_struct_assignment.cc:21: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/memory:63, - from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, - from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, - from /usr/include/boost/shared_ptr.hpp:17, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_handle.hh:32: + from /usr/include/c++/12/vector:60, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/sec_struct.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -30748,25 +30846,29 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 93%] Building CXX object modules/mol/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/test_block.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/test_block.cc.o -MF CMakeFiles/ost_mol_mm_tests.dir/test_block.cc.o.d -o CMakeFiles/ost_mol_mm_tests.dir/test_block.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/tests/test_block.cc +...... +---------------------------------------------------------------------- +Ran 6 tests in 0.004s + +OK make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 93%] Built target ost_img_alg_tests -make -f modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/build.make modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/depend +[ 93%] Built target test_stutil.py_run +make -f modules/base/tests/CMakeFiles/test_table.py_run.dir/build.make modules/base/tests/CMakeFiles/test_table.py_run.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/mm/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/DependInfo.cmake --color= -[ 93%] Building CXX object modules/mol/alg/tests/CMakeFiles/ost_mol_alg_tests.dir/test_consistency_checks.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/alg/tests/CMakeFiles/ost_mol_alg_tests.dir/test_consistency_checks.cc.o -MF CMakeFiles/ost_mol_alg_tests.dir/test_consistency_checks.cc.o.d -o CMakeFiles/ost_mol_alg_tests.dir/test_consistency_checks.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/tests/test_consistency_checks.cc +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/base/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/tests/CMakeFiles/test_table.py_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/build.make modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/build +make -f modules/base/tests/CMakeFiles/test_table.py_run.dir/build.make modules/base/tests/CMakeFiles/test_table.py_run.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/build'. -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[ 93%] running checks test_table.py +cd /build/openstructure-2.3.1/modules/base/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/base/tests/test_table.py" In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec_mat_predicates.hh:28, - from /build/openstructure-2.3.1/modules/io/tests/test_io_pdb.cc:24: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/coord_frame.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/coord_source.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/coord_group.hh:29, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/dcd_io.hh:28, + from /build/openstructure-2.3.1/modules/io/tests/test_io_dcd.cc:23: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -30779,7 +30881,7 @@ from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, - from /build/openstructure-2.3.1/modules/io/tests/test_io_pdb.cc:20: + from /build/openstructure-2.3.1/modules/io/tests/test_io_dcd.cc:21: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -30789,54 +30891,28 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 94%] Built target _ost_mol_mm -make -f scripts/CMakeFiles/ost_scripts.dir/build.make scripts/CMakeFiles/ost_scripts.dir/depend -make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/scripts /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/scripts /build/openstructure-2.3.1/obj-x86_64-linux-gnu/scripts/CMakeFiles/ost_scripts.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f scripts/CMakeFiles/ost_scripts.dir/build.make scripts/CMakeFiles/ost_scripts.dir/build -make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -E copy_if_different ost_config /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/openstructure/libexec/ost_config -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -E copy_if_different ost /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/bin/ost -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -E copy_if_different dng /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/bin/dng -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -E copy_if_different ost_startup.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/ost_startup.py -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/scripts/dng_startup.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/dng_startup.py -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 94%] Built target ost_scripts -[ 94%] Building CXX object modules/mol/alg/tests/CMakeFiles/ost_mol_alg_tests.dir/test_partial_sec_struct_assignment.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/alg/tests/CMakeFiles/ost_mol_alg_tests.dir/test_partial_sec_struct_assignment.cc.o -MF CMakeFiles/ost_mol_alg_tests.dir/test_partial_sec_struct_assignment.cc.o.d -o CMakeFiles/ost_mol_alg_tests.dir/test_partial_sec_struct_assignment.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/tests/test_partial_sec_struct_assignment.cc -make -f modules/img/alg/tests/CMakeFiles/ost_img_alg_tests_run.dir/build.make modules/img/alg/tests/CMakeFiles/ost_img_alg_tests_run.dir/depend -make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/img/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/tests/CMakeFiles/ost_img_alg_tests_run.dir/DependInfo.cmake --color= In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, - from /build/openstructure-2.3.1/modules/io/tests/test_io_pdb.cc:33: + from /build/openstructure-2.3.1/modules/mol/alg/tests/test_partial_sec_struct_assignment.cc:25: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/img/alg/tests/CMakeFiles/ost_img_alg_tests_run.dir/build.make modules/img/alg/tests/CMakeFiles/ost_img_alg_tests_run.dir/build -make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 94%] running checks for module img_alg -cd /build/openstructure-2.3.1/modules/img/alg/tests && env OST_ROOT=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage /build/openstructure-2.3.1/obj-x86_64-linux-gnu/tests/ost_img_alg_tests -[ 94%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/test_io_crd.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/io/tests/CMakeFiles/ost_io_tests.dir/test_io_crd.cc.o -MF CMakeFiles/ost_io_tests.dir/test_io_crd.cc.o.d -o CMakeFiles/ost_io_tests.dir/test_io_crd.cc.o -c /build/openstructure-2.3.1/modules/io/tests/test_io_crd.cc -Running 25 test cases... - -*** No errors detected -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 94%] Built target ost_img_alg_tests_run -make -f modules/io/tests/CMakeFiles/test_io_pdb.py_run.dir/build.make modules/io/tests/CMakeFiles/test_io_pdb.py_run.dir/depend +[ 93%] Linking CXX executable ../../../../tests/ost_mol_tests +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_mol_tests.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro CMakeFiles/ost_mol_tests.dir/test_atom_groups.cc.o CMakeFiles/ost_mol_tests.dir/test_chain.cc.o CMakeFiles/ost_mol_tests.dir/test_conn.cc.o CMakeFiles/ost_mol_tests.dir/test_coord_group.cc.o CMakeFiles/ost_mol_tests.dir/test_builder.cc.o CMakeFiles/ost_mol_tests.dir/test_delete.cc.o CMakeFiles/ost_mol_tests.dir/test_entity.cc.o CMakeFiles/ost_mol_tests.dir/test_ics.cc.o CMakeFiles/ost_mol_tests.dir/test_query.cc.o CMakeFiles/ost_mol_tests.dir/test_surface.cc.o CMakeFiles/ost_mol_tests.dir/test_residue.cc.o CMakeFiles/ost_mol_tests.dir/test_view.cc.o CMakeFiles/ost_mol_tests.dir/test_transfer_connectivity.cc.o CMakeFiles/ost_mol_tests.dir/test_view_op.cc.o CMakeFiles/ost_mol_tests.dir/tests.cc.o -o ../../../../tests/ost_mol_tests -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib /usr/lib/x86_64-linux-gnu/libboost_unit_test_framework.so ../../../../stage/lib/libost_mol.so.2.3.1 ../../../../stage/lib/libost_info.so.2.3.1 ../../../../stage/lib/libost_base.so.2.3.1 ../../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 +.......................make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[ 93%] Built target ost_mol_tests +make -f modules/base/tests/CMakeFiles/test_log.py_run.dir/build.make modules/base/tests/CMakeFiles/test_log.py_run.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/io/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/tests/CMakeFiles/test_io_pdb.py_run.dir/DependInfo.cmake --color= +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/base/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/tests/CMakeFiles/test_log.py_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/io/tests/CMakeFiles/test_io_pdb.py_run.dir/build.make modules/io/tests/CMakeFiles/test_io_pdb.py_run.dir/build +make -f modules/base/tests/CMakeFiles/test_log.py_run.dir/build.make modules/base/tests/CMakeFiles/test_log.py_run.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 94%] running checks test_io_pdb.py -cd /build/openstructure-2.3.1/modules/io/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/io/tests/test_io_pdb.py" +[ 93%] running checks test_log.py +cd /build/openstructure-2.3.1/modules/base/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/base/tests/test_log.py" In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -30844,7 +30920,7 @@ from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/interaction.hh:34, - from /build/openstructure-2.3.1/modules/mol/mm/tests/test_block.cc:21: + from /build/openstructure-2.3.1/modules/mol/mm/tests/test_interaction.cc:21: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -30857,7 +30933,7 @@ from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, - from /build/openstructure-2.3.1/modules/mol/mm/tests/test_block.cc:20: + from /build/openstructure-2.3.1/modules/mol/mm/tests/test_interaction.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -30867,16 +30943,29 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 94%] Building CXX object modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests.dir/tests.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests.dir/tests.cc.o -MF CMakeFiles/ost_seq_alg_tests.dir/tests.cc.o.d -o CMakeFiles/ost_seq_alg_tests.dir/tests.cc.o -c /build/openstructure-2.3.1/modules/seq/alg/tests/tests.cc -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, +.... +---------------------------------------------------------------------- +Ran 4 tests in 0.014s + +OK +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[ 93%] Built target test_log.py_run +make -f modules/bindings/tests/CMakeFiles/test_msms.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_msms.py_run.dir/depend +make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/bindings/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/tests/CMakeFiles/test_msms.py_run.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +make -f modules/bindings/tests/CMakeFiles/test_msms.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_msms.py_run.dir/build +make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +...........[ 93%] running checks test_msms.py +cd /build/openstructure-2.3.1/modules/bindings/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/bindings/tests/test_msms.py" +....In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/interaction.hh:34, - from /build/openstructure-2.3.1/modules/mol/mm/tests/test_interaction.cc:21: + from /build/openstructure-2.3.1/modules/mol/mm/tests/test_block_modifiers.cc:21: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -30889,7 +30978,7 @@ from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, - from /build/openstructure-2.3.1/modules/mol/mm/tests/test_interaction.cc:20: + from /build/openstructure-2.3.1/modules/mol/mm/tests/test_block_modifiers.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -30899,14 +30988,34 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +/usr/lib/python3.11/unittest/case.py:579: ResourceWarning: unclosed file <_io.BufferedReader name='testfiles/enrichment-out.png'> + if method() is not None: +ResourceWarning: Enable tracemalloc to get the object allocation traceback +.[ 93%] Building CXX object modules/gfx/tests/CMakeFiles/ost_gfx_tests.dir/test_color.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/gfx/tests/CMakeFiles/ost_gfx_tests.dir/test_color.cc.o -MF CMakeFiles/ost_gfx_tests.dir/test_color.cc.o.d -o CMakeFiles/ost_gfx_tests.dir/test_color.cc.o -c /build/openstructure-2.3.1/modules/gfx/tests/test_color.cc +[ 93%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/test_io_sdf.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/io/tests/CMakeFiles/ost_io_tests.dir/test_io_sdf.cc.o -MF CMakeFiles/ost_io_tests.dir/test_io_sdf.cc.o.d -o CMakeFiles/ost_io_tests.dir/test_io_sdf.cc.o -c /build/openstructure-2.3.1/modules/io/tests/test_io_sdf.cc +Could not find msms executable: ignoring unit tests +[ 93%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/test_io_sequence_profile.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/io/tests/CMakeFiles/ost_io_tests.dir/test_io_sequence_profile.cc.o -MF CMakeFiles/ost_io_tests.dir/test_io_sequence_profile.cc.o.d -o CMakeFiles/ost_io_tests.dir/test_io_sequence_profile.cc.o -c /build/openstructure-2.3.1/modules/io/tests/test_io_sequence_profile.cc +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[ 93%] Built target test_msms.py_run +make -f modules/bindings/tests/CMakeFiles/test_clustalw.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_clustalw.py_run.dir/depend +make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/bindings/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/tests/CMakeFiles/test_clustalw.py_run.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +make -f modules/bindings/tests/CMakeFiles/test_clustalw.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_clustalw.py_run.dir/build +make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +.[ 93%] running checks test_clustalw.py +cd /build/openstructure-2.3.1/modules/bindings/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/bindings/tests/test_clustalw.py" In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, - from /build/openstructure-2.3.1/modules/mol/alg/tests/test_consistency_checks.cc:26: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/interaction.hh:34, + from /build/openstructure-2.3.1/modules/mol/mm/tests/test_block.cc:21: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -30919,7 +31028,7 @@ from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, - from /build/openstructure-2.3.1/modules/mol/alg/tests/test_consistency_checks.cc:24: + from /build/openstructure-2.3.1/modules/mol/mm/tests/test_block.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -30929,20 +31038,30 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -make -f modules/io/tests/CMakeFiles/test_io_mmcif.py_run.dir/build.make modules/io/tests/CMakeFiles/test_io_mmcif.py_run.dir/depend -make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/io/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/tests/CMakeFiles/test_io_mmcif.py_run.dir/DependInfo.cmake --color= -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, +/usr/lib/python3.11/unittest/case.py:579: ResourceWarning: unclosed file <_io.BufferedReader name='testfiles/roc-out.png'> + if method() is not None: +ResourceWarning: Enable tracemalloc to get the object allocation traceback +.In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/sec_struct.hh:25, - from /build/openstructure-2.3.1/modules/mol/alg/tests/test_partial_sec_struct_assignment.cc:21: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/topology.hh:31, + from /build/openstructure-2.3.1/modules/mol/mm/tests/test_topology.cc:21: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/vector:60, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/sec_struct.hh:22: +In file included from /usr/include/c++/12/string:45, + from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, + from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, + from /usr/include/boost/test/detail/global_typedef.hpp:15, + from /usr/include/boost/test/tree/observer.hpp:17, + from /usr/include/boost/test/unit_test_log.hpp:18, + from /usr/include/boost/test/tools/old/impl.hpp:19, + from /usr/include/boost/test/test_tools.hpp:46, + from /usr/include/boost/test/unit_test.hpp:18, + from /build/openstructure-2.3.1/modules/mol/mm/tests/test_topology.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -30952,49 +31071,69 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +/usr/lib/python3.11/unittest/case.py:579: ResourceWarning: unclosed file <_io.BufferedReader name='testfiles/roc-same-val-out.png'> + if method() is not None: +ResourceWarning: Enable tracemalloc to get the object allocation traceback +................../build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ost/table.py:2186: DeprecationWarning: scipy.isnan is deprecated and will be removed in SciPy 2.0.0, use numpy.isnan instead + if scipy.isnan(correl): +......................... +---------------------------------------------------------------------- +Ran 83 tests in 11.018s + +OK make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/io/tests/CMakeFiles/test_io_mmcif.py_run.dir/build.make modules/io/tests/CMakeFiles/test_io_mmcif.py_run.dir/build +[ 93%] Built target test_table.py_run +make -f modules/bindings/tests/CMakeFiles/test_hhblits.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_hhblits.py_run.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 94%] running checks test_io_mmcif.py -cd /build/openstructure-2.3.1/modules/io/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/io/tests/test_io_mmcif.py" -[ 94%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/test_io_dcd.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/io/tests/CMakeFiles/ost_io_tests.dir/test_io_dcd.cc.o -MF CMakeFiles/ost_io_tests.dir/test_io_dcd.cc.o.d -o CMakeFiles/ost_io_tests.dir/test_io_dcd.cc.o -c /build/openstructure-2.3.1/modules/io/tests/test_io_dcd.cc -[ 94%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/test_io_sdf.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/io/tests/CMakeFiles/ost_io_tests.dir/test_io_sdf.cc.o -MF CMakeFiles/ost_io_tests.dir/test_io_sdf.cc.o.d -o CMakeFiles/ost_io_tests.dir/test_io_sdf.cc.o -c /build/openstructure-2.3.1/modules/io/tests/test_io_sdf.cc -[ 94%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/test_io_sequence_profile.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/io/tests/CMakeFiles/ost_io_tests.dir/test_io_sequence_profile.cc.o -MF CMakeFiles/ost_io_tests.dir/test_io_sequence_profile.cc.o.d -o CMakeFiles/ost_io_tests.dir/test_io_sequence_profile.cc.o -c /build/openstructure-2.3.1/modules/io/tests/test_io_sequence_profile.cc -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, - from /build/openstructure-2.3.1/modules/mol/alg/tests/test_partial_sec_struct_assignment.cc:25: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 32 | : public std::iterator{ - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -[ 94%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/test_pir.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/io/tests/CMakeFiles/ost_io_tests.dir/test_pir.cc.o -MF CMakeFiles/ost_io_tests.dir/test_pir.cc.o.d -o CMakeFiles/ost_io_tests.dir/test_pir.cc.o -c /build/openstructure-2.3.1/modules/io/tests/test_pir.cc +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/bindings/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/tests/CMakeFiles/test_hhblits.py_run.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +make -f modules/bindings/tests/CMakeFiles/test_hhblits.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_hhblits.py_run.dir/build +make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[ 93%] running checks test_hhblits.py +cd /build/openstructure-2.3.1/modules/bindings/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/bindings/tests/test_hhblits.py" +No HHblits installation found: skip unit tests +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[ 93%] Built target test_hhblits.py_run +make -f modules/bindings/tests/CMakeFiles/test_blast.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_blast.py_run.dir/depend +make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/bindings/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/tests/CMakeFiles/test_blast.py_run.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +make -f modules/bindings/tests/CMakeFiles/test_blast.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_blast.py_run.dir/build +make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[ 93%] running checks test_blast.py +cd /build/openstructure-2.3.1/modules/bindings/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/bindings/tests/test_blast.py" +.Could not find blast executable: ignoring unit tests +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +.[ 93%] Built target test_blast.py_run +make -f modules/bindings/tests/CMakeFiles/test_kclust.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_kclust.py_run.dir/depend +make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/bindings/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/tests/CMakeFiles/test_kclust.py_run.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +make -f modules/bindings/tests/CMakeFiles/test_kclust.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_kclust.py_run.dir/build +make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[ 93%] running checks test_kclust.py +cd /build/openstructure-2.3.1/modules/bindings/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/bindings/tests/test_kclust.py" +.... +---------------------------------------------------------------------- +Ran 7 tests in 6.761s + +OK +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[ 93%] Built target test_clustalw.py_run +make -f modules/bindings/tests/CMakeFiles/test_naccess.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_naccess.py_run.dir/depend +make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/bindings/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/tests/CMakeFiles/test_naccess.py_run.dir/DependInfo.cmake --color= In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, - from /build/openstructure-2.3.1/modules/io/tests/test_io_crd.cc:23: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color.hh:31, + from /build/openstructure-2.3.1/modules/gfx/tests/test_color.cc:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/12/string:45, - from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, - from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, - from /usr/include/boost/test/detail/global_typedef.hpp:15, - from /usr/include/boost/test/tree/observer.hpp:17, - from /usr/include/boost/test/unit_test_log.hpp:18, - from /usr/include/boost/test/tools/old/impl.hpp:19, - from /usr/include/boost/test/test_tools.hpp:46, - from /usr/include/boost/test/unit_test.hpp:18, - from /build/openstructure-2.3.1/modules/io/tests/test_io_crd.cc:20: +In file included from /usr/include/c++/12/iterator:61, + from /usr/include/boost/operators.hpp:98, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color.hh:28: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -31004,58 +31143,66 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 94%] Linking CXX executable ../../../../tests/ost_mol_tests -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_mol_tests.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro CMakeFiles/ost_mol_tests.dir/test_atom_groups.cc.o CMakeFiles/ost_mol_tests.dir/test_chain.cc.o CMakeFiles/ost_mol_tests.dir/test_conn.cc.o CMakeFiles/ost_mol_tests.dir/test_coord_group.cc.o CMakeFiles/ost_mol_tests.dir/test_builder.cc.o CMakeFiles/ost_mol_tests.dir/test_delete.cc.o CMakeFiles/ost_mol_tests.dir/test_entity.cc.o CMakeFiles/ost_mol_tests.dir/test_ics.cc.o CMakeFiles/ost_mol_tests.dir/test_query.cc.o CMakeFiles/ost_mol_tests.dir/test_surface.cc.o CMakeFiles/ost_mol_tests.dir/test_residue.cc.o CMakeFiles/ost_mol_tests.dir/test_view.cc.o CMakeFiles/ost_mol_tests.dir/test_transfer_connectivity.cc.o CMakeFiles/ost_mol_tests.dir/test_view_op.cc.o CMakeFiles/ost_mol_tests.dir/tests.cc.o -o ../../../../tests/ost_mol_tests -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib /usr/lib/x86_64-linux-gnu/libboost_unit_test_framework.so ../../../../stage/lib/libost_mol.so.2.3.1 ../../../../stage/lib/libost_info.so.2.3.1 ../../../../stage/lib/libost_base.so.2.3.1 ../../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 -[ 94%] Linking CXX executable ../../../tests/ost_gfx_tests -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_gfx_tests.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro CMakeFiles/ost_gfx_tests.dir/tests.cc.o CMakeFiles/ost_gfx_tests.dir/test_gfx_node.cc.o CMakeFiles/ost_gfx_tests.dir/test_color.cc.o CMakeFiles/ost_gfx_tests.dir/test_map_octree.cc.o -o ../../../tests/ost_gfx_tests -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib /usr/lib/x86_64-linux-gnu/libboost_unit_test_framework.so ../../../stage/lib/libost_gfx.so.2.3.1 ../../../stage/lib/libost_io.so.2.3.1 /usr/lib/x86_64-linux-gnu/libOpenGL.so /usr/lib/x86_64-linux-gnu/libGLX.so /usr/lib/x86_64-linux-gnu/libGLU.so ../../../stage/lib/libost_mol_alg.so.2.3.1 ../../../stage/lib/libost_conop.so.2.3.1 ../../../stage/lib/libost_db.so.2.3.1 /usr/lib/x86_64-linux-gnu/libsqlite3.so ../../../stage/lib/libost_img_alg.so.2.3.1 ../../../stage/lib/libost_img.so.2.3.1 /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libfftw3f_threads.so /usr/lib/x86_64-linux-gnu/libboost_program_options.so /usr/lib/x86_64-linux-gnu/libboost_thread.so /usr/lib/x86_64-linux-gnu/libboost_chrono.so /usr/lib/x86_64-linux-gnu/libboost_date_time.so /usr/lib/x86_64-linux-gnu/libboost_atomic.so ../../../stage/lib/libost_seq_alg.so.2.3.1 ../../../stage/lib/libost_seq.so.2.3.1 ../../../stage/lib/libost_mol.so.2.3.1 ../../../stage/lib/libost_info.so.2.3.1 ../../../stage/lib/libost_base.so.2.3.1 ../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libtiff.so /usr/lib/x86_64-linux-gnu/libpng.so /usr/lib/x86_64-linux-gnu/libz.so make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 94%] Built target ost_gfx_tests -make -f modules/io/tests/CMakeFiles/test_io_omf.py_run.dir/build.make modules/io/tests/CMakeFiles/test_io_omf.py_run.dir/depend +make -f modules/bindings/tests/CMakeFiles/test_naccess.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_naccess.py_run.dir/build +Could not find kClust executable: ignoring unit tests make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/io/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/tests/CMakeFiles/test_io_omf.py_run.dir/DependInfo.cmake --color= +[ 94%] running checks test_naccess.py +cd /build/openstructure-2.3.1/modules/bindings/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/bindings/tests/test_naccess.py" make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/io/tests/CMakeFiles/test_io_omf.py_run.dir/build.make modules/io/tests/CMakeFiles/test_io_omf.py_run.dir/build +[ 94%] Built target test_kclust.py_run +make -f modules/bindings/tests/CMakeFiles/test_cadscore.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_cadscore.py_run.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 94%] running checks test_io_omf.py -cd /build/openstructure-2.3.1/modules/io/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/io/tests/test_io_omf.py" +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/bindings/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/tests/CMakeFiles/test_cadscore.py_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 94%] Built target ost_mol_tests -make -f modules/mol/alg/tests/CMakeFiles/test_pdbize.py_run.dir/build.make modules/mol/alg/tests/CMakeFiles/test_pdbize.py_run.dir/depend +make -f modules/bindings/tests/CMakeFiles/test_cadscore.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_cadscore.py_run.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/tests/CMakeFiles/test_pdbize.py_run.dir/DependInfo.cmake --color= +[ 94%] running checks test_cadscore.py +cd /build/openstructure-2.3.1/modules/bindings/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/bindings/tests/test_cadscore.py" +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/modeller.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/topology_creator.hh:37, + from /build/openstructure-2.3.1/modules/mol/mm/tests/test_topology.cc:22: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 32 | : public std::iterator{ + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +Could not find NACCESS, could not test binding... +[ 94%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/test_pir.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/io/tests/CMakeFiles/ost_io_tests.dir/test_pir.cc.o -MF CMakeFiles/ost_io_tests.dir/test_pir.cc.o.d -o CMakeFiles/ost_io_tests.dir/test_pir.cc.o -c /build/openstructure-2.3.1/modules/io/tests/test_pir.cc make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/mol/alg/tests/CMakeFiles/test_pdbize.py_run.dir/build.make modules/mol/alg/tests/CMakeFiles/test_pdbize.py_run.dir/build +[ 94%] Built target test_naccess.py_run +make -f modules/bindings/tests/CMakeFiles/test_tmtools.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_tmtools.py_run.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 94%] running checks test_pdbize.py -cd /build/openstructure-2.3.1/modules/mol/alg/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/mol/alg/tests/test_pdbize.py" -........ +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/bindings/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/tests/CMakeFiles/test_tmtools.py_run.dir/DependInfo.cmake --color= +[ 94%] Linking CXX executable ../../../../tests/ost_mol_alg_tests +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_mol_alg_tests.dir/link.txt --verbose=1 +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +make -f modules/bindings/tests/CMakeFiles/test_tmtools.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_tmtools.py_run.dir/build +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro CMakeFiles/ost_mol_alg_tests.dir/test_superposition.cc.o CMakeFiles/ost_mol_alg_tests.dir/tests.cc.o CMakeFiles/ost_mol_alg_tests.dir/test_consistency_checks.cc.o CMakeFiles/ost_mol_alg_tests.dir/test_partial_sec_struct_assignment.cc.o -o ../../../../tests/ost_mol_alg_tests -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib /usr/lib/x86_64-linux-gnu/libboost_unit_test_framework.so ../../../../stage/lib/libost_io.so.2.3.1 ../../../../stage/lib/libost_mol_alg.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_program_options.so /usr/lib/x86_64-linux-gnu/libboost_thread.so /usr/lib/x86_64-linux-gnu/libboost_chrono.so /usr/lib/x86_64-linux-gnu/libboost_date_time.so /usr/lib/x86_64-linux-gnu/libboost_atomic.so ../../../../stage/lib/libost_seq_alg.so.2.3.1 ../../../../stage/lib/libost_img_alg.so.2.3.1 ../../../../stage/lib/libost_img.so.2.3.1 /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libfftw3f_threads.so ../../../../stage/lib/libost_conop.so.2.3.1 ../../../../stage/lib/libost_db.so.2.3.1 ../../../../stage/lib/libost_seq.so.2.3.1 ../../../../stage/lib/libost_mol.so.2.3.1 ../../../../stage/lib/libost_info.so.2.3.1 /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/x86_64-linux-gnu/libsqlite3.so ../../../../stage/lib/libost_base.so.2.3.1 ../../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libtiff.so /usr/lib/x86_64-linux-gnu/libpng.so /usr/lib/x86_64-linux-gnu/libz.so +make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[ 94%] running checks test_tmtools.py +cd /build/openstructure-2.3.1/modules/bindings/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/bindings/tests/test_tmtools.py" +... ---------------------------------------------------------------------- -Ran 8 tests in 0.449s +Ran 2 tests in 0.236s OK +Could not find tmalign executable: ignoring unit tests +Could not find tmalign executable: ignoring unit tests make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 94%] Built target test_pdbize.py_run -make -f modules/mol/alg/tests/CMakeFiles/test_convenient_superpose.py_run.dir/build.make modules/mol/alg/tests/CMakeFiles/test_convenient_superpose.py_run.dir/depend -make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/tests/CMakeFiles/test_convenient_superpose.py_run.dir/DependInfo.cmake --color= -[ 94%] Linking CXX executable ../../../../tests/ost_seq_alg_tests -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_seq_alg_tests.dir/link.txt --verbose=1 -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/mol/alg/tests/CMakeFiles/test_convenient_superpose.py_run.dir/build.make modules/mol/alg/tests/CMakeFiles/test_convenient_superpose.py_run.dir/build -make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro CMakeFiles/ost_seq_alg_tests.dir/test_distance_analysis.cc.o CMakeFiles/ost_seq_alg_tests.dir/test_merge_pairwise_alignments.cc.o CMakeFiles/ost_seq_alg_tests.dir/test_sequence_identity.cc.o CMakeFiles/ost_seq_alg_tests.dir/tests.cc.o -o ../../../../tests/ost_seq_alg_tests -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib /usr/lib/x86_64-linux-gnu/libboost_unit_test_framework.so ../../../../stage/lib/libost_io.so.2.3.1 ../../../../stage/lib/libost_mol_alg.so.2.3.1 ../../../../stage/lib/libost_seq_alg.so.2.3.1 ../../../../stage/lib/libost_conop.so.2.3.1 ../../../../stage/lib/libost_db.so.2.3.1 ../../../../stage/lib/libost_seq.so.2.3.1 ../../../../stage/lib/libost_mol.so.2.3.1 /usr/lib/x86_64-linux-gnu/libsqlite3.so /usr/lib/x86_64-linux-gnu/libboost_program_options.so /usr/lib/x86_64-linux-gnu/libboost_thread.so /usr/lib/x86_64-linux-gnu/libboost_chrono.so /usr/lib/x86_64-linux-gnu/libboost_date_time.so /usr/lib/x86_64-linux-gnu/libboost_atomic.so ../../../../stage/lib/libost_img_alg.so.2.3.1 ../../../../stage/lib/libost_img.so.2.3.1 ../../../../stage/lib/libost_info.so.2.3.1 ../../../../stage/lib/libost_base.so.2.3.1 ../../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libfftw3f_threads.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libtiff.so /usr/lib/x86_64-linux-gnu/libpng.so /usr/lib/x86_64-linux-gnu/libz.so -[ 94%] running checks test_convenient_superpose.py -cd /build/openstructure-2.3.1/modules/mol/alg/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/mol/alg/tests/test_convenient_superpose.py" -make -f modules/mol/alg/tests/CMakeFiles/test_hbond.py_run.dir/build.make modules/mol/alg/tests/CMakeFiles/test_hbond.py_run.dir/depend +[ 94%] Built target test_tmtools.py_run +make -f modules/bindings/tests/CMakeFiles/test_ialign.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_ialign.py_run.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/tests/CMakeFiles/test_hbond.py_run.dir/DependInfo.cmake --color= +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/bindings/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/tests/CMakeFiles/test_ialign.py_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/mol/alg/tests/CMakeFiles/test_hbond.py_run.dir/build.make modules/mol/alg/tests/CMakeFiles/test_hbond.py_run.dir/build +make -f modules/bindings/tests/CMakeFiles/test_ialign.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_ialign.py_run.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 94%] running checks test_hbond.py -cd /build/openstructure-2.3.1/modules/mol/alg/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/mol/alg/tests/test_hbond.py" +[ 94%] running checks test_ialign.py +cd /build/openstructure-2.3.1/modules/bindings/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/bindings/tests/test_ialign.py" In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/load.hh:27, from /build/openstructure-2.3.1/modules/io/tests/test_io_sequence_profile.cc:29: @@ -31075,47 +31222,72 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[ 94%] Built target ost_mol_alg_tests +make -f modules/bindings/tests/CMakeFiles/test_lga.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_lga.py_run.dir/depend +make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/bindings/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/tests/CMakeFiles/test_lga.py_run.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +make -f modules/bindings/tests/CMakeFiles/test_lga.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_lga.py_run.dir/build +make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[ 94%] running checks test_lga.py +cd /build/openstructure-2.3.1/modules/bindings/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/bindings/tests/test_lga.py" +[ 95%] Building CXX object modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests.dir/test_sequence_identity.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests.dir/test_sequence_identity.cc.o -MF CMakeFiles/ost_seq_alg_tests.dir/test_sequence_identity.cc.o.d -o CMakeFiles/ost_seq_alg_tests.dir/test_sequence_identity.cc.o -c /build/openstructure-2.3.1/modules/seq/alg/tests/test_sequence_identity.cc . ---------------------------------------------------------------------- -Ran 1 test in 2.837s +Ran 1 test in 0.185s OK +Could not find ialign master perl script: ignoring unit tests make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 94%] Built target test_io_omf.py_run -make -f modules/mol/alg/tests/CMakeFiles/test_accessibility.py_run.dir/build.make modules/mol/alg/tests/CMakeFiles/test_accessibility.py_run.dir/depend +[ 95%] Built target test_ialign.py_run +make -f modules/bindings/tests/CMakeFiles/test_hbplus.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_hbplus.py_run.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/tests/CMakeFiles/test_accessibility.py_run.dir/DependInfo.cmake --color= +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/bindings/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/tests/CMakeFiles/test_hbplus.py_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/mol/alg/tests/CMakeFiles/test_accessibility.py_run.dir/build.make modules/mol/alg/tests/CMakeFiles/test_accessibility.py_run.dir/build +make -f modules/bindings/tests/CMakeFiles/test_hbplus.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_hbplus.py_run.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 94%] running checks test_accessibility.py -cd /build/openstructure-2.3.1/modules/mol/alg/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/mol/alg/tests/test_accessibility.py" -... +[ 95%] running checks test_hbplus.py +cd /build/openstructure-2.3.1/modules/bindings/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/bindings/tests/test_hbplus.py" +. ---------------------------------------------------------------------- -Ran 2 tests in 0.255s +Ran 1 test in 0.181s OK +Could not find lga executable: ignoring unit tests make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 94%] Built target test_hbond.py_run -make -f modules/mol/alg/tests/CMakeFiles/test_sec_struct.py_run.dir/build.make modules/mol/alg/tests/CMakeFiles/test_sec_struct.py_run.dir/depend +[ 95%] Built target test_lga.py_run +make -f modules/conop/tests/CMakeFiles/test_processor.py_run.dir/build.make modules/conop/tests/CMakeFiles/test_processor.py_run.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/tests/CMakeFiles/test_sec_struct.py_run.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 94%] Built target ost_seq_alg_tests -make -f modules/mol/mm/tests/CMakeFiles/test_antechamber.py_run.dir/build.make modules/mol/mm/tests/CMakeFiles/test_antechamber.py_run.dir/depend +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/conop/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/tests/CMakeFiles/test_processor.py_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/mol/alg/tests/CMakeFiles/test_sec_struct.py_run.dir/build.make modules/mol/alg/tests/CMakeFiles/test_sec_struct.py_run.dir/build +make -f modules/conop/tests/CMakeFiles/test_processor.py_run.dir/build.make modules/conop/tests/CMakeFiles/test_processor.py_run.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[ 95%] running checks test_processor.py +cd /build/openstructure-2.3.1/modules/conop/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/conop/tests/test_processor.py" +Could not find hbplus, could not test binding... +. +---------------------------------------------------------------------- +Ran 1 test in 0.009s + +OK +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[ 95%] Built target test_processor.py_run +make -f modules/db/tests/CMakeFiles/test_linear_db.py_run.dir/build.make modules/db/tests/CMakeFiles/test_linear_db.py_run.dir/depend +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/mm/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/tests/CMakeFiles/test_antechamber.py_run.dir/DependInfo.cmake --color= -[ 94%] running checks test_sec_struct.py -cd /build/openstructure-2.3.1/modules/mol/alg/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/mol/alg/tests/test_sec_struct.py" +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/db/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/tests/CMakeFiles/test_linear_db.py_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/mol/mm/tests/CMakeFiles/test_antechamber.py_run.dir/build.make modules/mol/mm/tests/CMakeFiles/test_antechamber.py_run.dir/build +make -f modules/db/tests/CMakeFiles/test_linear_db.py_run.dir/build.make modules/db/tests/CMakeFiles/test_linear_db.py_run.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 94%] running checks test_antechamber.py -cd /build/openstructure-2.3.1/modules/mol/mm/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/mol/mm/tests/test_antechamber.py" -sIn file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, +[ 95%] Built target test_hbplus.py_run +make -f modules/geom/tests/CMakeFiles/test_geom.py_run.dir/build.make modules/geom/tests/CMakeFiles/test_geom.py_run.dir/depend +make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/geom/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/tests/CMakeFiles/test_geom.py_run.dir/DependInfo.cmake --color= +[ 95%] running checks test_linear_db.py +cd /build/openstructure-2.3.1/modules/db/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/db/tests/test_linear_db.py" +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, @@ -31135,14 +31307,73 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +make -f modules/geom/tests/CMakeFiles/test_geom.py_run.dir/build.make modules/geom/tests/CMakeFiles/test_geom.py_run.dir/build +make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[ 95%] running checks test_geom.py +cd /build/openstructure-2.3.1/modules/geom/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/geom/tests/test_geom.py" +... +---------------------------------------------------------------------- +Ran 3 tests in 0.051s + +OK +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +....[ 95%] Built target test_linear_db.py_run +.... +---------------------------------------------------------------------- +Ran 8 tests in 0.100s + +OK +[ 95%] Building CXX object modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests.dir/tests.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests.dir/tests.cc.o -MF CMakeFiles/ost_seq_alg_tests.dir/tests.cc.o.d -o CMakeFiles/ost_seq_alg_tests.dir/tests.cc.o -c /build/openstructure-2.3.1/modules/seq/alg/tests/tests.cc +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[ 95%] Built target test_geom.py_run +make -f modules/gfx/tests/CMakeFiles/test_gfx.py_run.dir/build.make modules/gfx/tests/CMakeFiles/test_gfx.py_run.dir/depend +make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/gfx/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/tests/CMakeFiles/test_gfx.py_run.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +make -f modules/gfx/tests/CMakeFiles/test_gfx.py_run.dir/build.make modules/gfx/tests/CMakeFiles/test_gfx.py_run.dir/build +make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[ 96%] running checks test_gfx.py +cd /build/openstructure-2.3.1/modules/gfx/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/gfx/tests/test_gfx.py" +...... +---------------------------------------------------------------------- +Ran 6 tests in 0.029s + +OK +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[ 96%] Built target test_gfx.py_run +make -f modules/io/tests/CMakeFiles/test_io_pdb.py_run.dir/build.make modules/io/tests/CMakeFiles/test_io_pdb.py_run.dir/depend +make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/io/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/tests/CMakeFiles/test_io_pdb.py_run.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +make -f modules/io/tests/CMakeFiles/test_io_pdb.py_run.dir/build.make modules/io/tests/CMakeFiles/test_io_pdb.py_run.dir/build +make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[ 96%] running checks test_io_pdb.py +cd /build/openstructure-2.3.1/modules/io/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/io/tests/test_io_pdb.py" +...s +---------------------------------------------------------------------- +Ran 4 tests in 0.033s + +OK (skipped=1) +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[ 96%] Built target test_io_pdb.py_run +make -f modules/io/tests/CMakeFiles/test_io_mmcif.py_run.dir/build.make modules/io/tests/CMakeFiles/test_io_mmcif.py_run.dir/depend +make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/io/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/tests/CMakeFiles/test_io_mmcif.py_run.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +make -f modules/io/tests/CMakeFiles/test_io_mmcif.py_run.dir/build.make modules/io/tests/CMakeFiles/test_io_mmcif.py_run.dir/build +make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[ 96%] running checks test_io_mmcif.py +cd /build/openstructure-2.3.1/modules/io/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/io/tests/test_io_mmcif.py" In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/coord_frame.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/coord_source.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/coord_group.hh:29, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/dcd_io.hh:28, - from /build/openstructure-2.3.1/modules/io/tests/test_io_dcd.cc:23: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, + from /build/openstructure-2.3.1/modules/io/tests/test_io_sdf.cc:26: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -31155,7 +31386,7 @@ from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, - from /build/openstructure-2.3.1/modules/io/tests/test_io_dcd.cc:21: + from /build/openstructure-2.3.1/modules/io/tests/test_io_sdf.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -31165,17 +31396,7 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -s ----------------------------------------------------------------------- -Ran 1 test in 0.009s - -OK (skipped=1) -..make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 94%] Built target test_sec_struct.py_run -make -f modules/seq/base/tests/CMakeFiles/test_seq.py_run.dir/build.make modules/seq/base/tests/CMakeFiles/test_seq.py_run.dir/depend -make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/seq/base/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/tests/CMakeFiles/test_seq.py_run.dir/DependInfo.cmake --color= -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, +.In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/pir_io_handler.hh:25, from /build/openstructure-2.3.1/modules/io/tests/test_pir.cc:27: @@ -31195,27 +31416,7 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/seq/base/tests/CMakeFiles/test_seq.py_run.dir/build.make modules/seq/base/tests/CMakeFiles/test_seq.py_run.dir/build -make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -.. ----------------------------------------------------------------------- -Ran 3 tests in 0.262s - -OK -[ 94%] running checks test_seq.py -cd /build/openstructure-2.3.1/modules/seq/base/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/seq/base/tests/test_seq.py" -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 94%] Built target test_antechamber.py_run -make -f modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests_run.dir/build.make modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests_run.dir/depend -make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/seq/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests_run.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests_run.dir/build.make modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests_run.dir/build -make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 94%] running checks for module seq_alg -cd /build/openstructure-2.3.1/modules/seq/alg/tests && env OST_ROOT=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage /build/openstructure-2.3.1/obj-x86_64-linux-gnu/tests/ost_seq_alg_tests -.In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, @@ -31235,30 +31436,35 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -.Running 19 test cases... +.[ 96%] Building CXX object modules/gfx/tests/CMakeFiles/ost_gfx_tests.dir/test_map_octree.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/gfx/tests/CMakeFiles/ost_gfx_tests.dir/test_map_octree.cc.o -MF CMakeFiles/ost_gfx_tests.dir/test_map_octree.cc.o.d -o CMakeFiles/ost_gfx_tests.dir/test_map_octree.cc.o -c /build/openstructure-2.3.1/modules/gfx/tests/test_map_octree.cc +.......s +---------------------------------------------------------------------- +Ran 10 tests in 6.106s -*** No errors detected -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 94%] Built target ost_seq_alg_tests_run -make -f modules/seq/alg/tests/CMakeFiles/test_renumber.py_run.dir/build.make modules/seq/alg/tests/CMakeFiles/test_renumber.py_run.dir/depend +OK (skipped=1) +[ 96%] Building CXX object modules/mol/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/test_forcefield.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/test_forcefield.cc.o -MF CMakeFiles/ost_mol_mm_tests.dir/test_forcefield.cc.o.d -o CMakeFiles/ost_mol_mm_tests.dir/test_forcefield.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/tests/test_forcefield.cc +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[ 96%] Built target test_io_mmcif.py_run +make -f modules/io/tests/CMakeFiles/test_io_omf.py_run.dir/build.make modules/io/tests/CMakeFiles/test_io_omf.py_run.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/seq/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/tests/CMakeFiles/test_renumber.py_run.dir/DependInfo.cmake --color= +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/io/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/tests/CMakeFiles/test_io_omf.py_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/seq/alg/tests/CMakeFiles/test_renumber.py_run.dir/build.make modules/seq/alg/tests/CMakeFiles/test_renumber.py_run.dir/build +make -f modules/io/tests/CMakeFiles/test_io_omf.py_run.dir/build.make modules/io/tests/CMakeFiles/test_io_omf.py_run.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 94%] running checks test_renumber.py -.cd /build/openstructure-2.3.1/modules/seq/alg/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/seq/alg/tests/test_renumber.py" -[ 94%] Linking CXX executable ../../../../tests/ost_mol_alg_tests -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_mol_alg_tests.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro CMakeFiles/ost_mol_alg_tests.dir/test_superposition.cc.o CMakeFiles/ost_mol_alg_tests.dir/tests.cc.o CMakeFiles/ost_mol_alg_tests.dir/test_consistency_checks.cc.o CMakeFiles/ost_mol_alg_tests.dir/test_partial_sec_struct_assignment.cc.o -o ../../../../tests/ost_mol_alg_tests -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib /usr/lib/x86_64-linux-gnu/libboost_unit_test_framework.so ../../../../stage/lib/libost_io.so.2.3.1 ../../../../stage/lib/libost_mol_alg.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_program_options.so /usr/lib/x86_64-linux-gnu/libboost_thread.so /usr/lib/x86_64-linux-gnu/libboost_chrono.so /usr/lib/x86_64-linux-gnu/libboost_date_time.so /usr/lib/x86_64-linux-gnu/libboost_atomic.so ../../../../stage/lib/libost_seq_alg.so.2.3.1 ../../../../stage/lib/libost_img_alg.so.2.3.1 ../../../../stage/lib/libost_img.so.2.3.1 /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libfftw3f_threads.so ../../../../stage/lib/libost_conop.so.2.3.1 ../../../../stage/lib/libost_db.so.2.3.1 ../../../../stage/lib/libost_seq.so.2.3.1 ../../../../stage/lib/libost_mol.so.2.3.1 ../../../../stage/lib/libost_info.so.2.3.1 /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/x86_64-linux-gnu/libsqlite3.so ../../../../stage/lib/libost_base.so.2.3.1 ../../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libtiff.so /usr/lib/x86_64-linux-gnu/libpng.so /usr/lib/x86_64-linux-gnu/libz.so -.In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, +[ 96%] running checks test_io_omf.py +cd /build/openstructure-2.3.1/modules/io/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/io/tests/test_io_omf.py" +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, - from /build/openstructure-2.3.1/modules/io/tests/test_io_sdf.cc:26: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/sequence_identity.hh:26, + from /build/openstructure-2.3.1/modules/seq/alg/tests/test_sequence_identity.cc:25: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -31271,7 +31477,7 @@ from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, - from /build/openstructure-2.3.1/modules/io/tests/test_io_sdf.cc:20: + from /build/openstructure-2.3.1/modules/seq/alg/tests/test_sequence_identity.cc:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -31281,367 +31487,184 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -.[ 94%] Building CXX object modules/mol/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/test_block_modifiers.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/test_block_modifiers.cc.o -MF CMakeFiles/ost_mol_mm_tests.dir/test_block_modifiers.cc.o.d -o CMakeFiles/ost_mol_mm_tests.dir/test_block_modifiers.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/tests/test_block_modifiers.cc -.. ----------------------------------------------------------------------- -Ran 9 tests in 6.979s - -OK -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 94%] Built target test_convenient_superpose.py_run -make -f modules/seq/alg/tests/CMakeFiles/test_local_align.py_run.dir/build.make modules/seq/alg/tests/CMakeFiles/test_local_align.py_run.dir/depend -make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/seq/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/tests/CMakeFiles/test_local_align.py_run.dir/DependInfo.cmake --color= -.........s ----------------------------------------------------------------------- -Ran 4 tests in 0.068s - -OK (skipped=1) -......... ----------------------------------------------------------------------- -Ran 14 tests in 0.101s - -OK -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/seq/alg/tests/CMakeFiles/test_local_align.py_run.dir/build.make modules/seq/alg/tests/CMakeFiles/test_local_align.py_run.dir/build +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 32 | : public std::iterator{ + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +make -f modules/mol/base/tests/CMakeFiles/ost_mol_tests_run.dir/build.make modules/mol/base/tests/CMakeFiles/ost_mol_tests_run.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 94%] running checks test_local_align.py -cd /build/openstructure-2.3.1/modules/seq/alg/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/seq/alg/tests/test_local_align.py" -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 94%] Built target ost_mol_alg_tests -make -f modules/seq/alg/tests/CMakeFiles/test_global_align.py_run.dir/build.make modules/seq/alg/tests/CMakeFiles/test_global_align.py_run.dir/depend -.make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/seq/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/tests/CMakeFiles/test_global_align.py_run.dir/DependInfo.cmake --color= -..make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/base/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/tests/CMakeFiles/ost_mol_tests_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/seq/alg/tests/CMakeFiles/test_global_align.py_run.dir/build.make modules/seq/alg/tests/CMakeFiles/test_global_align.py_run.dir/build +make -f modules/mol/base/tests/CMakeFiles/ost_mol_tests_run.dir/build.make modules/mol/base/tests/CMakeFiles/ost_mol_tests_run.dir/build .make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 94%] Built target test_io_pdb.py_run -[ 94%] Built target test_seq.py_run -make -f modules/seq/alg/tests/CMakeFiles/test_semiglobal_align.py_run.dir/build.make modules/seq/alg/tests/CMakeFiles/test_semiglobal_align.py_run.dir/depend -..make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/seq/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/tests/CMakeFiles/test_semiglobal_align.py_run.dir/DependInfo.cmake --color= -.. ----------------------------------------------------------------------- -Ran 8 tests in 0.779s - -OK -[ 94%] Building CXX object modules/mol/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/test_topology.cc.o -[ 94%] running checks test_global_align.py -cd /build/openstructure-2.3.1/modules/seq/alg/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/seq/alg/tests/test_global_align.py" -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/test_topology.cc.o -MF CMakeFiles/ost_mol_mm_tests.dir/test_topology.cc.o.d -o CMakeFiles/ost_mol_mm_tests.dir/test_topology.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/tests/test_topology.cc -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/seq/alg/tests/CMakeFiles/test_semiglobal_align.py_run.dir/build.make modules/seq/alg/tests/CMakeFiles/test_semiglobal_align.py_run.dir/build -make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 94%] running checks test_semiglobal_align.py -cd /build/openstructure-2.3.1/modules/seq/alg/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/seq/alg/tests/test_semiglobal_align.py" -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 94%] Built target test_renumber.py_run -make -f modules/seq/alg/tests/CMakeFiles/test_weight_matrix.py_run.dir/build.make modules/seq/alg/tests/CMakeFiles/test_weight_matrix.py_run.dir/depend -make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/seq/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/tests/CMakeFiles/test_weight_matrix.py_run.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/seq/alg/tests/CMakeFiles/test_weight_matrix.py_run.dir/build.make modules/seq/alg/tests/CMakeFiles/test_weight_matrix.py_run.dir/build -make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 94%] running checks test_weight_matrix.py -cd /build/openstructure-2.3.1/modules/seq/alg/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/seq/alg/tests/test_weight_matrix.py" -... ----------------------------------------------------------------------- -Ran 3 tests in 0.015s - -OK -. ----------------------------------------------------------------------- -Ran 1 test in 0.007s - -OK -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -... ----------------------------------------------------------------------- -Ran 3 tests in 0.008s -OK -.. ---------------------------------------------------------------------- -Ran 2 tests in 0.009s +Ran 1 test in 3.282s OK -[ 94%] Built target test_local_align.py_run -make -f modules/seq/alg/tests/CMakeFiles/test_alignment_from_chain_view.py_run.dir/build.make modules/seq/alg/tests/CMakeFiles/test_alignment_from_chain_view.py_run.dir/depend -make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/seq/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/tests/CMakeFiles/test_alignment_from_chain_view.py_run.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/seq/alg/tests/CMakeFiles/test_alignment_from_chain_view.py_run.dir/build.make modules/seq/alg/tests/CMakeFiles/test_alignment_from_chain_view.py_run.dir/build -make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 94%] Built target test_weight_matrix.py_run -make -f modules/seq/alg/tests/CMakeFiles/test_aaindex.py_run.dir/build.make modules/seq/alg/tests/CMakeFiles/test_aaindex.py_run.dir/depend -make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/seq/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/tests/CMakeFiles/test_aaindex.py_run.dir/DependInfo.cmake --color= -[ 94%] running checks test_alignment_from_chain_view.py -cd /build/openstructure-2.3.1/modules/seq/alg/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/seq/alg/tests/test_alignment_from_chain_view.py" -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/seq/alg/tests/CMakeFiles/test_aaindex.py_run.dir/build.make modules/seq/alg/tests/CMakeFiles/test_aaindex.py_run.dir/build -make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 94%] running checks test_aaindex.py -cd /build/openstructure-2.3.1/modules/seq/alg/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/seq/alg/tests/test_aaindex.py" +[ 96%] running checks for module mol +cd /build/openstructure-2.3.1/modules/mol/base/tests && env OST_ROOT=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage /build/openstructure-2.3.1/obj-x86_64-linux-gnu/tests/ost_mol_tests make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 94%] Built target test_semiglobal_align.py_run -make -f modules/base/tests/CMakeFiles/test_stutil.py_run.dir/build.make modules/base/tests/CMakeFiles/test_stutil.py_run.dir/depend +[ 96%] Built target test_io_omf.py_run +make -f modules/mol/alg/tests/CMakeFiles/ost_mol_alg_tests_run.dir/build.make modules/mol/alg/tests/CMakeFiles/ost_mol_alg_tests_run.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/base/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/tests/CMakeFiles/test_stutil.py_run.dir/DependInfo.cmake --color= -[ 94%] Built target test_global_align.py_run +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/tests/CMakeFiles/ost_mol_alg_tests_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/base/tests/CMakeFiles/test_stutil.py_run.dir/build.make modules/base/tests/CMakeFiles/test_stutil.py_run.dir/build +make -f modules/mol/alg/tests/CMakeFiles/ost_mol_alg_tests_run.dir/build.make modules/mol/alg/tests/CMakeFiles/ost_mol_alg_tests_run.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 94%] running checks test_stutil.py -cd /build/openstructure-2.3.1/modules/base/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/base/tests/test_stutil.py" -[ 94%] Building CXX object modules/mol/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/test_forcefield.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/test_forcefield.cc.o -MF CMakeFiles/ost_mol_mm_tests.dir/test_forcefield.cc.o.d -o CMakeFiles/ost_mol_mm_tests.dir/test_forcefield.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/tests/test_forcefield.cc -.. ----------------------------------------------------------------------- -Ran 1 test in 0.018s - -OK -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -...... ----------------------------------------------------------------------- -Ran 6 tests in 0.017s +Running 70 test cases... -OK -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 94%] Built target test_alignment_from_chain_view.py_run -make -f modules/base/tests/CMakeFiles/test_table.py_run.dir/build.make modules/base/tests/CMakeFiles/test_table.py_run.dir/depend -make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/base/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/tests/CMakeFiles/test_table.py_run.dir/DependInfo.cmake --color= -[ 94%] Built target test_stutil.py_run -make -f modules/base/tests/CMakeFiles/test_log.py_run.dir/build.make modules/base/tests/CMakeFiles/test_log.py_run.dir/depend -make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/base/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/tests/CMakeFiles/test_log.py_run.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/base/tests/CMakeFiles/test_table.py_run.dir/build.make modules/base/tests/CMakeFiles/test_table.py_run.dir/build +*** No errors detected +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[ 96%] running checks for module mol_alg +cd /build/openstructure-2.3.1/modules/mol/alg/tests && env OST_ROOT=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage /build/openstructure-2.3.1/obj-x86_64-linux-gnu/tests/ost_mol_alg_tests +[ 96%] Built target ost_mol_tests_run +make -f modules/mol/alg/tests/CMakeFiles/test_pdbize.py_run.dir/build.make modules/mol/alg/tests/CMakeFiles/test_pdbize.py_run.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/tests/CMakeFiles/test_pdbize.py_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/base/tests/CMakeFiles/test_log.py_run.dir/build.make modules/base/tests/CMakeFiles/test_log.py_run.dir/build -[ 94%] running checks test_table.py +make -f modules/mol/alg/tests/CMakeFiles/test_pdbize.py_run.dir/build.make modules/mol/alg/tests/CMakeFiles/test_pdbize.py_run.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/modules/base/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/base/tests/test_table.py" -. ----------------------------------------------------------------------- -Ran 1 test in 0.364s +[ 96%] running checks test_pdbize.py +cd /build/openstructure-2.3.1/modules/mol/alg/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/mol/alg/tests/test_pdbize.py" +Running 4 test cases... -OK -[ 94%] running checks test_log.py -cd /build/openstructure-2.3.1/modules/base/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/base/tests/test_log.py" -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 94%] Built target test_aaindex.py_run -make -f modules/bindings/tests/CMakeFiles/test_msms.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_msms.py_run.dir/depend +*** No errors detected +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[ 96%] Built target ost_mol_alg_tests_run +make -f modules/mol/alg/tests/CMakeFiles/test_convenient_superpose.py_run.dir/build.make modules/mol/alg/tests/CMakeFiles/test_convenient_superpose.py_run.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/bindings/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/tests/CMakeFiles/test_msms.py_run.dir/DependInfo.cmake --color= +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/tests/CMakeFiles/test_convenient_superpose.py_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/bindings/tests/CMakeFiles/test_msms.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_msms.py_run.dir/build +make -f modules/mol/alg/tests/CMakeFiles/test_convenient_superpose.py_run.dir/build.make modules/mol/alg/tests/CMakeFiles/test_convenient_superpose.py_run.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 94%] running checks test_msms.py -cd /build/openstructure-2.3.1/modules/bindings/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/bindings/tests/test_msms.py" -.... +[ 96%] running checks test_convenient_superpose.py +cd /build/openstructure-2.3.1/modules/mol/alg/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/mol/alg/tests/test_convenient_superpose.py" +........ ---------------------------------------------------------------------- -Ran 4 tests in 0.013s +Ran 8 tests in 0.038s OK make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 94%] Built target test_log.py_run -make -f modules/bindings/tests/CMakeFiles/test_clustalw.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_clustalw.py_run.dir/depend +[ 96%] Built target test_pdbize.py_run +make -f modules/mol/alg/tests/CMakeFiles/test_hbond.py_run.dir/build.make modules/mol/alg/tests/CMakeFiles/test_hbond.py_run.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/bindings/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/tests/CMakeFiles/test_clustalw.py_run.dir/DependInfo.cmake --color= +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/tests/CMakeFiles/test_hbond.py_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/bindings/tests/CMakeFiles/test_clustalw.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_clustalw.py_run.dir/build +make -f modules/mol/alg/tests/CMakeFiles/test_hbond.py_run.dir/build.make modules/mol/alg/tests/CMakeFiles/test_hbond.py_run.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 94%] running checks test_clustalw.py -cd /build/openstructure-2.3.1/modules/bindings/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/bindings/tests/test_clustalw.py" -Could not find msms executable: ignoring unit tests -.make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -.....[ 94%] Built target test_msms.py_run -make -f modules/bindings/tests/CMakeFiles/test_hhblits.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_hhblits.py_run.dir/depend -.s +[ 96%] running checks test_hbond.py +cd /build/openstructure-2.3.1/modules/mol/alg/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/mol/alg/tests/test_hbond.py" +... ---------------------------------------------------------------------- -Ran 10 tests in 5.225s +Ran 2 tests in 0.069s -OK (skipped=1) -make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/bindings/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/tests/CMakeFiles/test_hhblits.py_run.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/bindings/tests/CMakeFiles/test_hhblits.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_hhblits.py_run.dir/build -make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 94%] running checks test_hhblits.py -cd /build/openstructure-2.3.1/modules/bindings/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/bindings/tests/test_hhblits.py" -.make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 94%] Built target test_io_mmcif.py_run -make -f modules/bindings/tests/CMakeFiles/test_blast.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_blast.py_run.dir/depend -make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/bindings/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/tests/CMakeFiles/test_blast.py_run.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/bindings/tests/CMakeFiles/test_blast.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_blast.py_run.dir/build -make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 94%] running checks test_blast.py -cd /build/openstructure-2.3.1/modules/bindings/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/bindings/tests/test_blast.py" -No HHblits installation found: skip unit tests -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 94%] Built target test_hhblits.py_run -make -f modules/bindings/tests/CMakeFiles/test_kclust.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_kclust.py_run.dir/depend -make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/bindings/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/tests/CMakeFiles/test_kclust.py_run.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/bindings/tests/CMakeFiles/test_kclust.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_kclust.py_run.dir/build -make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 94%] running checks test_kclust.py -cd /build/openstructure-2.3.1/modules/bindings/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/bindings/tests/test_kclust.py" -Could not find blast executable: ignoring unit tests -Could not find kClust executable: ignoring unit tests -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 94%] Built target test_blast.py_run -make -f modules/bindings/tests/CMakeFiles/test_naccess.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_naccess.py_run.dir/depend +OK make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[ 96%] Built target test_hbond.py_run +make -f modules/mol/alg/tests/CMakeFiles/test_accessibility.py_run.dir/build.make modules/mol/alg/tests/CMakeFiles/test_accessibility.py_run.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/bindings/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/tests/CMakeFiles/test_naccess.py_run.dir/DependInfo.cmake --color= +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/tests/CMakeFiles/test_accessibility.py_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/bindings/tests/CMakeFiles/test_naccess.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_naccess.py_run.dir/build +make -f modules/mol/alg/tests/CMakeFiles/test_accessibility.py_run.dir/build.make modules/mol/alg/tests/CMakeFiles/test_accessibility.py_run.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 94%] Built target test_kclust.py_run -make -f modules/bindings/tests/CMakeFiles/test_cadscore.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_cadscore.py_run.dir/depend +[ 96%] running checks test_accessibility.py +cd /build/openstructure-2.3.1/modules/mol/alg/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/mol/alg/tests/test_accessibility.py" +[ 96%] Building CXX object modules/mol/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/test_simulation.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/test_simulation.cc.o -MF CMakeFiles/ost_mol_mm_tests.dir/test_simulation.cc.o.d -o CMakeFiles/ost_mol_mm_tests.dir/test_simulation.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/tests/test_simulation.cc +.smake -f modules/mol/alg/tests/CMakeFiles/test_sec_struct.py_run.dir/build.make modules/mol/alg/tests/CMakeFiles/test_sec_struct.py_run.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/bindings/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/tests/CMakeFiles/test_cadscore.py_run.dir/DependInfo.cmake --color= -[ 95%] running checks test_naccess.py -cd /build/openstructure-2.3.1/modules/bindings/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/bindings/tests/test_naccess.py" +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/tests/CMakeFiles/test_sec_struct.py_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/bindings/tests/CMakeFiles/test_cadscore.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_cadscore.py_run.dir/build +make -f modules/mol/alg/tests/CMakeFiles/test_sec_struct.py_run.dir/build.make modules/mol/alg/tests/CMakeFiles/test_sec_struct.py_run.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 95%] running checks test_cadscore.py -cd /build/openstructure-2.3.1/modules/bindings/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/bindings/tests/test_cadscore.py" -. +[ 96%] running checks test_sec_struct.py +cd /build/openstructure-2.3.1/modules/mol/alg/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/mol/alg/tests/test_sec_struct.py" +.s ---------------------------------------------------------------------- -Ran 2 tests in 14.146s +Ran 1 test in 0.000s OK (skipped=1) -Could not find NACCESS, could not compare Accessiblity function... -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -.[ 95%] Built target test_accessibility.py_run -make -f modules/bindings/tests/CMakeFiles/test_tmtools.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_tmtools.py_run.dir/depend -make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/bindings/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/tests/CMakeFiles/test_tmtools.py_run.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/bindings/tests/CMakeFiles/test_tmtools.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_tmtools.py_run.dir/build -make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -Could not find NACCESS, could not test binding... -[ 95%] running checks test_tmtools.py -cd /build/openstructure-2.3.1/modules/bindings/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/bindings/tests/test_tmtools.py" -.make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -.[ 95%] Built target test_naccess.py_run -make -f modules/bindings/tests/CMakeFiles/test_ialign.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_ialign.py_run.dir/depend -make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/bindings/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/tests/CMakeFiles/test_ialign.py_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/bindings/tests/CMakeFiles/test_ialign.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_ialign.py_run.dir/build +[ 96%] Built target test_sec_struct.py_run +make -f modules/mol/mm/tests/CMakeFiles/test_antechamber.py_run.dir/build.make modules/mol/mm/tests/CMakeFiles/test_antechamber.py_run.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -.[ 95%] running checks test_ialign.py -cd /build/openstructure-2.3.1/modules/bindings/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/bindings/tests/test_ialign.py" -... ----------------------------------------------------------------------- -Ran 2 tests in 0.144s - -OK -Could not find tmalign executable: ignoring unit tests -Could not find tmalign executable: ignoring unit tests +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/mm/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/tests/CMakeFiles/test_antechamber.py_run.dir/DependInfo.cmake --color= .make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 95%] Built target test_tmtools.py_run -.make -f modules/bindings/tests/CMakeFiles/test_lga.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_lga.py_run.dir/depend +make -f modules/mol/mm/tests/CMakeFiles/test_antechamber.py_run.dir/build.make modules/mol/mm/tests/CMakeFiles/test_antechamber.py_run.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/bindings/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/tests/CMakeFiles/test_lga.py_run.dir/DependInfo.cmake --color= - +[ 96%] running checks test_antechamber.py +cd /build/openstructure-2.3.1/modules/mol/mm/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/mol/mm/tests/test_antechamber.py" +.... ---------------------------------------------------------------------- -Ran 7 tests in 5.139s +Ran 3 tests in 0.262s OK make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/bindings/tests/CMakeFiles/test_lga.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_lga.py_run.dir/build -make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 95%] running checks test_lga.py -cd /build/openstructure-2.3.1/modules/bindings/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/bindings/tests/test_lga.py" -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 95%] Built target test_clustalw.py_run -make -f modules/bindings/tests/CMakeFiles/test_hbplus.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_hbplus.py_run.dir/depend +[ 96%] Built target test_antechamber.py_run +make -f modules/seq/base/tests/CMakeFiles/test_seq.py_run.dir/build.make modules/seq/base/tests/CMakeFiles/test_seq.py_run.dir/depend +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_handle.hh:38, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/map_octree.hh:22, + from /build/openstructure-2.3.1/modules/gfx/tests/test_map_octree.cc:24: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/memory:63, + from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, + from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, + from /usr/include/boost/shared_ptr.hpp:17, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_handle.hh:32: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/bindings/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/tests/CMakeFiles/test_hbplus.py_run.dir/DependInfo.cmake --color= +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/seq/base/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/tests/CMakeFiles/test_seq.py_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/bindings/tests/CMakeFiles/test_hbplus.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_hbplus.py_run.dir/build +make -f modules/seq/base/tests/CMakeFiles/test_seq.py_run.dir/build.make modules/seq/base/tests/CMakeFiles/test_seq.py_run.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 95%] running checks test_hbplus.py -cd /build/openstructure-2.3.1/modules/bindings/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/bindings/tests/test_hbplus.py" -. ----------------------------------------------------------------------- -Ran 1 test in 0.122s - -OK -Could not find ialign master perl script: ignoring unit tests -. +[ 96%] running checks test_seq.py +cd /build/openstructure-2.3.1/modules/seq/base/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/seq/base/tests/test_seq.py" +................ ---------------------------------------------------------------------- -Ran 1 test in 0.063s +Ran 14 tests in 0.049s OK -Could not find lga executable: ignoring unit tests -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 95%] Built target test_lga.py_run -make -f modules/conop/tests/CMakeFiles/test_processor.py_run.dir/build.make modules/conop/tests/CMakeFiles/test_processor.py_run.dir/depend -make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/conop/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/tests/CMakeFiles/test_processor.py_run.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 95%] Built target test_ialign.py_run -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/conop/tests/CMakeFiles/test_processor.py_run.dir/build.make modules/conop/tests/CMakeFiles/test_processor.py_run.dir/build -make -f modules/db/tests/CMakeFiles/test_linear_db.py_run.dir/build.make modules/db/tests/CMakeFiles/test_linear_db.py_run.dir/depend -make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/db/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/tests/CMakeFiles/test_linear_db.py_run.dir/DependInfo.cmake --color= -[ 95%] running checks test_processor.py -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/db/tests/CMakeFiles/test_linear_db.py_run.dir/build.make modules/db/tests/CMakeFiles/test_linear_db.py_run.dir/build -cd /build/openstructure-2.3.1/modules/conop/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/conop/tests/test_processor.py" -make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -Could not find hbplus, could not test binding... -[ 95%] running checks test_linear_db.py -cd /build/openstructure-2.3.1/modules/db/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/db/tests/test_linear_db.py" make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 95%] Built target test_hbplus.py_run -make -f modules/geom/tests/CMakeFiles/test_geom.py_run.dir/build.make modules/geom/tests/CMakeFiles/test_geom.py_run.dir/depend +[ 96%] Built target test_seq.py_run +make -f modules/seq/alg/tests/CMakeFiles/test_renumber.py_run.dir/build.make modules/seq/alg/tests/CMakeFiles/test_renumber.py_run.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/geom/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/tests/CMakeFiles/test_geom.py_run.dir/DependInfo.cmake --color= -[ 95%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/test_iomanager.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/io/tests/CMakeFiles/ost_io_tests.dir/test_iomanager.cc.o -MF CMakeFiles/ost_io_tests.dir/test_iomanager.cc.o.d -o CMakeFiles/ost_io_tests.dir/test_iomanager.cc.o -c /build/openstructure-2.3.1/modules/io/tests/test_iomanager.cc +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/seq/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/tests/CMakeFiles/test_renumber.py_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/geom/tests/CMakeFiles/test_geom.py_run.dir/build.make modules/geom/tests/CMakeFiles/test_geom.py_run.dir/build +make -f modules/seq/alg/tests/CMakeFiles/test_renumber.py_run.dir/build.make modules/seq/alg/tests/CMakeFiles/test_renumber.py_run.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 95%] running checks test_geom.py -cd /build/openstructure-2.3.1/modules/geom/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/geom/tests/test_geom.py" -. ----------------------------------------------------------------------- -Ran 1 test in 0.000s - -OK -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 95%] Built target test_processor.py_run -make -f modules/gfx/tests/CMakeFiles/ost_gfx_tests_run.dir/build.make modules/gfx/tests/CMakeFiles/ost_gfx_tests_run.dir/depend -.make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/gfx/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/tests/CMakeFiles/ost_gfx_tests_run.dir/DependInfo.cmake --color= +[ 96%] running checks test_renumber.py +cd /build/openstructure-2.3.1/modules/seq/alg/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/seq/alg/tests/test_renumber.py" .In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/interaction.hh:34, - from /build/openstructure-2.3.1/modules/mol/mm/tests/test_block_modifiers.cc:21: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/settings.hh:31, + from /build/openstructure-2.3.1/modules/mol/mm/tests/test_forcefield.cc:21: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -31654,7 +31677,7 @@ from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, - from /build/openstructure-2.3.1/modules/mol/mm/tests/test_block_modifiers.cc:20: + from /build/openstructure-2.3.1/modules/mol/mm/tests/test_forcefield.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -31664,114 +31687,132 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +. +---------------------------------------------------------------------- +Ran 9 tests in 10.537s + +OK make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/gfx/tests/CMakeFiles/ost_gfx_tests_run.dir/build.make modules/gfx/tests/CMakeFiles/ost_gfx_tests_run.dir/build +[ 96%] Built target test_convenient_superpose.py_run +make -f modules/seq/alg/tests/CMakeFiles/test_local_align.py_run.dir/build.make modules/seq/alg/tests/CMakeFiles/test_local_align.py_run.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -. +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/seq/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/tests/CMakeFiles/test_local_align.py_run.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +make -f modules/seq/alg/tests/CMakeFiles/test_local_align.py_run.dir/build.make modules/seq/alg/tests/CMakeFiles/test_local_align.py_run.dir/build +make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[ 96%] running checks test_local_align.py +cd /build/openstructure-2.3.1/modules/seq/alg/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/seq/alg/tests/test_local_align.py" +........ ---------------------------------------------------------------------- -Ran 3 tests in 0.259s +Ran 8 tests in 0.251s OK make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -..[ 95%] running checks for module gfx -cd /build/openstructure-2.3.1/modules/gfx/tests && env OST_ROOT=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage /build/openstructure-2.3.1/obj-x86_64-linux-gnu/tests/ost_gfx_tests -...[ 95%] Built target test_linear_db.py_run -..make -f modules/gfx/tests/CMakeFiles/test_gfx.py_run.dir/build.make modules/gfx/tests/CMakeFiles/test_gfx.py_run.dir/depend +[ 96%] Built target test_renumber.py_run +make -f modules/seq/alg/tests/CMakeFiles/test_global_align.py_run.dir/build.make modules/seq/alg/tests/CMakeFiles/test_global_align.py_run.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/gfx/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/tests/CMakeFiles/test_gfx.py_run.dir/DependInfo.cmake --color= -. +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/seq/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/tests/CMakeFiles/test_global_align.py_run.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +make -f modules/seq/alg/tests/CMakeFiles/test_global_align.py_run.dir/build.make modules/seq/alg/tests/CMakeFiles/test_global_align.py_run.dir/build +make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[ 96%] running checks test_global_align.py +cd /build/openstructure-2.3.1/modules/seq/alg/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/seq/alg/tests/test_global_align.py" +... ---------------------------------------------------------------------- -Ran 8 tests in 0.202s +Ran 3 tests in 0.002s OK make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/gfx/tests/CMakeFiles/test_gfx.py_run.dir/build.make modules/gfx/tests/CMakeFiles/test_gfx.py_run.dir/build +[ 96%] Built target test_local_align.py_run +make -f modules/seq/alg/tests/CMakeFiles/test_semiglobal_align.py_run.dir/build.make modules/seq/alg/tests/CMakeFiles/test_semiglobal_align.py_run.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/seq/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/tests/CMakeFiles/test_semiglobal_align.py_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -Running 13 test cases... +make -f modules/seq/alg/tests/CMakeFiles/test_semiglobal_align.py_run.dir/build.make modules/seq/alg/tests/CMakeFiles/test_semiglobal_align.py_run.dir/build +make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[ 96%] running checks test_semiglobal_align.py +cd /build/openstructure-2.3.1/modules/seq/alg/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/seq/alg/tests/test_semiglobal_align.py" +... +---------------------------------------------------------------------- +Ran 3 tests in 0.002s -*** No errors detected -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 96%] running checks test_gfx.py -cd /build/openstructure-2.3.1/modules/gfx/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/gfx/tests/test_gfx.py" -[ 96%] Built target ost_gfx_tests_run -[ 96%] Built target test_geom.py_run -make -f modules/mol/base/tests/CMakeFiles/ost_mol_tests_run.dir/build.make modules/mol/base/tests/CMakeFiles/ost_mol_tests_run.dir/depend +OK +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[ 96%] Built target test_global_align.py_run +make -f modules/seq/alg/tests/CMakeFiles/test_weight_matrix.py_run.dir/build.make modules/seq/alg/tests/CMakeFiles/test_weight_matrix.py_run.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/base/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/tests/CMakeFiles/ost_mol_tests_run.dir/DependInfo.cmake --color= -[ 96%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/tests.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/io/tests/CMakeFiles/ost_io_tests.dir/tests.cc.o -MF CMakeFiles/ost_io_tests.dir/tests.cc.o.d -o CMakeFiles/ost_io_tests.dir/tests.cc.o -c /build/openstructure-2.3.1/modules/io/tests/tests.cc +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/seq/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/tests/CMakeFiles/test_weight_matrix.py_run.dir/DependInfo.cmake --color= +. +---------------------------------------------------------------------- +Ran 1 test in 0.006s + +OK make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/mol/base/tests/CMakeFiles/ost_mol_tests_run.dir/build.make modules/mol/base/tests/CMakeFiles/ost_mol_tests_run.dir/build +make -f modules/seq/alg/tests/CMakeFiles/test_weight_matrix.py_run.dir/build.make modules/seq/alg/tests/CMakeFiles/test_weight_matrix.py_run.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 96%] running checks for module mol -cd /build/openstructure-2.3.1/modules/mol/base/tests && env OST_ROOT=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage /build/openstructure-2.3.1/obj-x86_64-linux-gnu/tests/ost_mol_tests -..[ 96%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/test_star_parser.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/io/tests/CMakeFiles/ost_io_tests.dir/test_star_parser.cc.o -MF CMakeFiles/ost_io_tests.dir/test_star_parser.cc.o.d -o CMakeFiles/ost_io_tests.dir/test_star_parser.cc.o -c /build/openstructure-2.3.1/modules/io/tests/test_star_parser.cc -.... +[ 96%] running checks test_weight_matrix.py +cd /build/openstructure-2.3.1/modules/seq/alg/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/seq/alg/tests/test_weight_matrix.py" +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[ 96%] Built target test_semiglobal_align.py_run +make -f modules/seq/alg/tests/CMakeFiles/test_alignment_from_chain_view.py_run.dir/build.make modules/seq/alg/tests/CMakeFiles/test_alignment_from_chain_view.py_run.dir/depend +make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/seq/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/tests/CMakeFiles/test_alignment_from_chain_view.py_run.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +make -f modules/seq/alg/tests/CMakeFiles/test_alignment_from_chain_view.py_run.dir/build.make modules/seq/alg/tests/CMakeFiles/test_alignment_from_chain_view.py_run.dir/build +make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[ 96%] running checks test_alignment_from_chain_view.py +cd /build/openstructure-2.3.1/modules/seq/alg/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/seq/alg/tests/test_alignment_from_chain_view.py" +. ---------------------------------------------------------------------- -Ran 6 tests in 0.280s +Ran 1 test in 0.015s OK make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -Running 70 test cases... +[ 96%] Built target test_alignment_from_chain_view.py_run +[ 96%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/test_iomanager.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/io/tests/CMakeFiles/ost_io_tests.dir/test_iomanager.cc.o -MF CMakeFiles/ost_io_tests.dir/test_iomanager.cc.o.d -o CMakeFiles/ost_io_tests.dir/test_iomanager.cc.o -c /build/openstructure-2.3.1/modules/io/tests/test_iomanager.cc +.. +---------------------------------------------------------------------- +Ran 2 tests in 0.000s -*** No errors detected -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 96%] Built target test_gfx.py_run -make -f modules/mol/alg/tests/CMakeFiles/ost_mol_alg_tests_run.dir/build.make modules/mol/alg/tests/CMakeFiles/ost_mol_alg_tests_run.dir/depend +OK +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[ 97%] Linking CXX executable ../../../tests/ost_conop_tests +[ 97%] Built target test_weight_matrix.py_run +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_conop_tests.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro CMakeFiles/ost_conop_tests.dir/test_amino_acids.cc.o CMakeFiles/ost_conop_tests.dir/test_heuristic_conop.cc.o CMakeFiles/ost_conop_tests.dir/tests.cc.o CMakeFiles/ost_conop_tests.dir/test_rule_based_conop.cc.o CMakeFiles/ost_conop_tests.dir/helper.cc.o -o ../../../tests/ost_conop_tests -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib /usr/lib/x86_64-linux-gnu/libboost_unit_test_framework.so ../../../stage/lib/libost_conop.so.2.3.1 ../../../stage/lib/libost_db.so.2.3.1 /usr/lib/x86_64-linux-gnu/libsqlite3.so ../../../stage/lib/libost_seq.so.2.3.1 ../../../stage/lib/libost_mol.so.2.3.1 ../../../stage/lib/libost_info.so.2.3.1 ../../../stage/lib/libost_base.so.2.3.1 ../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so +[ 98%] Building CXX object modules/mol/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/tests.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/tests.cc.o -MF CMakeFiles/ost_mol_mm_tests.dir/tests.cc.o.d -o CMakeFiles/ost_mol_mm_tests.dir/tests.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/tests/tests.cc +[ 98%] Linking CXX executable ../../../../tests/ost_seq_alg_tests +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_seq_alg_tests.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro CMakeFiles/ost_seq_alg_tests.dir/test_distance_analysis.cc.o CMakeFiles/ost_seq_alg_tests.dir/test_merge_pairwise_alignments.cc.o CMakeFiles/ost_seq_alg_tests.dir/test_sequence_identity.cc.o CMakeFiles/ost_seq_alg_tests.dir/tests.cc.o -o ../../../../tests/ost_seq_alg_tests -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib /usr/lib/x86_64-linux-gnu/libboost_unit_test_framework.so ../../../../stage/lib/libost_io.so.2.3.1 ../../../../stage/lib/libost_mol_alg.so.2.3.1 ../../../../stage/lib/libost_seq_alg.so.2.3.1 ../../../../stage/lib/libost_conop.so.2.3.1 ../../../../stage/lib/libost_db.so.2.3.1 ../../../../stage/lib/libost_seq.so.2.3.1 ../../../../stage/lib/libost_mol.so.2.3.1 /usr/lib/x86_64-linux-gnu/libsqlite3.so /usr/lib/x86_64-linux-gnu/libboost_program_options.so /usr/lib/x86_64-linux-gnu/libboost_thread.so /usr/lib/x86_64-linux-gnu/libboost_chrono.so /usr/lib/x86_64-linux-gnu/libboost_date_time.so /usr/lib/x86_64-linux-gnu/libboost_atomic.so ../../../../stage/lib/libost_img_alg.so.2.3.1 ../../../../stage/lib/libost_img.so.2.3.1 ../../../../stage/lib/libost_info.so.2.3.1 ../../../../stage/lib/libost_base.so.2.3.1 ../../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libfftw3f_threads.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libtiff.so /usr/lib/x86_64-linux-gnu/libpng.so /usr/lib/x86_64-linux-gnu/libz.so +[ 98%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/tests.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/io/tests/CMakeFiles/ost_io_tests.dir/tests.cc.o -MF CMakeFiles/ost_io_tests.dir/tests.cc.o.d -o CMakeFiles/ost_io_tests.dir/tests.cc.o -c /build/openstructure-2.3.1/modules/io/tests/tests.cc +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[ 98%] Built target ost_conop_tests +make -f modules/conop/tests/CMakeFiles/ost_conop_tests_run.dir/build.make modules/conop/tests/CMakeFiles/ost_conop_tests_run.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/tests/CMakeFiles/ost_mol_alg_tests_run.dir/DependInfo.cmake --color= -[ 96%] Built target ost_mol_tests_run +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/conop/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/tests/CMakeFiles/ost_conop_tests_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/mol/alg/tests/CMakeFiles/ost_mol_alg_tests_run.dir/build.make modules/mol/alg/tests/CMakeFiles/ost_mol_alg_tests_run.dir/build +make -f modules/conop/tests/CMakeFiles/ost_conop_tests_run.dir/build.make modules/conop/tests/CMakeFiles/ost_conop_tests_run.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 97%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/test_mmcif_reader.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/io/tests/CMakeFiles/ost_io_tests.dir/test_mmcif_reader.cc.o -MF CMakeFiles/ost_io_tests.dir/test_mmcif_reader.cc.o.d -o CMakeFiles/ost_io_tests.dir/test_mmcif_reader.cc.o -c /build/openstructure-2.3.1/modules/io/tests/test_mmcif_reader.cc -[ 97%] running checks for module mol_alg -cd /build/openstructure-2.3.1/modules/mol/alg/tests && env OST_ROOT=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage /build/openstructure-2.3.1/obj-x86_64-linux-gnu/tests/ost_mol_alg_tests -[ 97%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/test_mmcif_info.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/io/tests/CMakeFiles/ost_io_tests.dir/test_mmcif_info.cc.o -MF CMakeFiles/ost_io_tests.dir/test_mmcif_info.cc.o.d -o CMakeFiles/ost_io_tests.dir/test_mmcif_info.cc.o -c /build/openstructure-2.3.1/modules/io/tests/test_mmcif_info.cc -Running 4 test cases... +[ 98%] running checks for module conop +cd /build/openstructure-2.3.1/modules/conop/tests && env OST_ROOT=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage /build/openstructure-2.3.1/obj-x86_64-linux-gnu/tests/ost_conop_tests +Running 16 test cases... +unable to open database file +unable to open database file +unable to open database file +unable to open database file +unable to open database file +unable to open database file +unable to open database file +unable to open database file *** No errors detected make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 97%] Built target ost_mol_alg_tests_run -[ 97%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/test_io_img.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/io/tests/CMakeFiles/ost_io_tests.dir/test_io_img.cc.o -MF CMakeFiles/ost_io_tests.dir/test_io_img.cc.o.d -o CMakeFiles/ost_io_tests.dir/test_io_img.cc.o -c /build/openstructure-2.3.1/modules/io/tests/test_io_img.cc -[ 98%] Linking CXX executable ../../../tests/ost_conop_tests -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_conop_tests.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro CMakeFiles/ost_conop_tests.dir/test_amino_acids.cc.o CMakeFiles/ost_conop_tests.dir/test_heuristic_conop.cc.o CMakeFiles/ost_conop_tests.dir/tests.cc.o CMakeFiles/ost_conop_tests.dir/test_rule_based_conop.cc.o CMakeFiles/ost_conop_tests.dir/helper.cc.o -o ../../../tests/ost_conop_tests -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib /usr/lib/x86_64-linux-gnu/libboost_unit_test_framework.so ../../../stage/lib/libost_conop.so.2.3.1 ../../../stage/lib/libost_db.so.2.3.1 /usr/lib/x86_64-linux-gnu/libsqlite3.so ../../../stage/lib/libost_seq.so.2.3.1 ../../../stage/lib/libost_mol.so.2.3.1 ../../../stage/lib/libost_info.so.2.3.1 ../../../stage/lib/libost_base.so.2.3.1 ../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/topology.hh:31, - from /build/openstructure-2.3.1/modules/mol/mm/tests/test_topology.cc:21: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/12/string:45, - from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, - from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, - from /usr/include/boost/test/detail/global_typedef.hpp:15, - from /usr/include/boost/test/tree/observer.hpp:17, - from /usr/include/boost/test/unit_test_log.hpp:18, - from /usr/include/boost/test/tools/old/impl.hpp:19, - from /usr/include/boost/test/test_tools.hpp:46, - from /usr/include/boost/test/unit_test.hpp:18, - from /build/openstructure-2.3.1/modules/mol/mm/tests/test_topology.cc:20: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ +[ 98%] Built target ost_conop_tests_run +[ 98%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/test_star_parser.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/io/tests/CMakeFiles/ost_io_tests.dir/test_star_parser.cc.o -MF CMakeFiles/ost_io_tests.dir/test_star_parser.cc.o.d -o CMakeFiles/ost_io_tests.dir/test_star_parser.cc.o -c /build/openstructure-2.3.1/modules/io/tests/test_star_parser.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -31779,7 +31820,7 @@ from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/settings.hh:31, - from /build/openstructure-2.3.1/modules/mol/mm/tests/test_forcefield.cc:21: + from /build/openstructure-2.3.1/modules/mol/mm/tests/test_simulation.cc:21: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -31792,7 +31833,7 @@ from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, - from /build/openstructure-2.3.1/modules/mol/mm/tests/test_forcefield.cc:20: + from /build/openstructure-2.3.1/modules/mol/mm/tests/test_simulation.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -31803,31 +31844,44 @@ 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 98%] Built target ost_conop_tests -make -f modules/conop/tests/CMakeFiles/ost_conop_tests_run.dir/build.make modules/conop/tests/CMakeFiles/ost_conop_tests_run.dir/depend +[ 98%] Built target ost_seq_alg_tests +make -f modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests_run.dir/build.make modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests_run.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/conop/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/tests/CMakeFiles/ost_conop_tests_run.dir/DependInfo.cmake --color= +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/seq/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/conop/tests/CMakeFiles/ost_conop_tests_run.dir/build.make modules/conop/tests/CMakeFiles/ost_conop_tests_run.dir/build +make -f modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests_run.dir/build.make modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests_run.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 98%] running checks for module conop -cd /build/openstructure-2.3.1/modules/conop/tests && env OST_ROOT=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage /build/openstructure-2.3.1/obj-x86_64-linux-gnu/tests/ost_conop_tests -Running 16 test cases... -unable to open database file -unable to open database file -unable to open database file -unable to open database file -unable to open database file -unable to open database file -unable to open database file -unable to open database file +[ 98%] running checks for module seq_alg +cd /build/openstructure-2.3.1/modules/seq/alg/tests && env OST_ROOT=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage /build/openstructure-2.3.1/obj-x86_64-linux-gnu/tests/ost_seq_alg_tests +Running 19 test cases... *** No errors detected make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[ 98%] Built target ost_conop_tests_run -[ 98%] Building CXX object modules/mol/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/test_simulation.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/test_simulation.cc.o -MF CMakeFiles/ost_mol_mm_tests.dir/test_simulation.cc.o.d -o CMakeFiles/ost_mol_mm_tests.dir/test_simulation.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/tests/test_simulation.cc -[ 98%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/test_exceptions.cc.o +[ 98%] Built target ost_seq_alg_tests_run +[100%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/test_mmcif_reader.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/io/tests/CMakeFiles/ost_io_tests.dir/test_mmcif_reader.cc.o -MF CMakeFiles/ost_io_tests.dir/test_mmcif_reader.cc.o.d -o CMakeFiles/ost_io_tests.dir/test_mmcif_reader.cc.o -c /build/openstructure-2.3.1/modules/io/tests/test_mmcif_reader.cc +. +---------------------------------------------------------------------- +Ran 2 tests in 19.938s + +OK (skipped=1) +Could not find NACCESS, could not compare Accessiblity function... +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[100%] Built target test_accessibility.py_run +[100%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/test_mmcif_info.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/io/tests/CMakeFiles/ost_io_tests.dir/test_mmcif_info.cc.o -MF CMakeFiles/ost_io_tests.dir/test_mmcif_info.cc.o.d -o CMakeFiles/ost_io_tests.dir/test_mmcif_info.cc.o -c /build/openstructure-2.3.1/modules/io/tests/test_mmcif_info.cc +[100%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/test_io_img.cc.o +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/io/tests/CMakeFiles/ost_io_tests.dir/test_io_img.cc.o -MF CMakeFiles/ost_io_tests.dir/test_io_img.cc.o.d -o CMakeFiles/ost_io_tests.dir/test_io_img.cc.o -c /build/openstructure-2.3.1/modules/io/tests/test_io_img.cc +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, + from /build/openstructure-2.3.1/modules/mol/mm/tests/test_simulation.cc:29: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 32 | : public std::iterator{ + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[100%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/test_exceptions.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/io/tests/CMakeFiles/ost_io_tests.dir/test_exceptions.cc.o -MF CMakeFiles/ost_io_tests.dir/test_exceptions.cc.o.d -o CMakeFiles/ost_io_tests.dir/test_exceptions.cc.o -c /build/openstructure-2.3.1/modules/io/tests/test_exceptions.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/mmcif_info.hh:25, @@ -31849,18 +31903,28 @@ 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/modeller.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/topology_creator.hh:37, - from /build/openstructure-2.3.1/modules/mol/mm/tests/test_topology.cc:22: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/io_manager.hh:28, + from /build/openstructure-2.3.1/modules/io/tests/test_iomanager.cc:22: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ +In file included from /usr/include/c++/12/string:45, + from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, + from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, + from /usr/include/boost/test/detail/global_typedef.hpp:15, + from /usr/include/boost/test/tree/observer.hpp:17, + from /usr/include/boost/test/unit_test_log.hpp:18, + from /usr/include/boost/test/tools/old/impl.hpp:19, + from /usr/include/boost/test/test_tools.hpp:46, + from /usr/include/boost/test/unit_test.hpp:18, + from /build/openstructure-2.3.1/modules/io/tests/test_iomanager.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[100%] Building CXX object modules/mol/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/tests.cc.o -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/tests.cc.o -MF CMakeFiles/ost_mol_mm_tests.dir/tests.cc.o.d -o CMakeFiles/ost_mol_mm_tests.dir/tests.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/tests/tests.cc +[100%] Linking CXX executable ../../../tests/ost_gfx_tests +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_gfx_tests.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro CMakeFiles/ost_gfx_tests.dir/tests.cc.o CMakeFiles/ost_gfx_tests.dir/test_gfx_node.cc.o CMakeFiles/ost_gfx_tests.dir/test_color.cc.o CMakeFiles/ost_gfx_tests.dir/test_map_octree.cc.o -o ../../../tests/ost_gfx_tests -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib /usr/lib/x86_64-linux-gnu/libboost_unit_test_framework.so ../../../stage/lib/libost_gfx.so.2.3.1 ../../../stage/lib/libost_io.so.2.3.1 /usr/lib/x86_64-linux-gnu/libOpenGL.so /usr/lib/x86_64-linux-gnu/libGLX.so /usr/lib/x86_64-linux-gnu/libGLU.so ../../../stage/lib/libost_mol_alg.so.2.3.1 ../../../stage/lib/libost_conop.so.2.3.1 ../../../stage/lib/libost_db.so.2.3.1 /usr/lib/x86_64-linux-gnu/libsqlite3.so ../../../stage/lib/libost_img_alg.so.2.3.1 ../../../stage/lib/libost_img.so.2.3.1 /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libfftw3f_threads.so /usr/lib/x86_64-linux-gnu/libboost_program_options.so /usr/lib/x86_64-linux-gnu/libboost_thread.so /usr/lib/x86_64-linux-gnu/libboost_chrono.so /usr/lib/x86_64-linux-gnu/libboost_date_time.so /usr/lib/x86_64-linux-gnu/libboost_atomic.so ../../../stage/lib/libost_seq_alg.so.2.3.1 ../../../stage/lib/libost_seq.so.2.3.1 ../../../stage/lib/libost_mol.so.2.3.1 ../../../stage/lib/libost_info.so.2.3.1 ../../../stage/lib/libost_base.so.2.3.1 ../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libtiff.so /usr/lib/x86_64-linux-gnu/libpng.so /usr/lib/x86_64-linux-gnu/libz.so In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -31884,61 +31948,6 @@ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/mmcif_reader.hh:24, - from /build/openstructure-2.3.1/modules/io/tests/test_mmcif_reader.cc:26: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/12/string:45, - from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, - from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, - from /usr/include/boost/test/detail/global_typedef.hpp:15, - from /usr/include/boost/test/tree/observer.hpp:17, - from /usr/include/boost/test/unit_test_log.hpp:18, - from /usr/include/boost/test/tools/old/impl.hpp:19, - from /usr/include/boost/test/test_tools.hpp:46, - from /usr/include/boost/test/unit_test.hpp:18, - from /build/openstructure-2.3.1/modules/io/tests/test_mmcif_reader.cc:21: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/mmcif_reader.hh:25: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 32 | : public std::iterator{ - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/io_manager.hh:28, - from /build/openstructure-2.3.1/modules/io/tests/test_iomanager.cc:22: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 32 | : public std::iterator{ - | ^~~~~~~~ -In file included from /usr/include/c++/12/string:45, - from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, - from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, - from /usr/include/boost/test/detail/global_typedef.hpp:15, - from /usr/include/boost/test/tree/observer.hpp:17, - from /usr/include/boost/test/unit_test_log.hpp:18, - from /usr/include/boost/test/tools/old/impl.hpp:19, - from /usr/include/boost/test/test_tools.hpp:46, - from /usr/include/boost/test/unit_test.hpp:18, - from /build/openstructure-2.3.1/modules/io/tests/test_iomanager.cc:20: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, @@ -31956,6 +31965,21 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[100%] Built target ost_gfx_tests +make -f modules/gfx/tests/CMakeFiles/ost_gfx_tests_run.dir/build.make modules/gfx/tests/CMakeFiles/ost_gfx_tests_run.dir/depend +make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/gfx/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/tests/CMakeFiles/ost_gfx_tests_run.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +make -f modules/gfx/tests/CMakeFiles/ost_gfx_tests_run.dir/build.make modules/gfx/tests/CMakeFiles/ost_gfx_tests_run.dir/build +make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[100%] running checks for module gfx +cd /build/openstructure-2.3.1/modules/gfx/tests && env OST_ROOT=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage /build/openstructure-2.3.1/obj-x86_64-linux-gnu/tests/ost_gfx_tests +Running 13 test cases... + +*** No errors detected +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[100%] Built target ost_gfx_tests_run In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -31990,11 +32014,8 @@ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, - from /build/openstructure-2.3.1/modules/io/tests/test_star_parser.cc:27: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/mmcif_reader.hh:24, + from /build/openstructure-2.3.1/modules/io/tests/test_mmcif_reader.cc:26: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -32007,7 +32028,7 @@ from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, - from /build/openstructure-2.3.1/modules/io/tests/test_star_parser.cc:23: + from /build/openstructure-2.3.1/modules/io/tests/test_mmcif_reader.cc:21: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -32017,14 +32038,22 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/mmcif_reader.hh:25: +/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 32 | : public std::iterator{ + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/settings.hh:31, - from /build/openstructure-2.3.1/modules/mol/mm/tests/test_simulation.cc:21: + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, + from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, + from /build/openstructure-2.3.1/modules/io/tests/test_star_parser.cc:27: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -32037,7 +32066,7 @@ from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, - from /build/openstructure-2.3.1/modules/mol/mm/tests/test_simulation.cc:20: + from /build/openstructure-2.3.1/modules/io/tests/test_star_parser.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -32078,59 +32107,18 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, - from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, - from /build/openstructure-2.3.1/modules/mol/mm/tests/test_simulation.cc:29: -/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 32 | : public std::iterator{ - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -.......................Matplotlib is building the font cache; this may take a moment. -.............../usr/lib/python3.11/unittest/case.py:579: ResourceWarning: unclosed file <_io.BufferedReader name='testfiles/enrichment-out.png'> - if method() is not None: -ResourceWarning: Enable tracemalloc to get the object allocation traceback -../usr/lib/python3.11/unittest/case.py:579: ResourceWarning: unclosed file <_io.BufferedReader name='testfiles/roc-out.png'> - if method() is not None: -ResourceWarning: Enable tracemalloc to get the object allocation traceback -./usr/lib/python3.11/unittest/case.py:579: ResourceWarning: unclosed file <_io.BufferedReader name='testfiles/roc-same-val-out.png'> - if method() is not None: -ResourceWarning: Enable tracemalloc to get the object allocation traceback -................./build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ost/table.py:2186: DeprecationWarning: scipy.isnan is deprecated and will be removed in SciPy 2.0.0, use numpy.isnan instead - if scipy.isnan(correl): -......................... ----------------------------------------------------------------------- -Ran 83 tests in 22.929s - -OK -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[100%] Built target test_table.py_run . ---------------------------------------------------------------------- -Ran 2 tests in 91.890s +Ran 2 tests in 133.069s OK Could not find CAD score classic executables: ignoring unit tests make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [100%] Built target test_cadscore.py_run -[100%] Linking CXX executable ../../../tests/ost_io_tests -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_io_tests.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro CMakeFiles/ost_io_tests.dir/test_clustal.cc.o CMakeFiles/ost_io_tests.dir/test_io_pdb.cc.o CMakeFiles/ost_io_tests.dir/test_io_crd.cc.o CMakeFiles/ost_io_tests.dir/test_io_dcd.cc.o CMakeFiles/ost_io_tests.dir/test_io_sdf.cc.o CMakeFiles/ost_io_tests.dir/test_io_sequence_profile.cc.o CMakeFiles/ost_io_tests.dir/test_pir.cc.o CMakeFiles/ost_io_tests.dir/test_iomanager.cc.o CMakeFiles/ost_io_tests.dir/tests.cc.o CMakeFiles/ost_io_tests.dir/test_star_parser.cc.o CMakeFiles/ost_io_tests.dir/test_mmcif_reader.cc.o CMakeFiles/ost_io_tests.dir/test_mmcif_info.cc.o CMakeFiles/ost_io_tests.dir/test_io_img.cc.o CMakeFiles/ost_io_tests.dir/test_exceptions.cc.o -o ../../../tests/ost_io_tests -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib /usr/lib/x86_64-linux-gnu/libboost_unit_test_framework.so ../../../stage/lib/libost_io.so.2.3.1 ../../../stage/lib/libost_mol_alg.so.2.3.1 ../../../stage/lib/libost_conop.so.2.3.1 ../../../stage/lib/libost_db.so.2.3.1 /usr/lib/x86_64-linux-gnu/libsqlite3.so /usr/lib/x86_64-linux-gnu/libboost_program_options.so /usr/lib/x86_64-linux-gnu/libboost_thread.so /usr/lib/x86_64-linux-gnu/libboost_chrono.so /usr/lib/x86_64-linux-gnu/libboost_date_time.so /usr/lib/x86_64-linux-gnu/libboost_atomic.so ../../../stage/lib/libost_seq_alg.so.2.3.1 ../../../stage/lib/libost_seq.so.2.3.1 ../../../stage/lib/libost_mol.so.2.3.1 ../../../stage/lib/libost_img_alg.so.2.3.1 ../../../stage/lib/libost_img.so.2.3.1 ../../../stage/lib/libost_info.so.2.3.1 ../../../stage/lib/libost_base.so.2.3.1 ../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libfftw3f_threads.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libtiff.so /usr/lib/x86_64-linux-gnu/libpng.so /usr/lib/x86_64-linux-gnu/libz.so [100%] Linking CXX executable ../../../../tests/ost_mol_mm_tests cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_mol_mm_tests.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro CMakeFiles/ost_mol_mm_tests.dir/test_interaction.cc.o CMakeFiles/ost_mol_mm_tests.dir/test_block.cc.o CMakeFiles/ost_mol_mm_tests.dir/test_block_modifiers.cc.o CMakeFiles/ost_mol_mm_tests.dir/test_topology.cc.o CMakeFiles/ost_mol_mm_tests.dir/test_forcefield.cc.o CMakeFiles/ost_mol_mm_tests.dir/test_simulation.cc.o CMakeFiles/ost_mol_mm_tests.dir/tests.cc.o -o ../../../../tests/ost_mol_mm_tests -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib /usr/lib/x86_64-linux-gnu/libboost_unit_test_framework.so ../../../../stage/lib/libost_mol_mm.so.2.3.1 ../../../../stage/lib/libost_io.so.2.3.1 ../../../../stage/lib/libost_mol_alg.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_program_options.so ../../../../stage/lib/libost_conop.so.2.3.1 ../../../../stage/lib/libost_db.so.2.3.1 /usr/lib/x86_64-linux-gnu/libsqlite3.so /usr/lib/x86_64-linux-gnu/libboost_thread.so /usr/lib/x86_64-linux-gnu/libboost_chrono.so /usr/lib/x86_64-linux-gnu/libboost_date_time.so /usr/lib/x86_64-linux-gnu/libboost_atomic.so ../../../../stage/lib/libost_seq_alg.so.2.3.1 ../../../../stage/lib/libost_seq.so.2.3.1 ../../../../stage/lib/libost_mol.so.2.3.1 ../../../../stage/lib/libost_img_alg.so.2.3.1 ../../../../stage/lib/libost_img.so.2.3.1 ../../../../stage/lib/libost_info.so.2.3.1 ../../../../stage/lib/libost_base.so.2.3.1 ../../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libfftw3f_threads.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libtiff.so /usr/lib/x86_64-linux-gnu/libpng.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libOpenMM.so make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[100%] Built target ost_io_tests -make -f modules/io/tests/CMakeFiles/ost_io_tests_run.dir/build.make modules/io/tests/CMakeFiles/ost_io_tests_run.dir/depend -make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/io/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/tests/CMakeFiles/ost_io_tests_run.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -make -f modules/io/tests/CMakeFiles/ost_io_tests_run.dir/build.make modules/io/tests/CMakeFiles/ost_io_tests_run.dir/build -make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[100%] running checks for module io -cd /build/openstructure-2.3.1/modules/io/tests && env OST_ROOT=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage /build/openstructure-2.3.1/obj-x86_64-linux-gnu/tests/ost_io_tests -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [100%] Built target ost_mol_mm_tests make -f modules/mol/mm/tests/CMakeFiles/ost_mol_mm_tests_run.dir/build.make modules/mol/mm/tests/CMakeFiles/ost_mol_mm_tests_run.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' @@ -32140,6 +32128,24 @@ make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [100%] running checks for module mol_mm cd /build/openstructure-2.3.1/modules/mol/mm/tests && env OST_ROOT=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage /build/openstructure-2.3.1/obj-x86_64-linux-gnu/tests/ost_mol_mm_tests +Running 13 test cases... + +*** No errors detected +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[100%] Built target ost_mol_mm_tests_run +[100%] Linking CXX executable ../../../tests/ost_io_tests +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_io_tests.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro CMakeFiles/ost_io_tests.dir/test_clustal.cc.o CMakeFiles/ost_io_tests.dir/test_io_pdb.cc.o CMakeFiles/ost_io_tests.dir/test_io_crd.cc.o CMakeFiles/ost_io_tests.dir/test_io_dcd.cc.o CMakeFiles/ost_io_tests.dir/test_io_sdf.cc.o CMakeFiles/ost_io_tests.dir/test_io_sequence_profile.cc.o CMakeFiles/ost_io_tests.dir/test_pir.cc.o CMakeFiles/ost_io_tests.dir/test_iomanager.cc.o CMakeFiles/ost_io_tests.dir/tests.cc.o CMakeFiles/ost_io_tests.dir/test_star_parser.cc.o CMakeFiles/ost_io_tests.dir/test_mmcif_reader.cc.o CMakeFiles/ost_io_tests.dir/test_mmcif_info.cc.o CMakeFiles/ost_io_tests.dir/test_io_img.cc.o CMakeFiles/ost_io_tests.dir/test_exceptions.cc.o -o ../../../tests/ost_io_tests -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib /usr/lib/x86_64-linux-gnu/libboost_unit_test_framework.so ../../../stage/lib/libost_io.so.2.3.1 ../../../stage/lib/libost_mol_alg.so.2.3.1 ../../../stage/lib/libost_conop.so.2.3.1 ../../../stage/lib/libost_db.so.2.3.1 /usr/lib/x86_64-linux-gnu/libsqlite3.so /usr/lib/x86_64-linux-gnu/libboost_program_options.so /usr/lib/x86_64-linux-gnu/libboost_thread.so /usr/lib/x86_64-linux-gnu/libboost_chrono.so /usr/lib/x86_64-linux-gnu/libboost_date_time.so /usr/lib/x86_64-linux-gnu/libboost_atomic.so ../../../stage/lib/libost_seq_alg.so.2.3.1 ../../../stage/lib/libost_seq.so.2.3.1 ../../../stage/lib/libost_mol.so.2.3.1 ../../../stage/lib/libost_img_alg.so.2.3.1 ../../../stage/lib/libost_img.so.2.3.1 ../../../stage/lib/libost_info.so.2.3.1 ../../../stage/lib/libost_base.so.2.3.1 ../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libfftw3f_threads.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libtiff.so /usr/lib/x86_64-linux-gnu/libpng.so /usr/lib/x86_64-linux-gnu/libz.so +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[100%] Built target ost_io_tests +make -f modules/io/tests/CMakeFiles/ost_io_tests_run.dir/build.make modules/io/tests/CMakeFiles/ost_io_tests_run.dir/depend +make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/io/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/tests/CMakeFiles/ost_io_tests_run.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +make -f modules/io/tests/CMakeFiles/ost_io_tests_run.dir/build.make modules/io/tests/CMakeFiles/ost_io_tests_run.dir/build +make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' +[100%] running checks for module io +cd /build/openstructure-2.3.1/modules/io/tests && env OST_ROOT=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage /build/openstructure-2.3.1/obj-x86_64-linux-gnu/tests/ost_io_tests Running 159 test cases... unable to open database file WARNING: skipping SEQRES import unit test. Compound lib is required @@ -32152,11 +32158,6 @@ *** No errors detected make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [100%] Built target ost_io_tests_run -Running 13 test cases... - -*** No errors detected -make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' -[100%] Built target ost_mol_mm_tests_run make -f CMakeFiles/check.dir/build.make CMakeFiles/check.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1 /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/CMakeFiles/check.dir/DependInfo.cmake --color= @@ -32176,7 +32177,7 @@ debian/rules override_dh_auto_install make[1]: Entering directory '/build/openstructure-2.3.1' dh_auto_install - cd obj-x86_64-linux-gnu && make -j16 install DESTDIR=/build/openstructure-2.3.1/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd obj-x86_64-linux-gnu && make -j15 install DESTDIR=/build/openstructure-2.3.1/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/openstructure-2.3.1 -B/build/openstructure-2.3.1/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -33291,47 +33292,47 @@ dpkg-gencontrol: warning: Provides field of package python3-ost: substitution variable ${python3:Provides} used, but is not defined dh_md5sums dh_builddeb -dpkg-deb: building package 'openstructure' in '../openstructure_2.3.1-9_amd64.deb'. -dpkg-deb: building package 'libost-mol-mm-dev' in '../libost-mol-mm-dev_2.3.1-9_amd64.deb'. -dpkg-deb: building package 'libost-gui2.3' in '../libost-gui2.3_2.3.1-9_amd64.deb'. -dpkg-deb: building package 'libost-io2.3' in '../libost-io2.3_2.3.1-9_amd64.deb'. -dpkg-deb: building package 'libost-geom-dev' in '../libost-geom-dev_2.3.1-9_amd64.deb'. -dpkg-deb: building package 'libost-base-dev' in '../libost-base-dev_2.3.1-9_amd64.deb'. +dpkg-deb: building package 'libost-base2.3' in '../libost-base2.3_2.3.1-9_amd64.deb'. dpkg-deb: building package 'libost-img2.3' in '../libost-img2.3_2.3.1-9_amd64.deb'. dpkg-deb: building package 'libost-geom2.3' in '../libost-geom2.3_2.3.1-9_amd64.deb'. -dpkg-deb: building package 'libost-base2.3' in '../libost-base2.3_2.3.1-9_amd64.deb'. dpkg-deb: building package 'libost-conop2.3' in '../libost-conop2.3_2.3.1-9_amd64.deb'. +dpkg-deb: building package 'libost-gui2.3' in '../libost-gui2.3_2.3.1-9_amd64.deb'. +dpkg-deb: building package 'openstructure' in '../openstructure_2.3.1-9_amd64.deb'. +dpkg-deb: building package 'libost-io2.3' in '../libost-io2.3_2.3.1-9_amd64.deb'. +dpkg-deb: building package 'libost-base-dev' in '../libost-base-dev_2.3.1-9_amd64.deb'. +dpkg-deb: building package 'libost-mol-mm-dev' in '../libost-mol-mm-dev_2.3.1-9_amd64.deb'. +dpkg-deb: building package 'libost-geom-dev' in '../libost-geom-dev_2.3.1-9_amd64.deb'. +dpkg-deb: building package 'libost-img-dev' in '../libost-img-dev_2.3.1-9_amd64.deb'. dpkg-deb: building package 'libost-mol-mm2.3' in '../libost-mol-mm2.3_2.3.1-9_amd64.deb'. dpkg-deb: building package 'libost-seq-alg2.3' in '../libost-seq-alg2.3_2.3.1-9_amd64.deb'. -dpkg-deb: building package 'libost-img-dev' in '../libost-img-dev_2.3.1-9_amd64.deb'. -dpkg-deb: building package 'libost-base2.3-dbgsym' in '../libost-base2.3-dbgsym_2.3.1-9_amd64.deb'. -dpkg-deb: building package 'libost-mol-dev' in '../libost-mol-dev_2.3.1-9_amd64.deb'. -dpkg-deb: building package 'libost-gfx-dev' in '../libost-gfx-dev_2.3.1-9_amd64.deb'. dpkg-deb: building package 'libost-bindings-dev' in '../libost-bindings-dev_2.3.1-9_amd64.deb'. -dpkg-deb: building package 'libost-info-dev' in '../libost-info-dev_2.3.1-9_amd64.deb'. +dpkg-deb: building package 'libost-gfx-dev' in '../libost-gfx-dev_2.3.1-9_amd64.deb'. +dpkg-deb: building package 'libost-mol-dev' in '../libost-mol-dev_2.3.1-9_amd64.deb'. +dpkg-deb: building package 'libost-base2.3-dbgsym' in '../libost-base2.3-dbgsym_2.3.1-9_amd64.deb'. dpkg-deb: building package 'libost-geom2.3-dbgsym' in '../libost-geom2.3-dbgsym_2.3.1-9_amd64.deb'. dpkg-deb: building package 'libost-conop-dev' in '../libost-conop-dev_2.3.1-9_amd64.deb'. -dpkg-deb: building package 'libost-bindings2.3' in '../libost-bindings2.3_2.3.1-9_amd64.deb'. -dpkg-deb: building package 'libost-io-dev' in '../libost-io-dev_2.3.1-9_amd64.deb'. +dpkg-deb: building package 'libost-info-dev' in '../libost-info-dev_2.3.1-9_amd64.deb'. dpkg-deb: building package 'libost-db-dev' in '../libost-db-dev_2.3.1-9_amd64.deb'. -dpkg-deb: building package 'libost-img2.3-dbgsym' in '../libost-img2.3-dbgsym_2.3.1-9_amd64.deb'. +dpkg-deb: building package 'libost-io-dev' in '../libost-io-dev_2.3.1-9_amd64.deb'. +dpkg-deb: building package 'libost-bindings2.3' in '../libost-bindings2.3_2.3.1-9_amd64.deb'. dpkg-deb: building package 'libost-seq-alg-dev' in '../libost-seq-alg-dev_2.3.1-9_amd64.deb'. dpkg-deb: building package 'libost-bindings2.3-dbgsym' in '../libost-bindings2.3-dbgsym_2.3.1-9_amd64.deb'. +dpkg-deb: building package 'libost-img2.3-dbgsym' in '../libost-img2.3-dbgsym_2.3.1-9_amd64.deb'. dpkg-deb: building package 'libost-mol-alg-dev' in '../libost-mol-alg-dev_2.3.1-9_amd64.deb'. dpkg-deb: building package 'libost-gui-dev' in '../libost-gui-dev_2.3.1-9_amd64.deb'. dpkg-deb: building package 'libost-conop2.3-dbgsym' in '../libost-conop2.3-dbgsym_2.3.1-9_amd64.deb'. -dpkg-deb: building package 'libost-img-alg-dev' in '../libost-img-alg-dev_2.3.1-9_amd64.deb'. -dpkg-deb: building package 'libost-gfx2.3' in '../libost-gfx2.3_2.3.1-9_amd64.deb'. dpkg-deb: building package 'libost-seq-alg2.3-dbgsym' in '../libost-seq-alg2.3-dbgsym_2.3.1-9_amd64.deb'. dpkg-deb: building package 'libost-mol-mm2.3-dbgsym' in '../libost-mol-mm2.3-dbgsym_2.3.1-9_amd64.deb'. +dpkg-deb: building package 'libost-gfx2.3' in '../libost-gfx2.3_2.3.1-9_amd64.deb'. +dpkg-deb: building package 'libost-img-alg-dev' in '../libost-img-alg-dev_2.3.1-9_amd64.deb'. dpkg-deb: building package 'libost-gui2.3-dbgsym' in '../libost-gui2.3-dbgsym_2.3.1-9_amd64.deb'. -dpkg-deb: building package 'libost-gfx2.3-dbgsym' in '../libost-gfx2.3-dbgsym_2.3.1-9_amd64.deb'. dpkg-deb: building package 'libost-info2.3' in '../libost-info2.3_2.3.1-9_amd64.deb'. -dpkg-deb: building package 'libost-seq2.3' in '../libost-seq2.3_2.3.1-9_amd64.deb'. +dpkg-deb: building package 'libost-gfx2.3-dbgsym' in '../libost-gfx2.3-dbgsym_2.3.1-9_amd64.deb'. dpkg-deb: building package 'libost-info2.3-dbgsym' in '../libost-info2.3-dbgsym_2.3.1-9_amd64.deb'. +dpkg-deb: building package 'libost-seq2.3' in '../libost-seq2.3_2.3.1-9_amd64.deb'. dpkg-deb: building package 'libost-seq-dev' in '../libost-seq-dev_2.3.1-9_amd64.deb'. -dpkg-deb: building package 'libost-seq2.3-dbgsym' in '../libost-seq2.3-dbgsym_2.3.1-9_amd64.deb'. dpkg-deb: building package 'libost-io2.3-dbgsym' in '../libost-io2.3-dbgsym_2.3.1-9_amd64.deb'. +dpkg-deb: building package 'libost-seq2.3-dbgsym' in '../libost-seq2.3-dbgsym_2.3.1-9_amd64.deb'. dpkg-deb: building package 'libost-db2.3' in '../libost-db2.3_2.3.1-9_amd64.deb'. dpkg-deb: building package 'libost-db2.3-dbgsym' in '../libost-db2.3-dbgsym_2.3.1-9_amd64.deb'. dpkg-deb: building package 'libost-mol2.3' in '../libost-mol2.3_2.3.1-9_amd64.deb'. @@ -33350,12 +33351,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/1244763/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1244763/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/2995182 and its subdirectories -I: Current time: Fri Jul 5 01:09:47 -12 2024 -I: pbuilder-time-stamp: 1720184987 +I: removing directory /srv/workspace/pbuilder/1244763 and its subdirectories +I: Current time: Sat Jun 3 21:59:42 +14 2023 +I: pbuilder-time-stamp: 1685779182