Diff of the two buildlogs: -- --- b1/build.log 2023-06-05 13:42:22.495717628 +0000 +++ b2/build.log 2023-06-05 13:56:41.042119591 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Jul 7 07:41:50 -12 2024 -I: pbuilder-time-stamp: 1720381310 +I: Current time: Tue Jun 6 03:42:34 +14 2023 +I: pbuilder-time-stamp: 1685972554 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -16,7 +16,7 @@ I: copying [./promod3_3.2.1+ds.orig.tar.xz] I: copying [./promod3_3.2.1+ds-6.debian.tar.xz] I: Extracting source -gpgv: Signature made Mon Nov 21 20:20:26 2022 -12 +gpgv: Signature made Tue Nov 22 22:20:26 2022 +14 gpgv: using RSA key 772292F6F7AC85FAE041D41EE5F43F9C2734F287 gpgv: issuer "merkys@debian.org" gpgv: Can't check signature: No public key @@ -32,135 +32,167 @@ dpkg-source: info: applying promod-executable.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/273034/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3094074/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 6 03:43 /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/3094074/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3094074/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='276e93feb8f444bfbf58fd54fd13e8fa' - 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='273034' - PS1='# ' - PS2='> ' + INVOCATION_ID=8b386341f8da42ffa83a31cfa049a8a0 + 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=3094074 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.EpZkSHqo/pbuilderrc_yPTm --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.EpZkSHqo/b1 --logfile b1/build.log promod3_3.2.1+ds-6.dsc' - SUDO_GID='110' - SUDO_UID='105' - 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.EpZkSHqo/pbuilderrc_aZRT --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.EpZkSHqo/b2 --logfile b2/build.log --extrapackages usrmerge promod3_3.2.1+ds-6.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 ionos5-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/273034/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 6 03:43 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/3094074/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -536,7 +568,7 @@ Get: 294 http://deb.debian.org/debian bookworm/main amd64 python3-pyqt5 amd64 5.15.9+dfsg-1 [2489 kB] Get: 295 http://deb.debian.org/debian bookworm/main amd64 python3-ost amd64 2.3.1-9 [3726 kB] Get: 296 http://deb.debian.org/debian bookworm/main amd64 openstructure amd64 2.3.1-9 [84.8 MB] -Fetched 301 MB in 7s (46.3 MB/s) +Fetched 301 MB in 4s (72.8 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.) @@ -1749,8 +1781,19 @@ 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/promod3-3.2.1+ds/ && 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 > ../promod3_3.2.1+ds-6_source.changes +I: user script /srv/workspace/pbuilder/3094074/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/3094074/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/promod3-3.2.1+ds/ && 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 > ../promod3_3.2.1+ds-6_source.changes dpkg-buildpackage: info: source package promod3 dpkg-buildpackage: info: source version 3.2.1+ds-6 dpkg-buildpackage: info: source distribution unstable @@ -1821,7 +1864,7 @@ -- Build files have been written to: /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu make[1]: Leaving directory '/build/promod3-3.2.1+ds' 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/promod3-3.2.1+ds/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/promod3-3.2.1+ds -B/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/CMakeFiles /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu//CMakeFiles/progress.marks @@ -1830,348 +1873,348 @@ make -f modelling/pymod/CMakeFiles/modelling_pymod.dir/build.make modelling/pymod/CMakeFiles/modelling_pymod.dir/depend make -f core/src/CMakeFiles/create_stage.dir/build.make core/src/CMakeFiles/create_stage.dir/depend make -f config/src/CMakeFiles/config_header.dir/build.make config/src/CMakeFiles/config_header.dir/depend +make -f core/pymod/CMakeFiles/core_pymod.dir/build.make core/pymod/CMakeFiles/core_pymod.dir/depend make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/modelling/pymod /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod/CMakeFiles/modelling_pymod.dir/DependInfo.cmake --color= +make -f loop/pymod/CMakeFiles/loop_pymod.dir/build.make loop/pymod/CMakeFiles/loop_pymod.dir/depend make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/core/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src/CMakeFiles/create_stage.dir/DependInfo.cmake --color= +make -f scoring/pymod/CMakeFiles/scoring_pymod.dir/build.make scoring/pymod/CMakeFiles/scoring_pymod.dir/depend make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/config/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/config/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/config/src/CMakeFiles/config_header.dir/DependInfo.cmake --color= -make -f core/pymod/CMakeFiles/core_pymod.dir/build.make core/pymod/CMakeFiles/core_pymod.dir/depend +make -f sidechain/pymod/CMakeFiles/sidechain_pymod.dir/build.make sidechain/pymod/CMakeFiles/sidechain_pymod.dir/depend +make -f core/init/CMakeFiles/init___init__.py_pymod.dir/build.make core/init/CMakeFiles/init___init__.py_pymod.dir/depend make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/core/pymod /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/pymod /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/pymod/CMakeFiles/core_pymod.dir/DependInfo.cmake --color= -make -f loop/pymod/CMakeFiles/loop_pymod.dir/build.make loop/pymod/CMakeFiles/loop_pymod.dir/depend -make -f scoring/pymod/CMakeFiles/scoring_pymod.dir/build.make scoring/pymod/CMakeFiles/scoring_pymod.dir/depend +make -f loop/data/CMakeFiles/loop_data_dir.dir/build.make loop/data/CMakeFiles/loop_data_dir.dir/depend make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/loop/pymod /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/pymod /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/pymod/CMakeFiles/loop_pymod.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/scoring/pymod /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/pymod /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/pymod/CMakeFiles/scoring_pymod.dir/DependInfo.cmake --color= -make -f sidechain/pymod/CMakeFiles/sidechain_pymod.dir/build.make sidechain/pymod/CMakeFiles/sidechain_pymod.dir/depend -make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +make -f scoring/data/CMakeFiles/scoring_data_dir.dir/build.make scoring/data/CMakeFiles/scoring_data_dir.dir/depend +make -f sidechain/data/CMakeFiles/sidechain_data_dir.dir/build.make sidechain/data/CMakeFiles/sidechain_data_dir.dir/depend make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +make -f scripts/CMakeFiles/subst_pm.dir/build.make scripts/CMakeFiles/subst_pm.dir/depend cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/sidechain/pymod /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/pymod /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/pymod/CMakeFiles/sidechain_pymod.dir/DependInfo.cmake --color= -make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -make -f core/src/CMakeFiles/create_stage.dir/build.make core/src/CMakeFiles/create_stage.dir/build -make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64 -make -f modelling/pymod/CMakeFiles/modelling_pymod.dir/build.make modelling/pymod/CMakeFiles/modelling_pymod.dir/build -make -f core/init/CMakeFiles/init___init__.py_pymod.dir/build.make core/init/CMakeFiles/init___init__.py_pymod.dir/depend +make -f actions/CMakeFiles/actions.dir/build.make actions/CMakeFiles/actions.dir/depend make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/pymod/__init__.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/__init__.py +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/loop/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/loop_data_dir.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/core/init /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/init /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/init/CMakeFiles/init___init__.py_pymod.dir/DependInfo.cmake --color= -make -f loop/data/CMakeFiles/loop_data_dir.dir/build.make loop/data/CMakeFiles/loop_data_dir.dir/depend -make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/loop/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/loop_data_dir.dir/DependInfo.cmake --color= -make -f config/src/CMakeFiles/config_header.dir/build.make config/src/CMakeFiles/config_header.dir/build +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/scoring/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/data 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+cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/scripts /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scripts /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scripts/CMakeFiles/subst_pm.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/actions /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/actions /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/actions/CMakeFiles/actions.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds 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/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/bin make -f loop/pymod/CMakeFiles/loop_pymod.dir/build.make loop/pymod/CMakeFiles/loop_pymod.dir/build +make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +make -f scoring/pymod/CMakeFiles/scoring_pymod.dir/build.make scoring/pymod/CMakeFiles/scoring_pymod.dir/build +make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +make -f sidechain/pymod/CMakeFiles/sidechain_pymod.dir/build.make sidechain/pymod/CMakeFiles/sidechain_pymod.dir/build make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/scoring/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu 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core/init/CMakeFiles/init___init__.py_pymod.dir/build.make core/init/CMakeFiles/init___init__.py_pymod.dir/build make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/pymod/__init__.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/sidechain/__init__.py make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/data && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data +make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/data && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data +make -f core/pymod/CMakeFiles/core_pymod.dir/build.make core/pymod/CMakeFiles/core_pymod.dir/build +make -f core/init/CMakeFiles/init___init__.py_pymod.dir/build.make core/init/CMakeFiles/init___init__.py_pymod.dir/build +make -f sidechain/data/CMakeFiles/sidechain_data_dir.dir/build.make sidechain/data/CMakeFiles/sidechain_data_dir.dir/build +make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/pymod/__init__.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/core/__init__.py +make -f scripts/CMakeFiles/subst_pm.dir/build.make scripts/CMakeFiles/subst_pm.dir/build +make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/data && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/share/promod3/sidechain_data make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/libexec/promod3 make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -make -f loop/data/CMakeFiles/loop_data_dir.dir/build.make loop/data/CMakeFiles/loop_data_dir.dir/build -make -f scoring/data/CMakeFiles/scoring_data_dir.dir/build.make scoring/data/CMakeFiles/scoring_data_dir.dir/build +make -f config/src/CMakeFiles/config_header.dir/build.make config/src/CMakeFiles/config_header.dir/build make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/data && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -DINPUT_FILE=/build/promod3-3.2.1+ds/scripts/pm.in -DOUT_FILE=pm -DOST_ROOT="/usr" -DLIBDIR=lib64 -DLIBEXECPATH=libexec/promod3 -DPYTHON_MODULE_PATH=python3.11/site-packages/ -DOST_PYMOD_PATH=/usr/lib/python3/dist-packages -DPython_EXECUTABLE=/usr/bin/python3 -P /build/promod3-3.2.1+ds/cmake_support/substitute.cmake +make -f actions/CMakeFiles/actions.dir/build.make actions/CMakeFiles/actions.dir/build make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/data && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/pymod/helper.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/core/helper.py -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/pymod/_molprobity.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_molprobity.py +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/config/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/config/src/config.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/config.hh +make -f extras/CMakeFiles/bash-completion.dir/build.make extras/CMakeFiles/bash-completion.dir/build +make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/actions/pm-build-model /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/libexec/promod3/pm-build-model +make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/bin make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -[ 1%] Generating ../../stage/lib64/python3.11/site-packages/promod3/__init__.py -make -f sidechain/data/CMakeFiles/sidechain_data_dir.dir/build.make sidechain/data/CMakeFiles/sidechain_data_dir.dir/depend -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/init && /usr/bin/cmake -DINPUT_FILE=/build/promod3-3.2.1+ds/core/init/__init__.py.in -DOUT_FILE=/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/promod3/__init__.py -DOST_COMPOUNDS_CHEMLIB_PATH="\"/var/cache/openstructure/compounds.chemlib\"" -DOST_ROOT=/usr -DPROMOD3_VERSION_STRING=3.2.1 -DGIT_BRANCH= -DGIT_COMMIT_HASH= -P /build/promod3-3.2.1+ds/cmake_support/substitute.cmake +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/pymod/_closegaps.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_closegaps.py make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/sidechain/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/data/CMakeFiles/sidechain_data_dir.dir/DependInfo.cmake --color= -[ 1%] Built target config_header -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/pymod/pm3argparse.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/core/pm3argparse.py -make -f scripts/CMakeFiles/subst_pm.dir/build.make scripts/CMakeFiles/subst_pm.dir/depend make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/pymod/_pipeline.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_pipeline.py -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests -[ 1%] Built target loop_pymod -make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/scripts /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scripts /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scripts/CMakeFiles/subst_pm.dir/DependInfo.cmake --color= -[ 1%] Built target scoring_pymod +[ 1%] Generating ../../stage/lib64/python3.11/site-packages/promod3/__init__.py make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -make -f actions/CMakeFiles/actions.dir/build.make actions/CMakeFiles/actions.dir/depend -[ 1%] Built target sidechain_pymod make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/pymod/helper.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/core/helper.py make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/actions /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/actions /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/actions/CMakeFiles/actions.dir/DependInfo.cmake --color= +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/init && /usr/bin/cmake -DINPUT_FILE=/build/promod3-3.2.1+ds/core/init/__init__.py.in -DOUT_FILE=/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/promod3/__init__.py -DOST_COMPOUNDS_CHEMLIB_PATH="\"/var/cache/openstructure/compounds.chemlib\"" -DOST_ROOT=/usr -DPROMOD3_VERSION_STRING=3.2.1 -DGIT_BRANCH= -DGIT_COMMIT_HASH= -P /build/promod3-3.2.1+ds/cmake_support/substitute.cmake +[ 1%] Generating ../stage/etc/bash_completion.d/pm-completion.bash make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -make -f sidechain/data/CMakeFiles/sidechain_data_dir.dir/build.make sidechain/data/CMakeFiles/sidechain_data_dir.dir/build -make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/data && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/share/promod3/sidechain_data +make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +[ 1%] Built target sidechain_pymod +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/libexec/promod3 +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/extras && /usr/bin/cmake -DINPUT_FILE=/build/promod3-3.2.1+ds/extras/pm-completion.bash.in -DOUT_FILE=/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/etc/bash_completion.d/pm-completion.bash -DPM3_ACTION_NAMES=build-model\ build-rawmodel\ help\ build-sidechains -P /build/promod3-3.2.1+ds/cmake_support/substitute.cmake +[ 1%] Built target sidechain_data_dir +[ 1%] Built target loop_pymod +[ 1%] Built target scoring_pymod +[ 1%] Built target scoring_data_dir [ 1%] Built target loop_data_dir -make -f extras/CMakeFiles/bash-completion.dir/build.make extras/CMakeFiles/bash-completion.dir/depend -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/pymod/_ring_punches.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_ring_punches.py +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/pymod/_molprobity.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_molprobity.py +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/pymod/pm3argparse.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/core/pm3argparse.py +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/actions/pm-build-rawmodel /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/libexec/promod3/pm-build-rawmodel +[ 1%] Built target subst_pm make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +[ 1%] Built target config_header +make -f scripts/CMakeFiles/promod3_scripts.dir/build.make scripts/CMakeFiles/promod3_scripts.dir/depend +make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/actions/pm-help /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/libexec/promod3/pm-help +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/extras /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/extras /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/extras/CMakeFiles/bash-completion.dir/DependInfo.cmake --color= +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/scripts /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scripts /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scripts/CMakeFiles/promod3_scripts.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -make -f scripts/CMakeFiles/subst_pm.dir/build.make scripts/CMakeFiles/subst_pm.dir/build +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/pymod/_pipeline.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_pipeline.py [ 1%] Built target init___init__.py_pymod -make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -DINPUT_FILE=/build/promod3-3.2.1+ds/scripts/pm.in -DOUT_FILE=pm -DOST_ROOT="/usr" -DLIBDIR=lib64 -DLIBEXECPATH=libexec/promod3 -DPYTHON_MODULE_PATH=python3.11/site-packages/ -DOST_PYMOD_PATH=/usr/lib/python3/dist-packages -DPython_EXECUTABLE=/usr/bin/python3 -P /build/promod3-3.2.1+ds/cmake_support/substitute.cmake -make -f core/init/CMakeFiles/init_pymod.dir/build.make core/init/CMakeFiles/init_pymod.dir/depend [ 1%] Built target core_pymod -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/pymod/_denovo.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_denovo.py +[ 1%] Built target bash-completion +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/actions/pm-build-sidechains /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/libexec/promod3/pm-build-sidechains +make -f core/init/CMakeFiles/init_pymod.dir/build.make core/init/CMakeFiles/init_pymod.dir/depend +make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/core/init /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/init /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/init/CMakeFiles/init_pymod.dir/DependInfo.cmake --color= -[ 1%] Built target scoring_data_dir -[ 1%] Built target create_stage make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -make -f core/src/CMakeFiles/promod3_core_headers.dir/build.make core/src/CMakeFiles/promod3_core_headers.dir/depend +make -f scripts/CMakeFiles/promod3_scripts.dir/build.make scripts/CMakeFiles/promod3_scripts.dir/build make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/core/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src/CMakeFiles/promod3_core_headers.dir/DependInfo.cmake --color= -make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -make -f actions/CMakeFiles/actions.dir/build.make actions/CMakeFiles/actions.dir/build +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -E copy_if_different pm /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/bin/pm +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/pymod/_ring_punches.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_ring_punches.py +[ 1%] Built target create_stage make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +make -f core/src/CMakeFiles/promod3_core_headers.dir/build.make core/src/CMakeFiles/promod3_core_headers.dir/depend make -f loop/src/CMakeFiles/promod3_loop_headers.dir/build.make loop/src/CMakeFiles/promod3_loop_headers.dir/depend -make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/actions/pm-build-model /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/libexec/promod3/pm-build-model make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -[ 1%] Built target sidechain_data_dir +make -f scoring/src/CMakeFiles/promod3_scoring_headers.dir/build.make scoring/src/CMakeFiles/promod3_scoring_headers.dir/depend +make -f core/init/CMakeFiles/init_pymod.dir/build.make core/init/CMakeFiles/init_pymod.dir/build +make -f sidechain/src/CMakeFiles/promod3_sidechain_headers.dir/build.make sidechain/src/CMakeFiles/promod3_sidechain_headers.dir/depend make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/loop/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src/CMakeFiles/promod3_loop_headers.dir/DependInfo.cmake --color= -make -f extras/CMakeFiles/bash-completion.dir/build.make extras/CMakeFiles/bash-completion.dir/build -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/pymod/_fragger_handle.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_fragger_handle.py -make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/core/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src/CMakeFiles/promod3_core_headers.dir/DependInfo.cmake --color= +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scripts/pm /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/bin/pm +make -f modelling/src/CMakeFiles/promod3_modelling_headers.dir/build.make modelling/src/CMakeFiles/promod3_modelling_headers.dir/depend make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/actions/pm-build-rawmodel /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/libexec/promod3/pm-build-rawmodel -make -f core/src/CMakeFiles/promod3_core_headers.dir/build.make core/src/CMakeFiles/promod3_core_headers.dir/build -make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/loop/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src/CMakeFiles/promod3_loop_headers.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./check_io.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./check_io.hh -make -f core/init/CMakeFiles/init_pymod.dir/build.make core/init/CMakeFiles/init_pymod.dir/build -[ 1%] Generating ../stage/etc/bash_completion.d/pm-completion.bash -make -f scoring/src/CMakeFiles/promod3_scoring_headers.dir/build.make scoring/src/CMakeFiles/promod3_scoring_headers.dir/depend +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/scoring/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src/CMakeFiles/promod3_scoring_headers.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'core/init/CMakeFiles/init_pymod.dir/build'. make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/scoring/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src/CMakeFiles/promod3_scoring_headers.dir/DependInfo.cmake --color= -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/pymod/_reconstruct_sidechains.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_reconstruct_sidechains.py -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/extras && /usr/bin/cmake -DINPUT_FILE=/build/promod3-3.2.1+ds/extras/pm-completion.bash.in -DOUT_FILE=/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/etc/bash_completion.d/pm-completion.bash -DPM3_ACTION_NAMES=build-model\ build-rawmodel\ help\ build-sidechains -P /build/promod3-3.2.1+ds/cmake_support/substitute.cmake -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/actions/pm-help /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/libexec/promod3/pm-help +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/sidechain/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src/CMakeFiles/promod3_sidechain_headers.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/modelling/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src/CMakeFiles/promod3_modelling_headers.dir/DependInfo.cmake --color= +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/pymod/_denovo.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_denovo.py +[ 1%] Built target actions +make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +make -f core/src/CMakeFiles/promod3_core_headers.dir/build.make core/src/CMakeFiles/promod3_core_headers.dir/build make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -[ 1%] Built target subst_pm make -f loop/src/CMakeFiles/promod3_loop_headers.dir/build.make loop/src/CMakeFiles/promod3_loop_headers.dir/build make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +[ 1%] Built target init_pymod +make -f modelling/src/CMakeFiles/promod3_modelling_headers.dir/build.make modelling/src/CMakeFiles/promod3_modelling_headers.dir/build make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/pymod/_monte_carlo.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_monte_carlo.py -make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./all_atom_env.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./all_atom_env.hh -make -f scoring/src/CMakeFiles/promod3_scoring_headers.dir/build.make scoring/src/CMakeFiles/promod3_scoring_headers.dir/build -make -f sidechain/src/CMakeFiles/promod3_sidechain_headers.dir/build.make sidechain/src/CMakeFiles/promod3_sidechain_headers.dir/depend make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./backbone_score_base.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./backbone_score_base.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./cluster.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./cluster.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/actions/pm-build-sidechains /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/libexec/promod3/pm-build-sidechains -make -f modelling/src/CMakeFiles/promod3_modelling_headers.dir/build.make modelling/src/CMakeFiles/promod3_modelling_headers.dir/depend -make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/sidechain/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src/CMakeFiles/promod3_sidechain_headers.dir/DependInfo.cmake --color= -[ 1%] Built target init_pymod -make -f scripts/CMakeFiles/promod3_scripts.dir/build.make scripts/CMakeFiles/promod3_scripts.dir/depend +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./check_io.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./check_io.hh make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/modelling/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src/CMakeFiles/promod3_modelling_headers.dir/DependInfo.cmake --color= +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./all_atom_env.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./all_atom_env.hh make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/scripts /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scripts /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scripts/CMakeFiles/promod3_scripts.dir/DependInfo.cmake --color= -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./all_atom_positions.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./all_atom_positions.hh -[ 1%] Built target bash-completion -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/pymod/_mhandle_helper.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_mhandle_helper.py +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./extension_scheme.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./extension_scheme.hh make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./dynamic_spatial_organizer.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./dynamic_spatial_organizer.hh +make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +make -f scoring/src/CMakeFiles/promod3_scoring_headers.dir/build.make scoring/src/CMakeFiles/promod3_scoring_headers.dir/build make -f sidechain/src/CMakeFiles/promod3_sidechain_headers.dir/build.make sidechain/src/CMakeFiles/promod3_sidechain_headers.dir/build make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./backbone_score_base.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./backbone_score_base.hh +make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./bb_dep_rotamer_lib.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./bb_dep_rotamer_lib.hh -make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -make -f modelling/src/CMakeFiles/promod3_modelling_headers.dir/build.make modelling/src/CMakeFiles/promod3_modelling_headers.dir/build +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/pymod/_fragger_handle.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_fragger_handle.py +[ 1%] Built target promod3_scripts +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./cluster.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./cluster.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./gap.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./gap.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./all_atom_positions.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./all_atom_positions.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./backbone_overall_scorer.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./backbone_overall_scorer.hh -make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./extension_scheme.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./extension_scheme.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/pymod/_alignment_fiddling.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_alignment_fiddling.py -make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -make -f scripts/CMakeFiles/promod3_scripts.dir/build.make scripts/CMakeFiles/promod3_scripts.dir/build -make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -E copy_if_different pm /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/bin/pm -[ 1%] Built target actions -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./export_helper.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./export_helper.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./disulfid.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./disulfid.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./amino_acid_atoms.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./amino_acid_atoms.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/pymod/_reconstruct_sidechains.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_reconstruct_sidechains.py +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./dynamic_spatial_organizer.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./dynamic_spatial_organizer.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./gap_extender.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./gap_extender.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./scoring_object_loader.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./scoring_object_loader.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./gap.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./gap.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scripts/pm /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/bin/pm -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/pymod/_raw_model.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_raw_model.py -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./geom_base.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./geom_base.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./amino_acid_atoms.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./amino_acid_atoms.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./frame.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./frame.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/pymod/_monte_carlo.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_monte_carlo.py +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./export_helper.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./export_helper.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./model.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./model.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./cbeta_env_listener.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./cbeta_env_listener.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./backbone.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./backbone.hh -make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./gap_extender.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./gap_extender.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./rotamer_graph.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_graph.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./geom_base.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./geom_base.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./all_atom_relaxer.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./all_atom_relaxer.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/pymod/_mhandle_helper.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_mhandle_helper.py +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./cb_packing_score.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./cb_packing_score.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./bb_trace_param.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./bb_trace_param.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./geom_stems.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./geom_stems.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./cbeta_env_listener.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./cbeta_env_listener.hh -make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -[ 1%] Built target modelling_pymod -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./message.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./message.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./backbone_relaxer.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./backbone_relaxer.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./particle.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./particle.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./bb_trace_param.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./bb_trace_param.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./cb_packing_score.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./cb_packing_score.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./model.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./model.hh -[ 1%] Built target promod3_scripts -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./portable_binary_data_sink.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./portable_binary_data_sink.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./particle_scoring_base.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./particle_scoring_base.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./data_bag.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./data_bag.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./cbeta_score.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./cbeta_score.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./all_atom_relaxer.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./all_atom_relaxer.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./portable_binary_data_source.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./portable_binary_data_source.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./particle_scoring.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./particle_scoring.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/pymod/_alignment_fiddling.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_alignment_fiddling.py +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./data_bag.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./data_bag.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./message.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./message.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./ccd.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./ccd.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./reduced_env_listener.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./reduced_env_listener.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./particle_scoring_base.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./particle_scoring_base.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/pymod/_raw_model.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_raw_model.py cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./dense_hash_table.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./dense_hash_table.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./backbone_relaxer.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./backbone_relaxer.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./portable_binary_data_sink.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./portable_binary_data_sink.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./kic.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./kic.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./reduced_score.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./reduced_score.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./portable_binary_serializer.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./portable_binary_serializer.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./particle_scoring.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./particle_scoring.hh +make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./portable_binary_data_source.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./portable_binary_data_source.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./clash_env_listener.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./clash_env_listener.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./loop_candidate.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./loop_candidate.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./dense_map.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./dense_map.hh +[ 1%] Built target modelling_pymod cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./scwrl4_particle_scoring.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./scwrl4_particle_scoring.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./clash_score.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./clash_score.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./portable_binary_serializer.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./portable_binary_serializer.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./monte_carlo.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./dense_map.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./dense_map.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./clash_env_listener.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./clash_env_listener.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./scwrl3_particle_scoring.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./scwrl3_particle_scoring.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./ccd.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./ccd.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./dense_map.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./dense_map.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./density_score.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./density_score.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./runtime_profiling.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./runtime_profiling.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./vina_particle_scoring.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./vina_particle_scoring.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./clash_score.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./clash_score.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./kic.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./kic.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./monte_carlo_closer.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo_closer.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./density_creator.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./density_creator.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./rotamer.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./vina_particle_scoring.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./vina_particle_scoring.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./hbond_env_listener.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./hbond_env_listener.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./superpose.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./superpose.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./loop_candidate.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./loop_candidate.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./density_score.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./density_score.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./forcefield_lookup.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./forcefield_lookup.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./rotamer_cruncher.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_cruncher.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./enumerator.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./enumerator.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./monte_carlo.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./hbond_env_listener.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./hbond_env_listener.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./rotamer_density.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_density.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./frag_db.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./frag_db.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./monte_carlo_closer.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo_closer.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./hbond_score.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./hbond_score.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./graph.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./graph.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./rotamer_group.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_group.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./fragger.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./fragger.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./monte_carlo_cooler.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo_cooler.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./hbond_score.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./hbond_score.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./monte_carlo_sampler.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo_sampler.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./rotamer.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./frag_db.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./frag_db.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./enumerator.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./enumerator.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./ss_agreement_score.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./ss_agreement_score.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./monte_carlo_scorer.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo_scorer.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./fragger.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./fragger.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./graph.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./graph.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./rotamer_cruncher.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_cruncher.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./ss_agreement_env_listener.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./ss_agreement_env_listener.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./rigid_blocks.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./rigid_blocks.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./tree.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./tree.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./hydrogen_constructor.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./hydrogen_constructor.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./monte_carlo_sampler.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo_sampler.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./rotamer_id.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_id.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./rotamer_density.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_density.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./torsion_score.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./torsion_score.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./score_container.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./score_container.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./hydrogen_rule_lookup.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./hydrogen_rule_lookup.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./tetrahedral_polytope.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./tetrahedral_polytope.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./ss_agreement_env_listener.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./ss_agreement_env_listener.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./rotamer_lib.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_lib.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./rotamer_group.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_group.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./pairwise_scoring_function.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./pairwise_scoring_function.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./scoring_weights.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./scoring_weights.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./graph_minimizer.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./graph_minimizer.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./monte_carlo_scorer.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo_scorer.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./hydrogen_rule_lookup.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./hydrogen_rule_lookup.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./torsion_score.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./torsion_score.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./rotamer_lib_entry.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_lib_entry.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./idx_handler.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./idx_handler.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./rotamer_id.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_id.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./pairwise_score.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./pairwise_score.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./sidechain_reconstructor.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./sidechain_reconstructor.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./eigen_types.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./eigen_types.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./rigid_blocks.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./rigid_blocks.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./pairwise_scoring_function.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./pairwise_scoring_function.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./loop_object_loader.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./loop_object_loader.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./rotamer_lib_reader.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_lib_reader.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./rotamer_lib.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_lib.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./constraint_constructor.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./constraint_constructor.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./sidechain_env_listener.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./sidechain_env_listener.hh make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./score_container.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./score_container.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./mm_system_creator.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./mm_system_creator.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./pairwise_score.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./pairwise_score.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./all_atom_score_base.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_score_base.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./motif_finder.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./motif_finder.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./rotamer_lib_entry.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_lib_entry.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./psipred_prediction.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./psipred_prediction.hh [ 1%] Built target promod3_core_headers make -f core/src/CMakeFiles/promod3_core.dir/build.make core/src/CMakeFiles/promod3_core.dir/depend -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./scoring_weights.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./scoring_weights.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./sidechain_connector.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./sidechain_connector.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./all_atom_overall_scorer.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_overall_scorer.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./robin_hood.h /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./robin_hood.h make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/core/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src/CMakeFiles/promod3_core.dir/DependInfo.cmake --color= -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./psipred_prediction.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./psipred_prediction.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./sidechain_object_loader.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./sidechain_object_loader.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./constraint_constructor.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./constraint_constructor.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./sidechain_reconstructor.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./sidechain_reconstructor.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./rotamer_lib_reader.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_lib_reader.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./all_atom_interaction_env_listener.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_interaction_env_listener.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./stem_geom.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./stem_geom.hh make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make -f core/src/CMakeFiles/promod3_core.dir/build.make core/src/CMakeFiles/promod3_core.dir/build -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./sidechain_env_listener.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./sidechain_env_listener.hh make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./rotamer_constructor.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_constructor.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./all_atom_score_base.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_score_base.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./motif_finder.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./motif_finder.hh -[ 1%] Building CXX object core/src/CMakeFiles/promod3_core.dir/geom_base.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./sidechain_connector.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./sidechain_connector.hh +[ 1%] Built target promod3_modelling_headers +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./all_atom_interaction_score.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_interaction_score.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./structure_db.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./structure_db.hh -[ 2%] Building CXX object core/src/CMakeFiles/promod3_core.dir/geom_stems.cc.o -[ 2%] Building CXX object core/src/CMakeFiles/promod3_core.dir/cluster.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_CORE -Dpromod3_core_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/src/CMakeFiles/promod3_core.dir/cluster.cc.o -MF CMakeFiles/promod3_core.dir/cluster.cc.o.d -o CMakeFiles/promod3_core.dir/cluster.cc.o -c /build/promod3-3.2.1+ds/core/src/cluster.cc -[ 2%] Building CXX object core/src/CMakeFiles/promod3_core.dir/superpose.cc.o +[ 1%] Building CXX object core/src/CMakeFiles/promod3_core.dir/superpose.cc.o +[ 1%] Building CXX object core/src/CMakeFiles/promod3_core.dir/geom_base.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_CORE -Dpromod3_core_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/src/CMakeFiles/promod3_core.dir/superpose.cc.o -MF CMakeFiles/promod3_core.dir/superpose.cc.o.d -o CMakeFiles/promod3_core.dir/superpose.cc.o -c /build/promod3-3.2.1+ds/core/src/superpose.cc +[ 1%] Building CXX object core/src/CMakeFiles/promod3_core.dir/cluster.cc.o +[ 1%] Building CXX object core/src/CMakeFiles/promod3_core.dir/tree.cc.o [ 4%] Building CXX object core/src/CMakeFiles/promod3_core.dir/graph.cc.o +[ 4%] Building CXX object core/src/CMakeFiles/promod3_core.dir/geom_stems.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_CORE -Dpromod3_core_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/src/CMakeFiles/promod3_core.dir/geom_base.cc.o -MF CMakeFiles/promod3_core.dir/geom_base.cc.o.d -o CMakeFiles/promod3_core.dir/geom_base.cc.o -c /build/promod3-3.2.1+ds/core/src/geom_base.cc -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./all_atom_overall_scorer.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_overall_scorer.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_CORE -Dpromod3_core_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/src/CMakeFiles/promod3_core.dir/cluster.cc.o -MF CMakeFiles/promod3_core.dir/cluster.cc.o.d -o CMakeFiles/promod3_core.dir/cluster.cc.o -c /build/promod3-3.2.1+ds/core/src/cluster.cc +[ 4%] Building CXX object core/src/CMakeFiles/promod3_core.dir/tetrahedral_polytope.cc.o +[ 5%] Building CXX object core/src/CMakeFiles/promod3_core.dir/graph_minimizer.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_CORE -Dpromod3_core_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/src/CMakeFiles/promod3_core.dir/tree.cc.o -MF CMakeFiles/promod3_core.dir/tree.cc.o.d -o CMakeFiles/promod3_core.dir/tree.cc.o -c /build/promod3-3.2.1+ds/core/src/tree.cc cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_CORE -Dpromod3_core_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/src/CMakeFiles/promod3_core.dir/geom_stems.cc.o -MF CMakeFiles/promod3_core.dir/geom_stems.cc.o.d -o CMakeFiles/promod3_core.dir/geom_stems.cc.o -c /build/promod3-3.2.1+ds/core/src/geom_stems.cc -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./rotamer_lookup.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_lookup.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_CORE -Dpromod3_core_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/src/CMakeFiles/promod3_core.dir/superpose.cc.o -MF CMakeFiles/promod3_core.dir/superpose.cc.o.d -o CMakeFiles/promod3_core.dir/superpose.cc.o -c /build/promod3-3.2.1+ds/core/src/superpose.cc cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_CORE -Dpromod3_core_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/src/CMakeFiles/promod3_core.dir/graph.cc.o -MF CMakeFiles/promod3_core.dir/graph.cc.o.d -o CMakeFiles/promod3_core.dir/graph.cc.o -c /build/promod3-3.2.1+ds/core/src/graph.cc -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./robin_hood.h /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./robin_hood.h -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./torsion_sampler.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./torsion_sampler.hh -[ 4%] Building CXX object core/src/CMakeFiles/promod3_core.dir/tree.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_CORE -Dpromod3_core_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/src/CMakeFiles/promod3_core.dir/tree.cc.o -MF CMakeFiles/promod3_core.dir/tree.cc.o.d -o CMakeFiles/promod3_core.dir/tree.cc.o -c /build/promod3-3.2.1+ds/core/src/tree.cc -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./scwrl4_rotamer_constructor.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./scwrl4_rotamer_constructor.hh -make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -[ 4%] Building CXX object core/src/CMakeFiles/promod3_core.dir/tetrahedral_polytope.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_CORE -Dpromod3_core_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/src/CMakeFiles/promod3_core.dir/tetrahedral_polytope.cc.o -MF CMakeFiles/promod3_core.dir/tetrahedral_polytope.cc.o.d -o CMakeFiles/promod3_core.dir/tetrahedral_polytope.cc.o -c /build/promod3-3.2.1+ds/core/src/tetrahedral_polytope.cc -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./ushort_vec.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./ushort_vec.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./all_atom_interaction_env_listener.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_interaction_env_listener.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./scwrl3_rotamer_constructor.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./scwrl3_rotamer_constructor.hh -[ 5%] Building CXX object core/src/CMakeFiles/promod3_core.dir/graph_minimizer.cc.o -[ 5%] Built target promod3_modelling_headers +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./sidechain_object_loader.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./sidechain_object_loader.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_CORE -Dpromod3_core_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/src/CMakeFiles/promod3_core.dir/graph_minimizer.cc.o -MF CMakeFiles/promod3_core.dir/graph_minimizer.cc.o.d -o CMakeFiles/promod3_core.dir/graph_minimizer.cc.o -c /build/promod3-3.2.1+ds/core/src/graph_minimizer.cc -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./sidechain_atom_rule_lookup.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./sidechain_atom_rule_lookup.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./all_atom_interaction_score.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_interaction_score.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./vina_rotamer_constructor.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./vina_rotamer_constructor.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./sidechain_atom_constructor.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./sidechain_atom_constructor.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./all_atom_packing_score.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_packing_score.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./subrotamer_optimizer.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./subrotamer_optimizer.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./structure_db_custom_types.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./structure_db_custom_types.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./torsion_sampler.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./torsion_sampler.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./rotamer_constructor.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_constructor.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./ushort_vec.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./ushort_vec.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./all_atom_clash_score.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_clash_score.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./rotamer_lookup.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_lookup.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./sidechain_atom_rule_lookup.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./sidechain_atom_rule_lookup.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./scwrl3_energy_functions.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./scwrl3_energy_functions.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./scwrl4_rotamer_constructor.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./scwrl4_rotamer_constructor.hh make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./sidechain_atom_constructor.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./sidechain_atom_constructor.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./scwrl3_rotamer_constructor.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./scwrl3_rotamer_constructor.hh +[ 5%] Built target promod3_scoring_headers +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./structure_db_custom_types.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./structure_db_custom_types.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./vina_rotamer_constructor.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./vina_rotamer_constructor.hh make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./scwrl3_energy_functions.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./scwrl3_energy_functions.hh -[ 5%] Built target promod3_sidechain_headers +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./subrotamer_optimizer.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./subrotamer_optimizer.hh [ 5%] Built target promod3_loop_headers make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -[ 5%] Built target promod3_scoring_headers +[ 5%] Built target promod3_sidechain_headers [ 5%] Linking CXX shared library ../../stage/lib64/libpromod3_core.so cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/promod3_core.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libpromod3_core.so.3.2 -o ../../stage/lib64/libpromod3_core.so.3.2.1 CMakeFiles/promod3_core.dir/cluster.cc.o CMakeFiles/promod3_core.dir/geom_base.cc.o CMakeFiles/promod3_core.dir/geom_stems.cc.o CMakeFiles/promod3_core.dir/superpose.cc.o CMakeFiles/promod3_core.dir/graph.cc.o CMakeFiles/promod3_core.dir/tree.cc.o CMakeFiles/promod3_core.dir/tetrahedral_polytope.cc.o CMakeFiles/promod3_core.dir/graph_minimizer.cc.o -L/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64: /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.74.0 @@ -2186,40 +2229,40 @@ cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/loop/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src/CMakeFiles/promod3_loop.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make -f core/pymod/CMakeFiles/_core.dir/build.make core/pymod/CMakeFiles/_core.dir/build -make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make -f loop/src/CMakeFiles/promod3_loop.dir/build.make loop/src/CMakeFiles/promod3_loop.dir/build make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +[ 5%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/amino_acid_atoms.cc.o +[ 5%] Building CXX object core/pymod/CMakeFiles/_core.dir/export_runtime_profiling.cc.o [ 7%] Building CXX object core/pymod/CMakeFiles/_core.dir/export_graph_minimizer.cc.o -[ 7%] Building CXX object core/pymod/CMakeFiles/_core.dir/export_geom.cc.o -[ 7%] Building CXX object core/pymod/CMakeFiles/_core.dir/wrap_core.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_core_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/pymod/CMakeFiles/_core.dir/export_graph_minimizer.cc.o -MF CMakeFiles/_core.dir/export_graph_minimizer.cc.o.d -o CMakeFiles/_core.dir/export_graph_minimizer.cc.o -c /build/promod3-3.2.1+ds/core/pymod/export_graph_minimizer.cc -[ 7%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/all_atom_positions.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_core_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/pymod/CMakeFiles/_core.dir/export_geom.cc.o -MF CMakeFiles/_core.dir/export_geom.cc.o.d -o CMakeFiles/_core.dir/export_geom.cc.o -c /build/promod3-3.2.1+ds/core/pymod/export_geom.cc -[ 8%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/backbone.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_core_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/pymod/CMakeFiles/_core.dir/wrap_core.cc.o -MF CMakeFiles/_core.dir/wrap_core.cc.o.d -o CMakeFiles/_core.dir/wrap_core.cc.o -c /build/promod3-3.2.1+ds/core/pymod/wrap_core.cc -[ 8%] Building CXX object core/pymod/CMakeFiles/_core.dir/export_runtime_profiling.cc.o -[ 9%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/all_atom_env.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_core_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/pymod/CMakeFiles/_core.dir/export_runtime_profiling.cc.o -MF CMakeFiles/_core.dir/export_runtime_profiling.cc.o.d -o CMakeFiles/_core.dir/export_runtime_profiling.cc.o -c /build/promod3-3.2.1+ds/core/pymod/export_runtime_profiling.cc -[ 9%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/amino_acid_atoms.cc.o +[ 8%] Building CXX object core/pymod/CMakeFiles/_core.dir/wrap_core.cc.o +[ 8%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/all_atom_env.cc.o +[ 9%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/backbone.cc.o [ 9%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/bb_trace_param.cc.o +[ 9%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/all_atom_positions.cc.o +[ 9%] Building CXX object core/pymod/CMakeFiles/_core.dir/export_geom.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/amino_acid_atoms.cc.o -MF CMakeFiles/promod3_loop.dir/amino_acid_atoms.cc.o.d -o CMakeFiles/promod3_loop.dir/amino_acid_atoms.cc.o -c /build/promod3-3.2.1+ds/loop/src/amino_acid_atoms.cc +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_core_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/pymod/CMakeFiles/_core.dir/export_runtime_profiling.cc.o -MF CMakeFiles/_core.dir/export_runtime_profiling.cc.o.d -o CMakeFiles/_core.dir/export_runtime_profiling.cc.o -c /build/promod3-3.2.1+ds/core/pymod/export_runtime_profiling.cc cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/all_atom_env.cc.o -MF CMakeFiles/promod3_loop.dir/all_atom_env.cc.o.d -o CMakeFiles/promod3_loop.dir/all_atom_env.cc.o -c /build/promod3-3.2.1+ds/loop/src/all_atom_env.cc +[ 9%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/frag_db.cc.o +[ 9%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/forcefield_lookup.cc.o +[ 11%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/fragger.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/all_atom_positions.cc.o -MF CMakeFiles/promod3_loop.dir/all_atom_positions.cc.o.d -o CMakeFiles/promod3_loop.dir/all_atom_positions.cc.o -c /build/promod3-3.2.1+ds/loop/src/all_atom_positions.cc -[ 11%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/density_creator.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/amino_acid_atoms.cc.o -MF CMakeFiles/promod3_loop.dir/amino_acid_atoms.cc.o.d -o CMakeFiles/promod3_loop.dir/amino_acid_atoms.cc.o -c /build/promod3-3.2.1+ds/loop/src/amino_acid_atoms.cc cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/backbone.cc.o -MF CMakeFiles/promod3_loop.dir/backbone.cc.o.d -o CMakeFiles/promod3_loop.dir/backbone.cc.o -c /build/promod3-3.2.1+ds/loop/src/backbone.cc -[ 11%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/forcefield_lookup.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/bb_trace_param.cc.o -MF CMakeFiles/promod3_loop.dir/bb_trace_param.cc.o.d -o CMakeFiles/promod3_loop.dir/bb_trace_param.cc.o -c /build/promod3-3.2.1+ds/loop/src/bb_trace_param.cc -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/density_creator.cc.o -MF CMakeFiles/promod3_loop.dir/density_creator.cc.o.d -o CMakeFiles/promod3_loop.dir/density_creator.cc.o -c /build/promod3-3.2.1+ds/loop/src/density_creator.cc -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/forcefield_lookup.cc.o -MF CMakeFiles/promod3_loop.dir/forcefield_lookup.cc.o.d -o CMakeFiles/promod3_loop.dir/forcefield_lookup.cc.o -c /build/promod3-3.2.1+ds/loop/src/forcefield_lookup.cc -[ 12%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/fragger.cc.o -[ 12%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/frag_db.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/frag_db.cc.o -MF CMakeFiles/promod3_loop.dir/frag_db.cc.o.d -o CMakeFiles/promod3_loop.dir/frag_db.cc.o -c /build/promod3-3.2.1+ds/loop/src/frag_db.cc +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_core_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/pymod/CMakeFiles/_core.dir/export_graph_minimizer.cc.o -MF CMakeFiles/_core.dir/export_graph_minimizer.cc.o.d -o CMakeFiles/_core.dir/export_graph_minimizer.cc.o -c /build/promod3-3.2.1+ds/core/pymod/export_graph_minimizer.cc +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/forcefield_lookup.cc.o -MF CMakeFiles/promod3_loop.dir/forcefield_lookup.cc.o.d -o CMakeFiles/promod3_loop.dir/forcefield_lookup.cc.o -c /build/promod3-3.2.1+ds/loop/src/forcefield_lookup.cc +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_core_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/pymod/CMakeFiles/_core.dir/wrap_core.cc.o -MF CMakeFiles/_core.dir/wrap_core.cc.o.d -o CMakeFiles/_core.dir/wrap_core.cc.o -c /build/promod3-3.2.1+ds/core/pymod/wrap_core.cc cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/fragger.cc.o -MF CMakeFiles/promod3_loop.dir/fragger.cc.o.d -o CMakeFiles/promod3_loop.dir/fragger.cc.o -c /build/promod3-3.2.1+ds/loop/src/fragger.cc -[ 14%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/hydrogen_rule_lookup.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_core_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/pymod/CMakeFiles/_core.dir/export_geom.cc.o -MF CMakeFiles/_core.dir/export_geom.cc.o.d -o CMakeFiles/_core.dir/export_geom.cc.o -c /build/promod3-3.2.1+ds/core/pymod/export_geom.cc +[ 12%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/hydrogen_rule_lookup.cc.o +[ 14%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/density_creator.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/density_creator.cc.o -MF CMakeFiles/promod3_loop.dir/density_creator.cc.o.d -o CMakeFiles/promod3_loop.dir/density_creator.cc.o -c /build/promod3-3.2.1+ds/loop/src/density_creator.cc [ 14%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/hydrogen_constructor.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/hydrogen_rule_lookup.cc.o -MF CMakeFiles/promod3_loop.dir/hydrogen_rule_lookup.cc.o.d -o CMakeFiles/promod3_loop.dir/hydrogen_rule_lookup.cc.o -c /build/promod3-3.2.1+ds/loop/src/hydrogen_rule_lookup.cc cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/hydrogen_constructor.cc.o -MF CMakeFiles/promod3_loop.dir/hydrogen_constructor.cc.o.d -o CMakeFiles/promod3_loop.dir/hydrogen_constructor.cc.o -c /build/promod3-3.2.1+ds/loop/src/hydrogen_constructor.cc +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/hydrogen_rule_lookup.cc.o -MF CMakeFiles/promod3_loop.dir/hydrogen_rule_lookup.cc.o.d -o CMakeFiles/promod3_loop.dir/hydrogen_rule_lookup.cc.o -c /build/promod3-3.2.1+ds/loop/src/hydrogen_rule_lookup.cc [ 14%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/idx_handler.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/idx_handler.cc.o -MF CMakeFiles/promod3_loop.dir/idx_handler.cc.o.d -o CMakeFiles/promod3_loop.dir/idx_handler.cc.o -c /build/promod3-3.2.1+ds/loop/src/idx_handler.cc [ 15%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/loop_object_loader.cc.o @@ -2239,17 +2282,10 @@ 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/promod3-3.2.1+ds/core/pymod/wrap_core.cc:17: + from /build/promod3-3.2.1+ds/core/pymod/export_graph_minimizer.cc:17: /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("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 15%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/psipred_prediction.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/psipred_prediction.cc.o -MF CMakeFiles/promod3_loop.dir/psipred_prediction.cc.o.d -o CMakeFiles/promod3_loop.dir/psipred_prediction.cc.o -c /build/promod3-3.2.1+ds/loop/src/psipred_prediction.cc -[ 16%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/structure_db.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/structure_db.cc.o -MF CMakeFiles/promod3_loop.dir/structure_db.cc.o.d -o CMakeFiles/promod3_loop.dir/structure_db.cc.o -c /build/promod3-3.2.1+ds/loop/src/structure_db.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, @@ -2263,13 +2299,16 @@ 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/promod3-3.2.1+ds/core/pymod/export_geom.cc:17: + from /build/promod3-3.2.1+ds/core/pymod/export_runtime_profiling.cc:17: /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, @@ -2283,17 +2322,13 @@ 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/promod3-3.2.1+ds/core/pymod/export_runtime_profiling.cc:17: + from /build/promod3-3.2.1+ds/core/pymod/export_geom.cc:17: /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("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 16%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/torsion_sampler.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/torsion_sampler.cc.o -MF CMakeFiles/promod3_loop.dir/torsion_sampler.cc.o.d -o CMakeFiles/promod3_loop.dir/torsion_sampler.cc.o -c /build/promod3-3.2.1+ds/loop/src/torsion_sampler.cc -[ 18%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/sidechain_atom_rule_lookup.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/sidechain_atom_rule_lookup.cc.o -MF CMakeFiles/promod3_loop.dir/sidechain_atom_rule_lookup.cc.o.d -o CMakeFiles/promod3_loop.dir/sidechain_atom_rule_lookup.cc.o -c /build/promod3-3.2.1+ds/loop/src/sidechain_atom_rule_lookup.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, @@ -2307,13 +2342,21 @@ 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/promod3-3.2.1+ds/core/pymod/export_graph_minimizer.cc:17: + from /build/promod3-3.2.1+ds/core/pymod/wrap_core.cc:17: /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("") | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 15%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/psipred_prediction.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/psipred_prediction.cc.o -MF CMakeFiles/promod3_loop.dir/psipred_prediction.cc.o.d -o CMakeFiles/promod3_loop.dir/psipred_prediction.cc.o -c /build/promod3-3.2.1+ds/loop/src/psipred_prediction.cc +[ 16%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/structure_db.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/structure_db.cc.o -MF CMakeFiles/promod3_loop.dir/structure_db.cc.o.d -o CMakeFiles/promod3_loop.dir/structure_db.cc.o -c /build/promod3-3.2.1+ds/loop/src/structure_db.cc +[ 16%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/torsion_sampler.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/torsion_sampler.cc.o -MF CMakeFiles/promod3_loop.dir/torsion_sampler.cc.o.d -o CMakeFiles/promod3_loop.dir/torsion_sampler.cc.o -c /build/promod3-3.2.1+ds/loop/src/torsion_sampler.cc +[ 18%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/sidechain_atom_rule_lookup.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/sidechain_atom_rule_lookup.cc.o -MF CMakeFiles/promod3_loop.dir/sidechain_atom_rule_lookup.cc.o.d -o CMakeFiles/promod3_loop.dir/sidechain_atom_rule_lookup.cc.o -c /build/promod3-3.2.1+ds/loop/src/sidechain_atom_rule_lookup.cc [ 18%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/sidechain_atom_constructor.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/sidechain_atom_constructor.cc.o -MF CMakeFiles/promod3_loop.dir/sidechain_atom_constructor.cc.o.d -o CMakeFiles/promod3_loop.dir/sidechain_atom_constructor.cc.o -c /build/promod3-3.2.1+ds/loop/src/sidechain_atom_constructor.cc [ 19%] Linking CXX shared module ../../stage/lib64/python3.11/site-packages/promod3/core/_core.so @@ -2429,57 +2472,53 @@ make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' [ 19%] Built target promod3_loop make -f loop/pymod/CMakeFiles/_loop.dir/build.make loop/pymod/CMakeFiles/_loop.dir/depend +make -f scoring/src/CMakeFiles/promod3_scoring.dir/build.make scoring/src/CMakeFiles/promod3_scoring.dir/depend +make -f sidechain/src/CMakeFiles/promod3_sidechain.dir/build.make sidechain/src/CMakeFiles/promod3_sidechain.dir/depend make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/loop/pymod /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/pymod /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/pymod/CMakeFiles/_loop.dir/DependInfo.cmake --color= -make -f scoring/src/CMakeFiles/promod3_scoring.dir/build.make scoring/src/CMakeFiles/promod3_scoring.dir/depend make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/scoring/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src/CMakeFiles/promod3_scoring.dir/DependInfo.cmake --color= -make -f sidechain/src/CMakeFiles/promod3_sidechain.dir/build.make sidechain/src/CMakeFiles/promod3_sidechain.dir/depend make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/sidechain/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src/CMakeFiles/promod3_sidechain.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make -f loop/pymod/CMakeFiles/_loop.dir/build.make loop/pymod/CMakeFiles/_loop.dir/build make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make -f scoring/src/CMakeFiles/promod3_scoring.dir/build.make scoring/src/CMakeFiles/promod3_scoring.dir/build make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make -f sidechain/src/CMakeFiles/promod3_sidechain.dir/build.make sidechain/src/CMakeFiles/promod3_sidechain.dir/build -make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -[ 19%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_all_atom_env.cc.o +[ 21%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_amino_acid_atoms.cc.o +[ 21%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_all_atom_env.cc.o +[ 21%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_all_atom_positions.cc.o +[ 21%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_frag_db.cc.o +[ 22%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_mm_system_creator.cc.o +[ 22%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_loop_object_loader.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_loop_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_all_atom_env.cc.o -MF CMakeFiles/_loop.dir/export_all_atom_env.cc.o.d -o CMakeFiles/_loop.dir/export_all_atom_env.cc.o -c /build/promod3-3.2.1+ds/loop/pymod/export_all_atom_env.cc -[ 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-ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_all_atom_positions.cc.o -MF CMakeFiles/_loop.dir/export_all_atom_positions.cc.o.d -o CMakeFiles/_loop.dir/export_all_atom_positions.cc.o -c /build/promod3-3.2.1+ds/loop/pymod/export_all_atom_positions.cc -[ 22%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_amino_acid_atoms.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/backbone_score_base.cc.o -MF CMakeFiles/promod3_scoring.dir/backbone_score_base.cc.o.d -o CMakeFiles/promod3_scoring.dir/backbone_score_base.cc.o -c /build/promod3-3.2.1+ds/scoring/src/backbone_score_base.cc -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/backbone_overall_scorer.cc.o -MF CMakeFiles/promod3_scoring.dir/backbone_overall_scorer.cc.o.d -o CMakeFiles/promod3_scoring.dir/backbone_overall_scorer.cc.o -c /build/promod3-3.2.1+ds/scoring/src/backbone_overall_scorer.cc -[ 22%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_backbone.cc.o -[ 22%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/scoring_object_loader.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_loop_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_amino_acid_atoms.cc.o -MF CMakeFiles/_loop.dir/export_amino_acid_atoms.cc.o.d -o CMakeFiles/_loop.dir/export_amino_acid_atoms.cc.o -c /build/promod3-3.2.1+ds/loop/pymod/export_amino_acid_atoms.cc -[ 22%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/bb_dep_rotamer_lib.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/scoring_object_loader.cc.o -MF CMakeFiles/promod3_scoring.dir/scoring_object_loader.cc.o.d -o CMakeFiles/promod3_scoring.dir/scoring_object_loader.cc.o -c /build/promod3-3.2.1+ds/scoring/src/scoring_object_loader.cc -[ 23%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/cbeta_env_listener.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/bb_dep_rotamer_lib.cc.o -MF CMakeFiles/promod3_sidechain.dir/bb_dep_rotamer_lib.cc.o.d -o CMakeFiles/promod3_sidechain.dir/bb_dep_rotamer_lib.cc.o -c /build/promod3-3.2.1+ds/sidechain/src/bb_dep_rotamer_lib.cc -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_loop_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_backbone.cc.o -MF CMakeFiles/_loop.dir/export_backbone.cc.o.d -o CMakeFiles/_loop.dir/export_backbone.cc.o -c /build/promod3-3.2.1+ds/loop/pymod/export_backbone.cc -[ 25%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_forcefield_lookup.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/cbeta_env_listener.cc.o -MF CMakeFiles/promod3_scoring.dir/cbeta_env_listener.cc.o.d -o CMakeFiles/promod3_scoring.dir/cbeta_env_listener.cc.o -c /build/promod3-3.2.1+ds/scoring/src/cbeta_env_listener.cc -[ 26%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/disulfid.cc.o -[ 26%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/frame.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/disulfid.cc.o -MF CMakeFiles/promod3_sidechain.dir/disulfid.cc.o.d -o CMakeFiles/promod3_sidechain.dir/disulfid.cc.o -c /build/promod3-3.2.1+ds/sidechain/src/disulfid.cc +make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_loop_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_forcefield_lookup.cc.o -MF CMakeFiles/_loop.dir/export_forcefield_lookup.cc.o.d -o CMakeFiles/_loop.dir/export_forcefield_lookup.cc.o -c /build/promod3-3.2.1+ds/loop/pymod/export_forcefield_lookup.cc -[ 26%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/cb_packing_score.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/frame.cc.o -MF CMakeFiles/promod3_sidechain.dir/frame.cc.o.d -o CMakeFiles/promod3_sidechain.dir/frame.cc.o -c /build/promod3-3.2.1+ds/sidechain/src/frame.cc -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/cb_packing_score.cc.o -MF CMakeFiles/promod3_scoring.dir/cb_packing_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/cb_packing_score.cc.o -c /build/promod3-3.2.1+ds/scoring/src/cb_packing_score.cc -[ 26%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_frag_db.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_loop_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_frag_db.cc.o -MF CMakeFiles/_loop.dir/export_frag_db.cc.o.d -o CMakeFiles/_loop.dir/export_frag_db.cc.o -c /build/promod3-3.2.1+ds/loop/pymod/export_frag_db.cc -[ 26%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/particle_scoring.cc.o -[ 26%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/cbeta_score.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/particle_scoring.cc.o -MF CMakeFiles/promod3_sidechain.dir/particle_scoring.cc.o.d -o CMakeFiles/promod3_sidechain.dir/particle_scoring.cc.o -c /build/promod3-3.2.1+ds/sidechain/src/particle_scoring.cc -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/cbeta_score.cc.o -MF CMakeFiles/promod3_scoring.dir/cbeta_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/cbeta_score.cc.o -c /build/promod3-3.2.1+ds/scoring/src/cbeta_score.cc -[ 28%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/scwrl4_particle_scoring.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/scwrl4_particle_scoring.cc.o -MF CMakeFiles/promod3_sidechain.dir/scwrl4_particle_scoring.cc.o.d -o CMakeFiles/promod3_sidechain.dir/scwrl4_particle_scoring.cc.o -c /build/promod3-3.2.1+ds/sidechain/src/scwrl4_particle_scoring.cc +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_loop_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_loop_object_loader.cc.o -MF CMakeFiles/_loop.dir/export_loop_object_loader.cc.o.d -o CMakeFiles/_loop.dir/export_loop_object_loader.cc.o -c /build/promod3-3.2.1+ds/loop/pymod/export_loop_object_loader.cc +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_loop_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_mm_system_creator.cc.o -MF CMakeFiles/_loop.dir/export_mm_system_creator.cc.o.d -o CMakeFiles/_loop.dir/export_mm_system_creator.cc.o -c /build/promod3-3.2.1+ds/loop/pymod/export_mm_system_creator.cc +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_loop_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_psipred_prediction.cc.o -MF CMakeFiles/_loop.dir/export_psipred_prediction.cc.o.d -o CMakeFiles/_loop.dir/export_psipred_prediction.cc.o -c /build/promod3-3.2.1+ds/loop/pymod/export_psipred_prediction.cc +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_loop_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_structure_db.cc.o -MF CMakeFiles/_loop.dir/export_structure_db.cc.o.d -o CMakeFiles/_loop.dir/export_structure_db.cc.o -c /build/promod3-3.2.1+ds/loop/pymod/export_structure_db.cc +[ 25%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_backbone.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_loop_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_torsion_sampler.cc.o -MF CMakeFiles/_loop.dir/export_torsion_sampler.cc.o.d -o CMakeFiles/_loop.dir/export_torsion_sampler.cc.o -c /build/promod3-3.2.1+ds/loop/pymod/export_torsion_sampler.cc +[ 25%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_fragger.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_loop_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_backbone.cc.o -MF CMakeFiles/_loop.dir/export_backbone.cc.o.d -o CMakeFiles/_loop.dir/export_backbone.cc.o -c /build/promod3-3.2.1+ds/loop/pymod/export_backbone.cc +[ 26%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/wrap_loop.cc.o +[ 26%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/backbone_score_base.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_loop_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_fragger.cc.o -MF CMakeFiles/_loop.dir/export_fragger.cc.o.d -o CMakeFiles/_loop.dir/export_fragger.cc.o -c /build/promod3-3.2.1+ds/loop/pymod/export_fragger.cc +[ 26%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/bb_dep_rotamer_lib.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/backbone_score_base.cc.o -MF CMakeFiles/promod3_scoring.dir/backbone_score_base.cc.o.d -o CMakeFiles/promod3_scoring.dir/backbone_score_base.cc.o -c /build/promod3-3.2.1+ds/scoring/src/backbone_score_base.cc +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_loop_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/wrap_loop.cc.o -MF CMakeFiles/_loop.dir/wrap_loop.cc.o.d -o CMakeFiles/_loop.dir/wrap_loop.cc.o -c /build/promod3-3.2.1+ds/loop/pymod/wrap_loop.cc +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/bb_dep_rotamer_lib.cc.o -MF CMakeFiles/promod3_sidechain.dir/bb_dep_rotamer_lib.cc.o.d -o CMakeFiles/promod3_sidechain.dir/bb_dep_rotamer_lib.cc.o -c /build/promod3-3.2.1+ds/sidechain/src/bb_dep_rotamer_lib.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, @@ -2493,15 +2532,13 @@ 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/promod3-3.2.1+ds/loop/pymod/export_amino_acid_atoms.cc:17: + from /build/promod3-3.2.1+ds/loop/pymod/wrap_loop.cc:17: /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("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 28%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/scwrl3_particle_scoring.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/scwrl3_particle_scoring.cc.o -MF CMakeFiles/promod3_sidechain.dir/scwrl3_particle_scoring.cc.o.d -o CMakeFiles/promod3_sidechain.dir/scwrl3_particle_scoring.cc.o -c /build/promod3-3.2.1+ds/sidechain/src/scwrl3_particle_scoring.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, @@ -2515,7 +2552,7 @@ 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/promod3-3.2.1+ds/loop/pymod/export_forcefield_lookup.cc:17: + from /build/promod3-3.2.1+ds/loop/pymod/export_structure_db.cc:17: /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( | ^~~~~~~~~~~~~~~~~~~~ @@ -2535,7 +2572,7 @@ 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/promod3-3.2.1+ds/loop/pymod/export_backbone.cc:17: + from /build/promod3-3.2.1+ds/loop/pymod/export_torsion_sampler.cc:17: /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( | ^~~~~~~~~~~~~~~~~~~~ @@ -2555,15 +2592,15 @@ 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/promod3-3.2.1+ds/loop/pymod/export_all_atom_positions.cc:17: + from /build/promod3-3.2.1+ds/loop/pymod/export_forcefield_lookup.cc:17: /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 sidechain/src/CMakeFiles/promod3_sidechain.dir/vina_particle_scoring.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/vina_particle_scoring.cc.o -MF CMakeFiles/promod3_sidechain.dir/vina_particle_scoring.cc.o.d -o CMakeFiles/promod3_sidechain.dir/vina_particle_scoring.cc.o -c /build/promod3-3.2.1+ds/sidechain/src/vina_particle_scoring.cc +[ 28%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/backbone_overall_scorer.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/backbone_overall_scorer.cc.o -MF CMakeFiles/promod3_scoring.dir/backbone_overall_scorer.cc.o.d -o CMakeFiles/promod3_scoring.dir/backbone_overall_scorer.cc.o -c /build/promod3-3.2.1+ds/scoring/src/backbone_overall_scorer.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, @@ -2577,10 +2614,13 @@ 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/promod3-3.2.1+ds/loop/pymod/export_frag_db.cc:17: + from /build/promod3-3.2.1+ds/loop/pymod/export_all_atom_env.cc:17: /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, @@ -2594,54 +2634,13 @@ 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/promod3-3.2.1+ds/loop/pymod/export_all_atom_env.cc:17: + from /build/promod3-3.2.1+ds/loop/pymod/export_amino_acid_atoms.cc:17: /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 sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer.cc.o -MF CMakeFiles/promod3_sidechain.dir/rotamer.cc.o.d -o CMakeFiles/promod3_sidechain.dir/rotamer.cc.o -c /build/promod3-3.2.1+ds/sidechain/src/rotamer.cc -[ 30%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/reduced_env_listener.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/reduced_env_listener.cc.o -MF CMakeFiles/promod3_scoring.dir/reduced_env_listener.cc.o.d -o CMakeFiles/promod3_scoring.dir/reduced_env_listener.cc.o -c /build/promod3-3.2.1+ds/scoring/src/reduced_env_listener.cc -[ 30%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_cruncher.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_cruncher.cc.o -MF CMakeFiles/promod3_sidechain.dir/rotamer_cruncher.cc.o.d -o CMakeFiles/promod3_sidechain.dir/rotamer_cruncher.cc.o -c /build/promod3-3.2.1+ds/sidechain/src/rotamer_cruncher.cc -[ 30%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/reduced_score.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/reduced_score.cc.o -MF CMakeFiles/promod3_scoring.dir/reduced_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/reduced_score.cc.o -c /build/promod3-3.2.1+ds/scoring/src/reduced_score.cc -[ 32%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/clash_env_listener.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/clash_env_listener.cc.o -MF CMakeFiles/promod3_scoring.dir/clash_env_listener.cc.o.d -o CMakeFiles/promod3_scoring.dir/clash_env_listener.cc.o -c /build/promod3-3.2.1+ds/scoring/src/clash_env_listener.cc -[ 33%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_density.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_density.cc.o -MF CMakeFiles/promod3_sidechain.dir/rotamer_density.cc.o.d -o CMakeFiles/promod3_sidechain.dir/rotamer_density.cc.o -c /build/promod3-3.2.1+ds/sidechain/src/rotamer_density.cc -[ 33%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/clash_score.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/clash_score.cc.o -MF CMakeFiles/promod3_scoring.dir/clash_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/clash_score.cc.o -c /build/promod3-3.2.1+ds/scoring/src/clash_score.cc -[ 33%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_group.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_group.cc.o -MF CMakeFiles/promod3_sidechain.dir/rotamer_group.cc.o.d -o CMakeFiles/promod3_sidechain.dir/rotamer_group.cc.o -c /build/promod3-3.2.1+ds/sidechain/src/rotamer_group.cc -[ 33%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/density_score.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/density_score.cc.o -MF CMakeFiles/promod3_scoring.dir/density_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/density_score.cc.o -c /build/promod3-3.2.1+ds/scoring/src/density_score.cc -[ 33%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_fragger.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_loop_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_fragger.cc.o -MF CMakeFiles/_loop.dir/export_fragger.cc.o.d -o CMakeFiles/_loop.dir/export_fragger.cc.o -c /build/promod3-3.2.1+ds/loop/pymod/export_fragger.cc -[ 35%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/hbond_env_listener.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/hbond_env_listener.cc.o -MF CMakeFiles/promod3_scoring.dir/hbond_env_listener.cc.o.d -o CMakeFiles/promod3_scoring.dir/hbond_env_listener.cc.o -c /build/promod3-3.2.1+ds/scoring/src/hbond_env_listener.cc -[ 36%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_loop_object_loader.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_loop_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_loop_object_loader.cc.o -MF CMakeFiles/_loop.dir/export_loop_object_loader.cc.o.d -o CMakeFiles/_loop.dir/export_loop_object_loader.cc.o -c /build/promod3-3.2.1+ds/loop/pymod/export_loop_object_loader.cc -[ 38%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_id.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_id.cc.o -MF CMakeFiles/promod3_sidechain.dir/rotamer_id.cc.o.d -o CMakeFiles/promod3_sidechain.dir/rotamer_id.cc.o -c /build/promod3-3.2.1+ds/sidechain/src/rotamer_id.cc -[ 38%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_lib.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_lib.cc.o -MF CMakeFiles/promod3_sidechain.dir/rotamer_lib.cc.o.d -o CMakeFiles/promod3_sidechain.dir/rotamer_lib.cc.o -c /build/promod3-3.2.1+ds/sidechain/src/rotamer_lib.cc -[ 38%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/hbond_score.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/hbond_score.cc.o -MF CMakeFiles/promod3_scoring.dir/hbond_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/hbond_score.cc.o -c /build/promod3-3.2.1+ds/scoring/src/hbond_score.cc -[ 38%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_lib_entry.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_lib_entry.cc.o -MF CMakeFiles/promod3_sidechain.dir/rotamer_lib_entry.cc.o.d -o CMakeFiles/promod3_sidechain.dir/rotamer_lib_entry.cc.o -c /build/promod3-3.2.1+ds/sidechain/src/rotamer_lib_entry.cc -[ 38%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_mm_system_creator.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_loop_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_mm_system_creator.cc.o -MF CMakeFiles/_loop.dir/export_mm_system_creator.cc.o.d -o CMakeFiles/_loop.dir/export_mm_system_creator.cc.o -c /build/promod3-3.2.1+ds/loop/pymod/export_mm_system_creator.cc -[ 39%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/ss_agreement_score.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/ss_agreement_score.cc.o -MF CMakeFiles/promod3_scoring.dir/ss_agreement_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/ss_agreement_score.cc.o -c /build/promod3-3.2.1+ds/scoring/src/ss_agreement_score.cc -[ 40%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_lib_reader.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_lib_reader.cc.o -MF CMakeFiles/promod3_sidechain.dir/rotamer_lib_reader.cc.o.d -o CMakeFiles/promod3_sidechain.dir/rotamer_lib_reader.cc.o -c /build/promod3-3.2.1+ds/sidechain/src/rotamer_lib_reader.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, @@ -2655,23 +2654,13 @@ 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/promod3-3.2.1+ds/loop/pymod/export_fragger.cc:17: + from /build/promod3-3.2.1+ds/loop/pymod/export_backbone.cc:17: /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("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 42%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_psipred_prediction.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_loop_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_psipred_prediction.cc.o -MF CMakeFiles/_loop.dir/export_psipred_prediction.cc.o.d -o CMakeFiles/_loop.dir/export_psipred_prediction.cc.o -c /build/promod3-3.2.1+ds/loop/pymod/export_psipred_prediction.cc -[ 42%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/ss_agreement_env_listener.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/ss_agreement_env_listener.cc.o -MF CMakeFiles/promod3_scoring.dir/ss_agreement_env_listener.cc.o.d -o CMakeFiles/promod3_scoring.dir/ss_agreement_env_listener.cc.o -c /build/promod3-3.2.1+ds/scoring/src/ss_agreement_env_listener.cc -[ 42%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/torsion_score.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/torsion_score.cc.o -MF CMakeFiles/promod3_scoring.dir/torsion_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/torsion_score.cc.o -c /build/promod3-3.2.1+ds/scoring/src/torsion_score.cc -[ 43%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/pairwise_score.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/pairwise_score.cc.o -MF CMakeFiles/promod3_scoring.dir/pairwise_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/pairwise_score.cc.o -c /build/promod3-3.2.1+ds/scoring/src/pairwise_score.cc -[ 43%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/sidechain_connector.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/sidechain_connector.cc.o -MF CMakeFiles/promod3_sidechain.dir/sidechain_connector.cc.o.d -o CMakeFiles/promod3_sidechain.dir/sidechain_connector.cc.o -c /build/promod3-3.2.1+ds/sidechain/src/sidechain_connector.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, @@ -2685,15 +2674,13 @@ 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/promod3-3.2.1+ds/loop/pymod/export_loop_object_loader.cc:17: + from /build/promod3-3.2.1+ds/loop/pymod/export_psipred_prediction.cc:17: /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("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 45%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/sidechain_object_loader.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/sidechain_object_loader.cc.o -MF CMakeFiles/promod3_sidechain.dir/sidechain_object_loader.cc.o.d -o CMakeFiles/promod3_sidechain.dir/sidechain_object_loader.cc.o -c /build/promod3-3.2.1+ds/sidechain/src/sidechain_object_loader.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, @@ -2707,17 +2694,10 @@ 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/promod3-3.2.1+ds/loop/pymod/export_mm_system_creator.cc:17: + from /build/promod3-3.2.1+ds/loop/pymod/export_frag_db.cc:17: /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("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 45%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/constraint_constructor.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/constraint_constructor.cc.o -MF CMakeFiles/promod3_scoring.dir/constraint_constructor.cc.o.d -o CMakeFiles/promod3_scoring.dir/constraint_constructor.cc.o -c /build/promod3-3.2.1+ds/scoring/src/constraint_constructor.cc -[ 45%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_structure_db.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_loop_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_structure_db.cc.o -MF CMakeFiles/_loop.dir/export_structure_db.cc.o.d -o CMakeFiles/_loop.dir/export_structure_db.cc.o -c /build/promod3-3.2.1+ds/loop/pymod/export_structure_db.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, @@ -2731,37 +2711,16 @@ 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/promod3-3.2.1+ds/loop/pymod/export_psipred_prediction.cc:17: + from /build/promod3-3.2.1+ds/loop/pymod/export_all_atom_positions.cc:17: /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( | ^~~~~~~~~~~~~~~~~~~~ -[ 45%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_constructor.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_constructor.cc.o -MF CMakeFiles/promod3_sidechain.dir/rotamer_constructor.cc.o.d -o CMakeFiles/promod3_sidechain.dir/rotamer_constructor.cc.o -c /build/promod3-3.2.1+ds/sidechain/src/rotamer_constructor.cc /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 46%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_overall_scorer.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_overall_scorer.cc.o -MF CMakeFiles/promod3_scoring.dir/all_atom_overall_scorer.cc.o.d -o CMakeFiles/promod3_scoring.dir/all_atom_overall_scorer.cc.o -c /build/promod3-3.2.1+ds/scoring/src/all_atom_overall_scorer.cc -[ 46%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_lookup.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_lookup.cc.o -MF CMakeFiles/promod3_sidechain.dir/rotamer_lookup.cc.o.d -o CMakeFiles/promod3_sidechain.dir/rotamer_lookup.cc.o -c /build/promod3-3.2.1+ds/sidechain/src/rotamer_lookup.cc -[ 46%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_interaction_env_listener.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_interaction_env_listener.cc.o -MF CMakeFiles/promod3_scoring.dir/all_atom_interaction_env_listener.cc.o.d -o CMakeFiles/promod3_scoring.dir/all_atom_interaction_env_listener.cc.o -c /build/promod3-3.2.1+ds/scoring/src/all_atom_interaction_env_listener.cc -[ 46%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_torsion_sampler.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_loop_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_torsion_sampler.cc.o -MF CMakeFiles/_loop.dir/export_torsion_sampler.cc.o.d -o CMakeFiles/_loop.dir/export_torsion_sampler.cc.o -c /build/promod3-3.2.1+ds/loop/pymod/export_torsion_sampler.cc -[ 47%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_interaction_score.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_interaction_score.cc.o -MF CMakeFiles/promod3_scoring.dir/all_atom_interaction_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/all_atom_interaction_score.cc.o -c /build/promod3-3.2.1+ds/scoring/src/all_atom_interaction_score.cc -[ 49%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/wrap_loop.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_loop_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/wrap_loop.cc.o -MF CMakeFiles/_loop.dir/wrap_loop.cc.o.d -o CMakeFiles/_loop.dir/wrap_loop.cc.o -c /build/promod3-3.2.1+ds/loop/pymod/wrap_loop.cc -[ 49%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_packing_score.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_packing_score.cc.o -MF CMakeFiles/promod3_scoring.dir/all_atom_packing_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/all_atom_packing_score.cc.o -c /build/promod3-3.2.1+ds/scoring/src/all_atom_packing_score.cc -[ 50%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/scwrl4_rotamer_constructor.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/scwrl4_rotamer_constructor.cc.o -MF CMakeFiles/promod3_sidechain.dir/scwrl4_rotamer_constructor.cc.o.d -o CMakeFiles/promod3_sidechain.dir/scwrl4_rotamer_constructor.cc.o -c /build/promod3-3.2.1+ds/sidechain/src/scwrl4_rotamer_constructor.cc -[ 50%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/scwrl3_rotamer_constructor.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/scwrl3_rotamer_constructor.cc.o -MF CMakeFiles/promod3_sidechain.dir/scwrl3_rotamer_constructor.cc.o.d -o CMakeFiles/promod3_sidechain.dir/scwrl3_rotamer_constructor.cc.o -c /build/promod3-3.2.1+ds/sidechain/src/scwrl3_rotamer_constructor.cc -[ 52%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/vina_rotamer_constructor.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/vina_rotamer_constructor.cc.o -MF CMakeFiles/promod3_sidechain.dir/vina_rotamer_constructor.cc.o.d -o CMakeFiles/promod3_sidechain.dir/vina_rotamer_constructor.cc.o -c /build/promod3-3.2.1+ds/sidechain/src/vina_rotamer_constructor.cc -[ 52%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_clash_score.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_clash_score.cc.o -MF CMakeFiles/promod3_scoring.dir/all_atom_clash_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/all_atom_clash_score.cc.o -c /build/promod3-3.2.1+ds/scoring/src/all_atom_clash_score.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, @@ -2775,15 +2734,13 @@ 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/promod3-3.2.1+ds/loop/pymod/export_structure_db.cc:17: + from /build/promod3-3.2.1+ds/loop/pymod/export_loop_object_loader.cc:17: /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%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/subrotamer_optimizer.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/subrotamer_optimizer.cc.o -MF CMakeFiles/promod3_sidechain.dir/subrotamer_optimizer.cc.o.d -o CMakeFiles/promod3_sidechain.dir/subrotamer_optimizer.cc.o -c /build/promod3-3.2.1+ds/sidechain/src/subrotamer_optimizer.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, @@ -2797,7 +2754,7 @@ 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/promod3-3.2.1+ds/loop/pymod/export_torsion_sampler.cc:17: + from /build/promod3-3.2.1+ds/loop/pymod/export_mm_system_creator.cc:17: /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( | ^~~~~~~~~~~~~~~~~~~~ @@ -2817,13 +2774,104 @@ 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/promod3-3.2.1+ds/loop/pymod/wrap_loop.cc:17: + from /build/promod3-3.2.1+ds/loop/pymod/export_fragger.cc:17: /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 sidechain/src/CMakeFiles/promod3_sidechain.dir/disulfid.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/disulfid.cc.o -MF CMakeFiles/promod3_sidechain.dir/disulfid.cc.o.d -o CMakeFiles/promod3_sidechain.dir/disulfid.cc.o -c /build/promod3-3.2.1+ds/sidechain/src/disulfid.cc +[ 29%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/frame.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/frame.cc.o -MF CMakeFiles/promod3_sidechain.dir/frame.cc.o.d -o CMakeFiles/promod3_sidechain.dir/frame.cc.o -c /build/promod3-3.2.1+ds/sidechain/src/frame.cc +[ 29%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/particle_scoring.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/particle_scoring.cc.o -MF CMakeFiles/promod3_sidechain.dir/particle_scoring.cc.o.d -o CMakeFiles/promod3_sidechain.dir/particle_scoring.cc.o -c /build/promod3-3.2.1+ds/sidechain/src/particle_scoring.cc +[ 29%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/scoring_object_loader.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/scoring_object_loader.cc.o -MF CMakeFiles/promod3_scoring.dir/scoring_object_loader.cc.o.d -o CMakeFiles/promod3_scoring.dir/scoring_object_loader.cc.o -c /build/promod3-3.2.1+ds/scoring/src/scoring_object_loader.cc +[ 30%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/scwrl4_particle_scoring.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/scwrl4_particle_scoring.cc.o -MF CMakeFiles/promod3_sidechain.dir/scwrl4_particle_scoring.cc.o.d -o CMakeFiles/promod3_sidechain.dir/scwrl4_particle_scoring.cc.o -c /build/promod3-3.2.1+ds/sidechain/src/scwrl4_particle_scoring.cc +[ 32%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/cbeta_env_listener.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/cbeta_env_listener.cc.o -MF CMakeFiles/promod3_scoring.dir/cbeta_env_listener.cc.o.d -o CMakeFiles/promod3_scoring.dir/cbeta_env_listener.cc.o -c /build/promod3-3.2.1+ds/scoring/src/cbeta_env_listener.cc +[ 32%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/scwrl3_particle_scoring.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/scwrl3_particle_scoring.cc.o -MF CMakeFiles/promod3_sidechain.dir/scwrl3_particle_scoring.cc.o.d -o CMakeFiles/promod3_sidechain.dir/scwrl3_particle_scoring.cc.o -c /build/promod3-3.2.1+ds/sidechain/src/scwrl3_particle_scoring.cc +[ 32%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/cb_packing_score.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/cb_packing_score.cc.o -MF CMakeFiles/promod3_scoring.dir/cb_packing_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/cb_packing_score.cc.o -c /build/promod3-3.2.1+ds/scoring/src/cb_packing_score.cc +[ 33%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/vina_particle_scoring.cc.o +[ 33%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer.cc.o -MF CMakeFiles/promod3_sidechain.dir/rotamer.cc.o.d -o CMakeFiles/promod3_sidechain.dir/rotamer.cc.o -c /build/promod3-3.2.1+ds/sidechain/src/rotamer.cc +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/vina_particle_scoring.cc.o -MF CMakeFiles/promod3_sidechain.dir/vina_particle_scoring.cc.o.d -o CMakeFiles/promod3_sidechain.dir/vina_particle_scoring.cc.o -c /build/promod3-3.2.1+ds/sidechain/src/vina_particle_scoring.cc +[ 33%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_cruncher.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_cruncher.cc.o -MF CMakeFiles/promod3_sidechain.dir/rotamer_cruncher.cc.o.d -o CMakeFiles/promod3_sidechain.dir/rotamer_cruncher.cc.o -c /build/promod3-3.2.1+ds/sidechain/src/rotamer_cruncher.cc +[ 35%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_density.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_density.cc.o -MF CMakeFiles/promod3_sidechain.dir/rotamer_density.cc.o.d -o CMakeFiles/promod3_sidechain.dir/rotamer_density.cc.o -c /build/promod3-3.2.1+ds/sidechain/src/rotamer_density.cc +[ 35%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_group.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_group.cc.o -MF CMakeFiles/promod3_sidechain.dir/rotamer_group.cc.o.d -o CMakeFiles/promod3_sidechain.dir/rotamer_group.cc.o -c /build/promod3-3.2.1+ds/sidechain/src/rotamer_group.cc +[ 36%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_id.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_id.cc.o -MF CMakeFiles/promod3_sidechain.dir/rotamer_id.cc.o.d -o CMakeFiles/promod3_sidechain.dir/rotamer_id.cc.o -c /build/promod3-3.2.1+ds/sidechain/src/rotamer_id.cc +[ 36%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/cbeta_score.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/cbeta_score.cc.o -MF CMakeFiles/promod3_scoring.dir/cbeta_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/cbeta_score.cc.o -c /build/promod3-3.2.1+ds/scoring/src/cbeta_score.cc +[ 38%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/reduced_env_listener.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/reduced_env_listener.cc.o -MF CMakeFiles/promod3_scoring.dir/reduced_env_listener.cc.o.d -o CMakeFiles/promod3_scoring.dir/reduced_env_listener.cc.o -c /build/promod3-3.2.1+ds/scoring/src/reduced_env_listener.cc +[ 38%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_lib.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_lib.cc.o -MF CMakeFiles/promod3_sidechain.dir/rotamer_lib.cc.o.d -o CMakeFiles/promod3_sidechain.dir/rotamer_lib.cc.o -c /build/promod3-3.2.1+ds/sidechain/src/rotamer_lib.cc +[ 38%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_lib_entry.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_lib_entry.cc.o -MF CMakeFiles/promod3_sidechain.dir/rotamer_lib_entry.cc.o.d -o CMakeFiles/promod3_sidechain.dir/rotamer_lib_entry.cc.o -c /build/promod3-3.2.1+ds/sidechain/src/rotamer_lib_entry.cc +[ 39%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_lib_reader.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_lib_reader.cc.o -MF CMakeFiles/promod3_sidechain.dir/rotamer_lib_reader.cc.o.d -o CMakeFiles/promod3_sidechain.dir/rotamer_lib_reader.cc.o -c /build/promod3-3.2.1+ds/sidechain/src/rotamer_lib_reader.cc +[ 39%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/sidechain_connector.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/sidechain_connector.cc.o -MF CMakeFiles/promod3_sidechain.dir/sidechain_connector.cc.o.d -o CMakeFiles/promod3_sidechain.dir/sidechain_connector.cc.o -c /build/promod3-3.2.1+ds/sidechain/src/sidechain_connector.cc +[ 39%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/reduced_score.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/reduced_score.cc.o -MF CMakeFiles/promod3_scoring.dir/reduced_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/reduced_score.cc.o -c /build/promod3-3.2.1+ds/scoring/src/reduced_score.cc +[ 40%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/sidechain_object_loader.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/sidechain_object_loader.cc.o -MF CMakeFiles/promod3_sidechain.dir/sidechain_object_loader.cc.o.d -o CMakeFiles/promod3_sidechain.dir/sidechain_object_loader.cc.o -c /build/promod3-3.2.1+ds/sidechain/src/sidechain_object_loader.cc +[ 40%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_constructor.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_constructor.cc.o -MF CMakeFiles/promod3_sidechain.dir/rotamer_constructor.cc.o.d -o CMakeFiles/promod3_sidechain.dir/rotamer_constructor.cc.o -c /build/promod3-3.2.1+ds/sidechain/src/rotamer_constructor.cc +[ 40%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_lookup.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_lookup.cc.o -MF CMakeFiles/promod3_sidechain.dir/rotamer_lookup.cc.o.d -o CMakeFiles/promod3_sidechain.dir/rotamer_lookup.cc.o -c /build/promod3-3.2.1+ds/sidechain/src/rotamer_lookup.cc +[ 42%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/clash_env_listener.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/clash_env_listener.cc.o -MF CMakeFiles/promod3_scoring.dir/clash_env_listener.cc.o.d -o CMakeFiles/promod3_scoring.dir/clash_env_listener.cc.o -c /build/promod3-3.2.1+ds/scoring/src/clash_env_listener.cc +[ 42%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/clash_score.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/clash_score.cc.o -MF CMakeFiles/promod3_scoring.dir/clash_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/clash_score.cc.o -c /build/promod3-3.2.1+ds/scoring/src/clash_score.cc +[ 43%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/scwrl4_rotamer_constructor.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/scwrl4_rotamer_constructor.cc.o -MF CMakeFiles/promod3_sidechain.dir/scwrl4_rotamer_constructor.cc.o.d -o CMakeFiles/promod3_sidechain.dir/scwrl4_rotamer_constructor.cc.o -c /build/promod3-3.2.1+ds/sidechain/src/scwrl4_rotamer_constructor.cc +[ 43%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/scwrl3_rotamer_constructor.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/scwrl3_rotamer_constructor.cc.o -MF CMakeFiles/promod3_sidechain.dir/scwrl3_rotamer_constructor.cc.o.d -o CMakeFiles/promod3_sidechain.dir/scwrl3_rotamer_constructor.cc.o -c /build/promod3-3.2.1+ds/sidechain/src/scwrl3_rotamer_constructor.cc +[ 45%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/vina_rotamer_constructor.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/vina_rotamer_constructor.cc.o -MF CMakeFiles/promod3_sidechain.dir/vina_rotamer_constructor.cc.o.d -o CMakeFiles/promod3_sidechain.dir/vina_rotamer_constructor.cc.o -c /build/promod3-3.2.1+ds/sidechain/src/vina_rotamer_constructor.cc +[ 45%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/subrotamer_optimizer.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/subrotamer_optimizer.cc.o -MF CMakeFiles/promod3_sidechain.dir/subrotamer_optimizer.cc.o.d -o CMakeFiles/promod3_sidechain.dir/subrotamer_optimizer.cc.o -c /build/promod3-3.2.1+ds/sidechain/src/subrotamer_optimizer.cc +[ 45%] Linking CXX shared module ../../stage/lib64/python3.11/site-packages/promod3/loop/_loop.so +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_loop.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -o ../../stage/lib64/python3.11/site-packages/promod3/loop/_loop.so CMakeFiles/_loop.dir/export_all_atom_env.cc.o CMakeFiles/_loop.dir/export_all_atom_positions.cc.o CMakeFiles/_loop.dir/export_amino_acid_atoms.cc.o CMakeFiles/_loop.dir/export_backbone.cc.o CMakeFiles/_loop.dir/export_forcefield_lookup.cc.o CMakeFiles/_loop.dir/export_frag_db.cc.o CMakeFiles/_loop.dir/export_fragger.cc.o CMakeFiles/_loop.dir/export_loop_object_loader.cc.o CMakeFiles/_loop.dir/export_mm_system_creator.cc.o CMakeFiles/_loop.dir/export_psipred_prediction.cc.o CMakeFiles/_loop.dir/export_structure_db.cc.o CMakeFiles/_loop.dir/export_torsion_sampler.cc.o CMakeFiles/_loop.dir/wrap_loop.cc.o -L/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64: ../../stage/lib64/libpromod3_loop.so.3.2.1 /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.74.0 ../../stage/lib64/libpromod3_core.so.3.2.1 /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.74.0 +[ 45%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/density_score.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/density_score.cc.o -MF CMakeFiles/promod3_scoring.dir/density_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/density_score.cc.o -c /build/promod3-3.2.1+ds/scoring/src/density_score.cc +[ 46%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/hbond_env_listener.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/hbond_env_listener.cc.o -MF CMakeFiles/promod3_scoring.dir/hbond_env_listener.cc.o.d -o CMakeFiles/promod3_scoring.dir/hbond_env_listener.cc.o -c /build/promod3-3.2.1+ds/scoring/src/hbond_env_listener.cc +[ 46%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/hbond_score.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/hbond_score.cc.o -MF CMakeFiles/promod3_scoring.dir/hbond_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/hbond_score.cc.o -c /build/promod3-3.2.1+ds/scoring/src/hbond_score.cc +make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +[ 46%] Built target _loop +[ 47%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/ss_agreement_score.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/ss_agreement_score.cc.o -MF CMakeFiles/promod3_scoring.dir/ss_agreement_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/ss_agreement_score.cc.o -c /build/promod3-3.2.1+ds/scoring/src/ss_agreement_score.cc +[ 47%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/ss_agreement_env_listener.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/ss_agreement_env_listener.cc.o -MF CMakeFiles/promod3_scoring.dir/ss_agreement_env_listener.cc.o.d -o CMakeFiles/promod3_scoring.dir/ss_agreement_env_listener.cc.o -c /build/promod3-3.2.1+ds/scoring/src/ss_agreement_env_listener.cc +[ 47%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/torsion_score.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/torsion_score.cc.o -MF CMakeFiles/promod3_scoring.dir/torsion_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/torsion_score.cc.o -c /build/promod3-3.2.1+ds/scoring/src/torsion_score.cc +[ 49%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/pairwise_score.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/pairwise_score.cc.o -MF CMakeFiles/promod3_scoring.dir/pairwise_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/pairwise_score.cc.o -c /build/promod3-3.2.1+ds/scoring/src/pairwise_score.cc +[ 49%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/constraint_constructor.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/constraint_constructor.cc.o -MF CMakeFiles/promod3_scoring.dir/constraint_constructor.cc.o.d -o CMakeFiles/promod3_scoring.dir/constraint_constructor.cc.o -c /build/promod3-3.2.1+ds/scoring/src/constraint_constructor.cc +[ 50%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_overall_scorer.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_overall_scorer.cc.o -MF CMakeFiles/promod3_scoring.dir/all_atom_overall_scorer.cc.o.d -o CMakeFiles/promod3_scoring.dir/all_atom_overall_scorer.cc.o -c /build/promod3-3.2.1+ds/scoring/src/all_atom_overall_scorer.cc +[ 50%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_interaction_env_listener.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_interaction_env_listener.cc.o -MF CMakeFiles/promod3_scoring.dir/all_atom_interaction_env_listener.cc.o.d -o CMakeFiles/promod3_scoring.dir/all_atom_interaction_env_listener.cc.o -c /build/promod3-3.2.1+ds/scoring/src/all_atom_interaction_env_listener.cc +[ 52%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_interaction_score.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_interaction_score.cc.o -MF CMakeFiles/promod3_scoring.dir/all_atom_interaction_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/all_atom_interaction_score.cc.o -c /build/promod3-3.2.1+ds/scoring/src/all_atom_interaction_score.cc +[ 52%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_packing_score.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_packing_score.cc.o -MF CMakeFiles/promod3_scoring.dir/all_atom_packing_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/all_atom_packing_score.cc.o -c /build/promod3-3.2.1+ds/scoring/src/all_atom_packing_score.cc +[ 52%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_clash_score.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_clash_score.cc.o -MF CMakeFiles/promod3_scoring.dir/all_atom_clash_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/all_atom_clash_score.cc.o -c /build/promod3-3.2.1+ds/scoring/src/all_atom_clash_score.cc [ 53%] Linking CXX shared library ../../stage/lib64/libpromod3_scoring.so cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/promod3_scoring.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libpromod3_scoring.so.3.2 -o ../../stage/lib64/libpromod3_scoring.so.3.2.1 CMakeFiles/promod3_scoring.dir/backbone_score_base.cc.o CMakeFiles/promod3_scoring.dir/backbone_overall_scorer.cc.o CMakeFiles/promod3_scoring.dir/scoring_object_loader.cc.o CMakeFiles/promod3_scoring.dir/cbeta_env_listener.cc.o CMakeFiles/promod3_scoring.dir/cb_packing_score.cc.o CMakeFiles/promod3_scoring.dir/cbeta_score.cc.o CMakeFiles/promod3_scoring.dir/reduced_env_listener.cc.o CMakeFiles/promod3_scoring.dir/reduced_score.cc.o CMakeFiles/promod3_scoring.dir/clash_env_listener.cc.o CMakeFiles/promod3_scoring.dir/clash_score.cc.o CMakeFiles/promod3_scoring.dir/density_score.cc.o CMakeFiles/promod3_scoring.dir/hbond_env_listener.cc.o CMakeFiles/promod3_scoring.dir/hbond_score.cc.o CMakeFiles/promod3_scoring.dir/ss_agreement_score.cc.o CMakeFiles/promod3_scoring.dir/ss_agreement_env_listener.cc.o CMakeFiles/promod3_scoring.dir/torsion_score.cc.o CMakeFiles/promod3_scoring.dir/pairwise_score.cc.o CMakeFiles/promod3_scoring.dir/constraint_constructor.cc.o CMakeFiles/promod3_scoring.dir/all_atom_overall_scorer.cc.o CMakeFiles/promod3_scoring.dir/all_atom_interaction_env_listener.cc.o CMakeFiles/promod3_scoring.dir/all_atom_interaction_score.cc.o CMakeFiles/promod3_scoring.dir/all_atom_packing_score.cc.o CMakeFiles/promod3_scoring.dir/all_atom_clash_score.cc.o -L/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64: /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so ../../stage/lib64/libpromod3_loop.so.3.2.1 ../../stage/lib64/libpromod3_core.so.3.2.1 /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.74.0 @@ -2838,20 +2886,54 @@ make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' [ 53%] Building CXX object scoring/pymod/CMakeFiles/_scoring.dir/export_backbone_score.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_scoring_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/pymod/CMakeFiles/_scoring.dir/export_backbone_score.cc.o -MF CMakeFiles/_scoring.dir/export_backbone_score.cc.o.d -o CMakeFiles/_scoring.dir/export_backbone_score.cc.o -c /build/promod3-3.2.1+ds/scoring/pymod/export_backbone_score.cc -[ 54%] Building CXX object scoring/pymod/CMakeFiles/_scoring.dir/export_all_atom_score.cc.o +[ 53%] Building CXX object scoring/pymod/CMakeFiles/_scoring.dir/export_constraint_constructor.cc.o +[ 54%] Building CXX object scoring/pymod/CMakeFiles/_scoring.dir/export_pairwise_functions.cc.o [ 54%] Building CXX object scoring/pymod/CMakeFiles/_scoring.dir/export_object_loader.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_scoring_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/pymod/CMakeFiles/_scoring.dir/export_all_atom_score.cc.o -MF CMakeFiles/_scoring.dir/export_all_atom_score.cc.o.d -o CMakeFiles/_scoring.dir/export_all_atom_score.cc.o -c /build/promod3-3.2.1+ds/scoring/pymod/export_all_atom_score.cc -[ 56%] Building CXX object scoring/pymod/CMakeFiles/_scoring.dir/export_pairwise_functions.cc.o +[ 56%] Building CXX object scoring/pymod/CMakeFiles/_scoring.dir/export_all_atom_score.cc.o +[ 56%] Building CXX object scoring/pymod/CMakeFiles/_scoring.dir/wrap_scoring.cc.o +[ 57%] Building CXX object scoring/pymod/CMakeFiles/_scoring.dir/export_scwrl3_energy_functions.cc.o +[ 57%] Building CXX object scoring/pymod/CMakeFiles/_scoring.dir/export_density_scorer.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_scoring_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/pymod/CMakeFiles/_scoring.dir/export_constraint_constructor.cc.o -MF CMakeFiles/_scoring.dir/export_constraint_constructor.cc.o.d -o CMakeFiles/_scoring.dir/export_constraint_constructor.cc.o -c /build/promod3-3.2.1+ds/scoring/pymod/export_constraint_constructor.cc cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_scoring_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/pymod/CMakeFiles/_scoring.dir/export_object_loader.cc.o -MF CMakeFiles/_scoring.dir/export_object_loader.cc.o.d -o CMakeFiles/_scoring.dir/export_object_loader.cc.o -c /build/promod3-3.2.1+ds/scoring/pymod/export_object_loader.cc -[ 56%] Building CXX object scoring/pymod/CMakeFiles/_scoring.dir/export_scwrl3_energy_functions.cc.o -[ 56%] Building CXX object scoring/pymod/CMakeFiles/_scoring.dir/export_constraint_constructor.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_scoring_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/pymod/CMakeFiles/_scoring.dir/export_pairwise_functions.cc.o -MF CMakeFiles/_scoring.dir/export_pairwise_functions.cc.o.d -o CMakeFiles/_scoring.dir/export_pairwise_functions.cc.o -c /build/promod3-3.2.1+ds/scoring/pymod/export_pairwise_functions.cc -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_scoring_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/pymod/CMakeFiles/_scoring.dir/export_constraint_constructor.cc.o -MF CMakeFiles/_scoring.dir/export_constraint_constructor.cc.o.d -o CMakeFiles/_scoring.dir/export_constraint_constructor.cc.o -c /build/promod3-3.2.1+ds/scoring/pymod/export_constraint_constructor.cc -[ 57%] Building CXX object scoring/pymod/CMakeFiles/_scoring.dir/export_density_scorer.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_scoring_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/pymod/CMakeFiles/_scoring.dir/export_all_atom_score.cc.o -MF CMakeFiles/_scoring.dir/export_all_atom_score.cc.o.d -o CMakeFiles/_scoring.dir/export_all_atom_score.cc.o -c /build/promod3-3.2.1+ds/scoring/pymod/export_all_atom_score.cc cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_scoring_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/pymod/CMakeFiles/_scoring.dir/export_scwrl3_energy_functions.cc.o -MF CMakeFiles/_scoring.dir/export_scwrl3_energy_functions.cc.o.d -o CMakeFiles/_scoring.dir/export_scwrl3_energy_functions.cc.o -c /build/promod3-3.2.1+ds/scoring/pymod/export_scwrl3_energy_functions.cc cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_scoring_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/pymod/CMakeFiles/_scoring.dir/export_density_scorer.cc.o -MF CMakeFiles/_scoring.dir/export_density_scorer.cc.o.d -o CMakeFiles/_scoring.dir/export_density_scorer.cc.o -c /build/promod3-3.2.1+ds/scoring/pymod/export_density_scorer.cc -[ 57%] Building CXX object scoring/pymod/CMakeFiles/_scoring.dir/wrap_scoring.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_scoring_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/pymod/CMakeFiles/_scoring.dir/wrap_scoring.cc.o -MF CMakeFiles/_scoring.dir/wrap_scoring.cc.o.d -o CMakeFiles/_scoring.dir/wrap_scoring.cc.o -c /build/promod3-3.2.1+ds/scoring/pymod/wrap_scoring.cc +[ 59%] Linking CXX shared library ../../stage/lib64/libpromod3_sidechain.so +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/promod3_sidechain.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libpromod3_sidechain.so.3.2 -o ../../stage/lib64/libpromod3_sidechain.so.3.2.1 CMakeFiles/promod3_sidechain.dir/bb_dep_rotamer_lib.cc.o CMakeFiles/promod3_sidechain.dir/disulfid.cc.o CMakeFiles/promod3_sidechain.dir/frame.cc.o CMakeFiles/promod3_sidechain.dir/particle_scoring.cc.o CMakeFiles/promod3_sidechain.dir/scwrl4_particle_scoring.cc.o CMakeFiles/promod3_sidechain.dir/scwrl3_particle_scoring.cc.o CMakeFiles/promod3_sidechain.dir/vina_particle_scoring.cc.o CMakeFiles/promod3_sidechain.dir/rotamer.cc.o CMakeFiles/promod3_sidechain.dir/rotamer_cruncher.cc.o CMakeFiles/promod3_sidechain.dir/rotamer_density.cc.o CMakeFiles/promod3_sidechain.dir/rotamer_group.cc.o CMakeFiles/promod3_sidechain.dir/rotamer_id.cc.o CMakeFiles/promod3_sidechain.dir/rotamer_lib.cc.o CMakeFiles/promod3_sidechain.dir/rotamer_lib_entry.cc.o CMakeFiles/promod3_sidechain.dir/rotamer_lib_reader.cc.o CMakeFiles/promod3_sidechain.dir/sidechain_connector.cc.o CMakeFiles/promod3_sidechain.dir/sidechain_object_loader.cc.o CMakeFiles/promod3_sidechain.dir/rotamer_constructor.cc.o CMakeFiles/promod3_sidechain.dir/rotamer_lookup.cc.o CMakeFiles/promod3_sidechain.dir/scwrl4_rotamer_constructor.cc.o CMakeFiles/promod3_sidechain.dir/scwrl3_rotamer_constructor.cc.o CMakeFiles/promod3_sidechain.dir/vina_rotamer_constructor.cc.o CMakeFiles/promod3_sidechain.dir/subrotamer_optimizer.cc.o -L/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64: /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so ../../stage/lib64/libpromod3_loop.so.3.2.1 ../../stage/lib64/libpromod3_core.so.3.2.1 /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.74.0 +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E cmake_symlink_library ../../stage/lib64/libpromod3_sidechain.so.3.2.1 ../../stage/lib64/libpromod3_sidechain.so.3.2 ../../stage/lib64/libpromod3_sidechain.so +make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +[ 59%] Built target promod3_sidechain +make -f sidechain/pymod/CMakeFiles/_sidechain.dir/build.make sidechain/pymod/CMakeFiles/_sidechain.dir/depend +make -f modelling/src/CMakeFiles/promod3_modelling.dir/build.make modelling/src/CMakeFiles/promod3_modelling.dir/depend +make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/sidechain/pymod /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/pymod /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/pymod/CMakeFiles/_sidechain.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/modelling/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src/CMakeFiles/promod3_modelling.dir/DependInfo.cmake --color= +make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +make -f sidechain/pymod/CMakeFiles/_sidechain.dir/build.make sidechain/pymod/CMakeFiles/_sidechain.dir/build +make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +make -f modelling/src/CMakeFiles/promod3_modelling.dir/build.make modelling/src/CMakeFiles/promod3_modelling.dir/build +make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +[ 59%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_disulfid.cc.o +[ 59%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_connector.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_disulfid.cc.o -MF CMakeFiles/_sidechain.dir/export_disulfid.cc.o.d -o CMakeFiles/_sidechain.dir/export_disulfid.cc.o -c /build/promod3-3.2.1+ds/sidechain/pymod/export_disulfid.cc +[ 60%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/extension_scheme.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_connector.cc.o -MF CMakeFiles/_sidechain.dir/export_connector.cc.o.d -o CMakeFiles/_sidechain.dir/export_connector.cc.o -c /build/promod3-3.2.1+ds/sidechain/pymod/export_connector.cc +[ 61%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_frame.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/extension_scheme.cc.o -MF CMakeFiles/promod3_modelling.dir/extension_scheme.cc.o.d -o CMakeFiles/promod3_modelling.dir/extension_scheme.cc.o -c /build/promod3-3.2.1+ds/modelling/src/extension_scheme.cc +[ 61%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/gap.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_frame.cc.o -MF CMakeFiles/_sidechain.dir/export_frame.cc.o.d -o CMakeFiles/_sidechain.dir/export_frame.cc.o -c /build/promod3-3.2.1+ds/sidechain/pymod/export_frame.cc +[ 63%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_particle.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/gap.cc.o -MF CMakeFiles/promod3_modelling.dir/gap.cc.o.d -o CMakeFiles/promod3_modelling.dir/gap.cc.o -c /build/promod3-3.2.1+ds/modelling/src/gap.cc +[ 63%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_graph.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_graph.cc.o -MF CMakeFiles/_sidechain.dir/export_rotamer_graph.cc.o.d -o CMakeFiles/_sidechain.dir/export_rotamer_graph.cc.o -c /build/promod3-3.2.1+ds/sidechain/pymod/export_rotamer_graph.cc +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_particle.cc.o -MF CMakeFiles/_sidechain.dir/export_particle.cc.o.d -o CMakeFiles/_sidechain.dir/export_particle.cc.o -c /build/promod3-3.2.1+ds/sidechain/pymod/export_particle.cc +[ 64%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/gap_extender.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/gap_extender.cc.o -MF CMakeFiles/promod3_modelling.dir/gap_extender.cc.o.d -o CMakeFiles/promod3_modelling.dir/gap_extender.cc.o -c /build/promod3-3.2.1+ds/modelling/src/gap_extender.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, @@ -2865,7 +2947,7 @@ 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/promod3-3.2.1+ds/scoring/pymod/wrap_scoring.cc:17: + from /build/promod3-3.2.1+ds/scoring/pymod/export_density_scorer.cc:17: /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( | ^~~~~~~~~~~~~~~~~~~~ @@ -2885,7 +2967,7 @@ 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/promod3-3.2.1+ds/scoring/pymod/export_all_atom_score.cc:17: + from /build/promod3-3.2.1+ds/scoring/pymod/export_pairwise_functions.cc:17: /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( | ^~~~~~~~~~~~~~~~~~~~ @@ -2905,7 +2987,7 @@ 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/promod3-3.2.1+ds/scoring/pymod/export_pairwise_functions.cc:17: + from /build/promod3-3.2.1+ds/scoring/pymod/wrap_scoring.cc:17: /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( | ^~~~~~~~~~~~~~~~~~~~ @@ -2945,7 +3027,7 @@ 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/promod3-3.2.1+ds/scoring/pymod/export_density_scorer.cc:17: + from /build/promod3-3.2.1+ds/scoring/pymod/export_all_atom_score.cc:17: /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( | ^~~~~~~~~~~~~~~~~~~~ @@ -2965,7 +3047,7 @@ 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/promod3-3.2.1+ds/scoring/pymod/export_constraint_constructor.cc:17: + from /build/promod3-3.2.1+ds/scoring/pymod/export_object_loader.cc:17: /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( | ^~~~~~~~~~~~~~~~~~~~ @@ -3005,66 +3087,17 @@ 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/promod3-3.2.1+ds/scoring/pymod/export_object_loader.cc:17: + from /build/promod3-3.2.1+ds/scoring/pymod/export_constraint_constructor.cc:17: /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("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 57%] Linking CXX shared module ../../stage/lib64/python3.11/site-packages/promod3/loop/_loop.so -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_loop.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -o ../../stage/lib64/python3.11/site-packages/promod3/loop/_loop.so CMakeFiles/_loop.dir/export_all_atom_env.cc.o CMakeFiles/_loop.dir/export_all_atom_positions.cc.o CMakeFiles/_loop.dir/export_amino_acid_atoms.cc.o CMakeFiles/_loop.dir/export_backbone.cc.o CMakeFiles/_loop.dir/export_forcefield_lookup.cc.o CMakeFiles/_loop.dir/export_frag_db.cc.o CMakeFiles/_loop.dir/export_fragger.cc.o CMakeFiles/_loop.dir/export_loop_object_loader.cc.o CMakeFiles/_loop.dir/export_mm_system_creator.cc.o CMakeFiles/_loop.dir/export_psipred_prediction.cc.o CMakeFiles/_loop.dir/export_structure_db.cc.o CMakeFiles/_loop.dir/export_torsion_sampler.cc.o CMakeFiles/_loop.dir/wrap_loop.cc.o -L/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64: ../../stage/lib64/libpromod3_loop.so.3.2.1 /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.74.0 ../../stage/lib64/libpromod3_core.so.3.2.1 /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.74.0 -[ 59%] Linking CXX shared library ../../stage/lib64/libpromod3_sidechain.so -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/promod3_sidechain.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libpromod3_sidechain.so.3.2 -o ../../stage/lib64/libpromod3_sidechain.so.3.2.1 CMakeFiles/promod3_sidechain.dir/bb_dep_rotamer_lib.cc.o CMakeFiles/promod3_sidechain.dir/disulfid.cc.o CMakeFiles/promod3_sidechain.dir/frame.cc.o CMakeFiles/promod3_sidechain.dir/particle_scoring.cc.o CMakeFiles/promod3_sidechain.dir/scwrl4_particle_scoring.cc.o CMakeFiles/promod3_sidechain.dir/scwrl3_particle_scoring.cc.o CMakeFiles/promod3_sidechain.dir/vina_particle_scoring.cc.o CMakeFiles/promod3_sidechain.dir/rotamer.cc.o CMakeFiles/promod3_sidechain.dir/rotamer_cruncher.cc.o CMakeFiles/promod3_sidechain.dir/rotamer_density.cc.o CMakeFiles/promod3_sidechain.dir/rotamer_group.cc.o CMakeFiles/promod3_sidechain.dir/rotamer_id.cc.o CMakeFiles/promod3_sidechain.dir/rotamer_lib.cc.o CMakeFiles/promod3_sidechain.dir/rotamer_lib_entry.cc.o CMakeFiles/promod3_sidechain.dir/rotamer_lib_reader.cc.o CMakeFiles/promod3_sidechain.dir/sidechain_connector.cc.o CMakeFiles/promod3_sidechain.dir/sidechain_object_loader.cc.o CMakeFiles/promod3_sidechain.dir/rotamer_constructor.cc.o CMakeFiles/promod3_sidechain.dir/rotamer_lookup.cc.o CMakeFiles/promod3_sidechain.dir/scwrl4_rotamer_constructor.cc.o CMakeFiles/promod3_sidechain.dir/scwrl3_rotamer_constructor.cc.o CMakeFiles/promod3_sidechain.dir/vina_rotamer_constructor.cc.o CMakeFiles/promod3_sidechain.dir/subrotamer_optimizer.cc.o -L/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64: /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so ../../stage/lib64/libpromod3_loop.so.3.2.1 ../../stage/lib64/libpromod3_core.so.3.2.1 /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.74.0 -make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -[ 59%] Built target _loop -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E cmake_symlink_library ../../stage/lib64/libpromod3_sidechain.so.3.2.1 ../../stage/lib64/libpromod3_sidechain.so.3.2 ../../stage/lib64/libpromod3_sidechain.so -make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -[ 59%] Built target promod3_sidechain -make -f sidechain/pymod/CMakeFiles/_sidechain.dir/build.make sidechain/pymod/CMakeFiles/_sidechain.dir/depend -make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -make -f modelling/src/CMakeFiles/promod3_modelling.dir/build.make modelling/src/CMakeFiles/promod3_modelling.dir/depend -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/sidechain/pymod /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/pymod /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/pymod/CMakeFiles/_sidechain.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/modelling/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src/CMakeFiles/promod3_modelling.dir/DependInfo.cmake --color= -make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -make -f modelling/src/CMakeFiles/promod3_modelling.dir/build.make modelling/src/CMakeFiles/promod3_modelling.dir/build -make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -make -f sidechain/pymod/CMakeFiles/_sidechain.dir/build.make sidechain/pymod/CMakeFiles/_sidechain.dir/build -make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -[ 60%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/extension_scheme.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong 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-DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/model.cc.o -MF CMakeFiles/promod3_modelling.dir/model.cc.o.d -o CMakeFiles/promod3_modelling.dir/model.cc.o -c /build/promod3-3.2.1+ds/modelling/src/model.cc -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_particle.cc.o -MF CMakeFiles/_sidechain.dir/export_particle.cc.o.d -o CMakeFiles/_sidechain.dir/export_particle.cc.o -c /build/promod3-3.2.1+ds/sidechain/pymod/export_particle.cc -[ 66%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/backbone_relaxer.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/backbone_relaxer.cc.o -MF CMakeFiles/promod3_modelling.dir/backbone_relaxer.cc.o.d -o CMakeFiles/promod3_modelling.dir/backbone_relaxer.cc.o -c /build/promod3-3.2.1+ds/modelling/src/backbone_relaxer.cc -[ 66%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer.cc.o +[ 64%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer.cc.o -MF CMakeFiles/_sidechain.dir/export_rotamer.cc.o.d -o CMakeFiles/_sidechain.dir/export_rotamer.cc.o -c /build/promod3-3.2.1+ds/sidechain/pymod/export_rotamer.cc -[ 67%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_cruncher.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_cruncher.cc.o -MF CMakeFiles/_sidechain.dir/export_rotamer_cruncher.cc.o.d -o CMakeFiles/_sidechain.dir/export_rotamer_cruncher.cc.o -c /build/promod3-3.2.1+ds/sidechain/pymod/export_rotamer_cruncher.cc -[ 67%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/ccd.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/ccd.cc.o -MF CMakeFiles/promod3_modelling.dir/ccd.cc.o.d -o CMakeFiles/promod3_modelling.dir/ccd.cc.o -c /build/promod3-3.2.1+ds/modelling/src/ccd.cc -[ 69%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/kic.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/kic.cc.o -MF CMakeFiles/promod3_modelling.dir/kic.cc.o.d -o CMakeFiles/promod3_modelling.dir/kic.cc.o -c /build/promod3-3.2.1+ds/modelling/src/kic.cc +[ 64%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/model.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/model.cc.o -MF CMakeFiles/promod3_modelling.dir/model.cc.o.d -o CMakeFiles/promod3_modelling.dir/model.cc.o -c /build/promod3-3.2.1+ds/modelling/src/model.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, @@ -3078,7 +3111,7 @@ 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/promod3-3.2.1+ds/sidechain/pymod/export_particle.cc:17: + from /build/promod3-3.2.1+ds/sidechain/pymod/export_frame.cc:17: /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( | ^~~~~~~~~~~~~~~~~~~~ @@ -3098,15 +3131,13 @@ 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/promod3-3.2.1+ds/sidechain/pymod/export_frame.cc:17: + from /build/promod3-3.2.1+ds/sidechain/pymod/export_connector.cc:17: /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("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 69%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_density.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_density.cc.o -MF CMakeFiles/_sidechain.dir/export_rotamer_density.cc.o.d -o CMakeFiles/_sidechain.dir/export_rotamer_density.cc.o -c /build/promod3-3.2.1+ds/sidechain/pymod/export_rotamer_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, @@ -3120,7 +3151,7 @@ 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/promod3-3.2.1+ds/sidechain/pymod/export_connector.cc:17: + from /build/promod3-3.2.1+ds/sidechain/pymod/export_disulfid.cc:17: /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( | ^~~~~~~~~~~~~~~~~~~~ @@ -3140,10 +3171,15 @@ 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/promod3-3.2.1+ds/sidechain/pymod/export_rotamer.cc:17: + from /build/promod3-3.2.1+ds/sidechain/pymod/export_rotamer_graph.cc:17: /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("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 66%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_cruncher.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_cruncher.cc.o -MF CMakeFiles/_sidechain.dir/export_rotamer_cruncher.cc.o.d -o CMakeFiles/_sidechain.dir/export_rotamer_cruncher.cc.o -c /build/promod3-3.2.1+ds/sidechain/pymod/export_rotamer_cruncher.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, @@ -3157,16 +3193,21 @@ 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/promod3-3.2.1+ds/sidechain/pymod/export_rotamer_cruncher.cc:17: + from /build/promod3-3.2.1+ds/sidechain/pymod/export_particle.cc:17: /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("") - | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 66%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/all_atom_relaxer.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/all_atom_relaxer.cc.o -MF CMakeFiles/promod3_modelling.dir/all_atom_relaxer.cc.o.d -o CMakeFiles/promod3_modelling.dir/all_atom_relaxer.cc.o -c /build/promod3-3.2.1+ds/modelling/src/all_atom_relaxer.cc +[ 67%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/backbone_relaxer.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/backbone_relaxer.cc.o -MF CMakeFiles/promod3_modelling.dir/backbone_relaxer.cc.o.d -o CMakeFiles/promod3_modelling.dir/backbone_relaxer.cc.o -c /build/promod3-3.2.1+ds/modelling/src/backbone_relaxer.cc +[ 67%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/ccd.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/ccd.cc.o -MF CMakeFiles/promod3_modelling.dir/ccd.cc.o.d -o CMakeFiles/promod3_modelling.dir/ccd.cc.o -c /build/promod3-3.2.1+ds/modelling/src/ccd.cc +[ 67%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_density.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_density.cc.o -MF CMakeFiles/_sidechain.dir/export_rotamer_density.cc.o.d -o CMakeFiles/_sidechain.dir/export_rotamer_density.cc.o -c /build/promod3-3.2.1+ds/sidechain/pymod/export_rotamer_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, @@ -3180,13 +3221,19 @@ 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/promod3-3.2.1+ds/sidechain/pymod/export_rotamer_graph.cc:17: + from /build/promod3-3.2.1+ds/sidechain/pymod/export_rotamer.cc:17: /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 sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_ids.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_ids.cc.o -MF CMakeFiles/_sidechain.dir/export_rotamer_ids.cc.o.d -o CMakeFiles/_sidechain.dir/export_rotamer_ids.cc.o -c /build/promod3-3.2.1+ds/sidechain/pymod/export_rotamer_ids.cc +[ 69%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_lib.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_lib.cc.o -MF CMakeFiles/_sidechain.dir/export_rotamer_lib.cc.o.d -o CMakeFiles/_sidechain.dir/export_rotamer_lib.cc.o -c /build/promod3-3.2.1+ds/sidechain/pymod/export_rotamer_lib.cc +[ 69%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_sidechain_object_loader.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_sidechain_object_loader.cc.o -MF CMakeFiles/_sidechain.dir/export_sidechain_object_loader.cc.o.d -o CMakeFiles/_sidechain.dir/export_sidechain_object_loader.cc.o -c /build/promod3-3.2.1+ds/sidechain/pymod/export_sidechain_object_loader.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, @@ -3200,17 +3247,17 @@ 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/promod3-3.2.1+ds/sidechain/pymod/export_disulfid.cc:17: + from /build/promod3-3.2.1+ds/sidechain/pymod/export_rotamer_cruncher.cc:17: /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("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 69%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/loop_candidate.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/loop_candidate.cc.o -MF CMakeFiles/promod3_modelling.dir/loop_candidate.cc.o.d -o CMakeFiles/promod3_modelling.dir/loop_candidate.cc.o -c /build/promod3-3.2.1+ds/modelling/src/loop_candidate.cc -[ 69%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_ids.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_ids.cc.o -MF CMakeFiles/_sidechain.dir/export_rotamer_ids.cc.o.d -o CMakeFiles/_sidechain.dir/export_rotamer_ids.cc.o -c /build/promod3-3.2.1+ds/sidechain/pymod/export_rotamer_ids.cc +[ 70%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/kic.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/kic.cc.o -MF CMakeFiles/promod3_modelling.dir/kic.cc.o.d -o CMakeFiles/promod3_modelling.dir/kic.cc.o -c /build/promod3-3.2.1+ds/modelling/src/kic.cc +[ 71%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_constructor.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_constructor.cc.o -MF CMakeFiles/_sidechain.dir/export_rotamer_constructor.cc.o.d -o CMakeFiles/_sidechain.dir/export_rotamer_constructor.cc.o -c /build/promod3-3.2.1+ds/sidechain/pymod/export_rotamer_constructor.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, @@ -3228,21 +3275,11 @@ /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( | ^~~~~~~~~~~~~~~~~~~~ -[ 69%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo.cc.o -MF CMakeFiles/promod3_modelling.dir/monte_carlo.cc.o.d -o CMakeFiles/promod3_modelling.dir/monte_carlo.cc.o -c /build/promod3-3.2.1+ds/modelling/src/monte_carlo.cc /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 sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_lib.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_lib.cc.o -MF CMakeFiles/_sidechain.dir/export_rotamer_lib.cc.o.d -o CMakeFiles/_sidechain.dir/export_rotamer_lib.cc.o -c /build/promod3-3.2.1+ds/sidechain/pymod/export_rotamer_lib.cc -[ 70%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_sidechain_object_loader.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_sidechain_object_loader.cc.o -MF CMakeFiles/_sidechain.dir/export_sidechain_object_loader.cc.o.d -o CMakeFiles/_sidechain.dir/export_sidechain_object_loader.cc.o -c /build/promod3-3.2.1+ds/sidechain/pymod/export_sidechain_object_loader.cc -[ 71%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_constructor.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_constructor.cc.o -MF CMakeFiles/_sidechain.dir/export_rotamer_constructor.cc.o.d -o CMakeFiles/_sidechain.dir/export_rotamer_constructor.cc.o -c /build/promod3-3.2.1+ds/sidechain/pymod/export_rotamer_constructor.cc [ 71%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_subrotamer_optimizer.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_subrotamer_optimizer.cc.o -MF CMakeFiles/_sidechain.dir/export_subrotamer_optimizer.cc.o.d -o CMakeFiles/_sidechain.dir/export_subrotamer_optimizer.cc.o -c /build/promod3-3.2.1+ds/sidechain/pymod/export_subrotamer_optimizer.cc -[ 71%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/wrap_sidechain.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/wrap_sidechain.cc.o -MF CMakeFiles/_sidechain.dir/wrap_sidechain.cc.o.d -o CMakeFiles/_sidechain.dir/wrap_sidechain.cc.o -c /build/promod3-3.2.1+ds/sidechain/pymod/wrap_sidechain.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, @@ -3263,12 +3300,6 @@ /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 modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo_closer.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo_closer.cc.o -MF CMakeFiles/promod3_modelling.dir/monte_carlo_closer.cc.o.d -o CMakeFiles/promod3_modelling.dir/monte_carlo_closer.cc.o -c /build/promod3-3.2.1+ds/modelling/src/monte_carlo_closer.cc -[ 73%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo_cooler.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo_cooler.cc.o -MF CMakeFiles/promod3_modelling.dir/monte_carlo_cooler.cc.o.d -o CMakeFiles/promod3_modelling.dir/monte_carlo_cooler.cc.o -c /build/promod3-3.2.1+ds/modelling/src/monte_carlo_cooler.cc -[ 74%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo_sampler.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo_sampler.cc.o -MF CMakeFiles/promod3_modelling.dir/monte_carlo_sampler.cc.o.d -o CMakeFiles/promod3_modelling.dir/monte_carlo_sampler.cc.o -c /build/promod3-3.2.1+ds/modelling/src/monte_carlo_sampler.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, @@ -3282,15 +3313,13 @@ 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/promod3-3.2.1+ds/sidechain/pymod/export_rotamer_lib.cc:17: + from /build/promod3-3.2.1+ds/sidechain/pymod/export_sidechain_object_loader.cc:17: /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 modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo_scorer.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo_scorer.cc.o -MF CMakeFiles/promod3_modelling.dir/monte_carlo_scorer.cc.o.d -o CMakeFiles/promod3_modelling.dir/monte_carlo_scorer.cc.o -c /build/promod3-3.2.1+ds/modelling/src/monte_carlo_scorer.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, @@ -3304,13 +3333,25 @@ 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/promod3-3.2.1+ds/sidechain/pymod/export_rotamer_constructor.cc:17: + from /build/promod3-3.2.1+ds/sidechain/pymod/export_rotamer_lib.cc:17: /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("") | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 71%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/loop_candidate.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/loop_candidate.cc.o -MF CMakeFiles/promod3_modelling.dir/loop_candidate.cc.o.d -o CMakeFiles/promod3_modelling.dir/loop_candidate.cc.o -c /build/promod3-3.2.1+ds/modelling/src/loop_candidate.cc +[ 71%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/wrap_sidechain.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/wrap_sidechain.cc.o -MF CMakeFiles/_sidechain.dir/wrap_sidechain.cc.o.d -o CMakeFiles/_sidechain.dir/wrap_sidechain.cc.o -c /build/promod3-3.2.1+ds/sidechain/pymod/wrap_sidechain.cc +[ 71%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo.cc.o -MF CMakeFiles/promod3_modelling.dir/monte_carlo.cc.o.d -o CMakeFiles/promod3_modelling.dir/monte_carlo.cc.o -c /build/promod3-3.2.1+ds/modelling/src/monte_carlo.cc +[ 73%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo_closer.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo_closer.cc.o -MF CMakeFiles/promod3_modelling.dir/monte_carlo_closer.cc.o.d -o CMakeFiles/promod3_modelling.dir/monte_carlo_closer.cc.o -c /build/promod3-3.2.1+ds/modelling/src/monte_carlo_closer.cc +[ 73%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo_cooler.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo_cooler.cc.o -MF CMakeFiles/promod3_modelling.dir/monte_carlo_cooler.cc.o.d -o CMakeFiles/promod3_modelling.dir/monte_carlo_cooler.cc.o -c /build/promod3-3.2.1+ds/modelling/src/monte_carlo_cooler.cc +[ 74%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo_sampler.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo_sampler.cc.o -MF CMakeFiles/promod3_modelling.dir/monte_carlo_sampler.cc.o.d -o CMakeFiles/promod3_modelling.dir/monte_carlo_sampler.cc.o -c /build/promod3-3.2.1+ds/modelling/src/monte_carlo_sampler.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, @@ -3324,15 +3365,15 @@ 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/promod3-3.2.1+ds/sidechain/pymod/export_sidechain_object_loader.cc:17: + from /build/promod3-3.2.1+ds/sidechain/pymod/export_rotamer_constructor.cc:17: /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 modelling/src/CMakeFiles/promod3_modelling.dir/rigid_blocks.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/rigid_blocks.cc.o -MF CMakeFiles/promod3_modelling.dir/rigid_blocks.cc.o.d -o CMakeFiles/promod3_modelling.dir/rigid_blocks.cc.o -c /build/promod3-3.2.1+ds/modelling/src/rigid_blocks.cc +[ 74%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo_scorer.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo_scorer.cc.o -MF CMakeFiles/promod3_modelling.dir/monte_carlo_scorer.cc.o.d -o CMakeFiles/promod3_modelling.dir/monte_carlo_scorer.cc.o -c /build/promod3-3.2.1+ds/modelling/src/monte_carlo_scorer.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, @@ -3353,8 +3394,8 @@ /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 modelling/src/CMakeFiles/promod3_modelling.dir/score_container.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/score_container.cc.o -MF CMakeFiles/promod3_modelling.dir/score_container.cc.o.d -o CMakeFiles/promod3_modelling.dir/score_container.cc.o -c /build/promod3-3.2.1+ds/modelling/src/score_container.cc +[ 74%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/rigid_blocks.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/rigid_blocks.cc.o -MF CMakeFiles/promod3_modelling.dir/rigid_blocks.cc.o.d -o CMakeFiles/promod3_modelling.dir/rigid_blocks.cc.o -c /build/promod3-3.2.1+ds/modelling/src/rigid_blocks.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, @@ -3375,6 +3416,8 @@ /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 modelling/src/CMakeFiles/promod3_modelling.dir/score_container.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/score_container.cc.o -MF CMakeFiles/promod3_modelling.dir/score_container.cc.o.d -o CMakeFiles/promod3_modelling.dir/score_container.cc.o -c /build/promod3-3.2.1+ds/modelling/src/score_container.cc [ 76%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/scoring_weights.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/scoring_weights.cc.o -MF CMakeFiles/promod3_modelling.dir/scoring_weights.cc.o.d -o CMakeFiles/promod3_modelling.dir/scoring_weights.cc.o -c /build/promod3-3.2.1+ds/modelling/src/scoring_weights.cc [ 77%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/sidechain_reconstructor.cc.o @@ -3437,26 +3480,26 @@ make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make -f modelling/pymod/CMakeFiles/_modelling.dir/build.make modelling/pymod/CMakeFiles/_modelling.dir/build make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -[ 81%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_gap_extender.cc.o -[ 81%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_gap.cc.o +[ 81%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_loop_closure.cc.o +[ 83%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_gap.cc.o [ 83%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_extension_scheme.cc.o -[ 84%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_model.cc.o -[ 84%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_loop_closure.cc.o -[ 85%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_rigid_blocks.cc.o -[ 87%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_loop_candidate.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_modelling_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/pymod/CMakeFiles/_modelling.dir/export_loop_closure.cc.o -MF CMakeFiles/_modelling.dir/export_loop_closure.cc.o.d -o CMakeFiles/_modelling.dir/export_loop_closure.cc.o -c /build/promod3-3.2.1+ds/modelling/pymod/export_loop_closure.cc +[ 84%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_loop_candidate.cc.o +[ 85%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_gap_extender.cc.o +[ 85%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_model.cc.o +[ 85%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_score_container.cc.o +[ 87%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_monte_carlo.cc.o +[ 87%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_rigid_blocks.cc.o +[ 87%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_scoring_weights.cc.o +[ 88%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/wrap_modelling.cc.o +[ 90%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_motif_finder.cc.o +[ 90%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_sidechain_reconstructor.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_modelling_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/pymod/CMakeFiles/_modelling.dir/export_extension_scheme.cc.o -MF CMakeFiles/_modelling.dir/export_extension_scheme.cc.o.d -o CMakeFiles/_modelling.dir/export_extension_scheme.cc.o -c /build/promod3-3.2.1+ds/modelling/pymod/export_extension_scheme.cc cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_modelling_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/pymod/CMakeFiles/_modelling.dir/export_gap.cc.o -MF CMakeFiles/_modelling.dir/export_gap.cc.o.d -o CMakeFiles/_modelling.dir/export_gap.cc.o -c /build/promod3-3.2.1+ds/modelling/pymod/export_gap.cc -[ 87%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_scoring_weights.cc.o -[ 87%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_monte_carlo.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_modelling_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/pymod/CMakeFiles/_modelling.dir/export_gap_extender.cc.o -MF CMakeFiles/_modelling.dir/export_gap_extender.cc.o.d -o CMakeFiles/_modelling.dir/export_gap_extender.cc.o -c /build/promod3-3.2.1+ds/modelling/pymod/export_gap_extender.cc -[ 87%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_score_container.cc.o -[ 88%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_sidechain_reconstructor.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_modelling_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/pymod/CMakeFiles/_modelling.dir/export_loop_candidate.cc.o -MF CMakeFiles/_modelling.dir/export_loop_candidate.cc.o.d -o CMakeFiles/_modelling.dir/export_loop_candidate.cc.o -c /build/promod3-3.2.1+ds/modelling/pymod/export_loop_candidate.cc -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_modelling_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/pymod/CMakeFiles/_modelling.dir/export_loop_closure.cc.o -MF CMakeFiles/_modelling.dir/export_loop_closure.cc.o.d -o CMakeFiles/_modelling.dir/export_loop_closure.cc.o -c /build/promod3-3.2.1+ds/modelling/pymod/export_loop_closure.cc -[ 88%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_motif_finder.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_modelling_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/pymod/CMakeFiles/_modelling.dir/export_model.cc.o -MF CMakeFiles/_modelling.dir/export_model.cc.o.d -o CMakeFiles/_modelling.dir/export_model.cc.o -c /build/promod3-3.2.1+ds/modelling/pymod/export_model.cc cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_modelling_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/pymod/CMakeFiles/_modelling.dir/export_monte_carlo.cc.o -MF CMakeFiles/_modelling.dir/export_monte_carlo.cc.o.d -o CMakeFiles/_modelling.dir/export_monte_carlo.cc.o -c /build/promod3-3.2.1+ds/modelling/pymod/export_monte_carlo.cc -[ 90%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/wrap_modelling.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_modelling_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/pymod/CMakeFiles/_modelling.dir/export_rigid_blocks.cc.o -MF CMakeFiles/_modelling.dir/export_rigid_blocks.cc.o.d -o CMakeFiles/_modelling.dir/export_rigid_blocks.cc.o -c /build/promod3-3.2.1+ds/modelling/pymod/export_rigid_blocks.cc cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_modelling_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/pymod/CMakeFiles/_modelling.dir/export_score_container.cc.o -MF CMakeFiles/_modelling.dir/export_score_container.cc.o.d -o CMakeFiles/_modelling.dir/export_score_container.cc.o -c /build/promod3-3.2.1+ds/modelling/pymod/export_score_container.cc cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_modelling_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/pymod/CMakeFiles/_modelling.dir/export_scoring_weights.cc.o -MF CMakeFiles/_modelling.dir/export_scoring_weights.cc.o.d -o CMakeFiles/_modelling.dir/export_scoring_weights.cc.o -c /build/promod3-3.2.1+ds/modelling/pymod/export_scoring_weights.cc @@ -3476,7 +3519,7 @@ 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/promod3-3.2.1+ds/modelling/pymod/export_score_container.cc:17: + from /build/promod3-3.2.1+ds/modelling/pymod/export_motif_finder.cc:17: /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( | ^~~~~~~~~~~~~~~~~~~~ @@ -3516,7 +3559,7 @@ 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/promod3-3.2.1+ds/modelling/pymod/export_gap_extender.cc:17: + from /build/promod3-3.2.1+ds/modelling/pymod/export_scoring_weights.cc:17: /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( | ^~~~~~~~~~~~~~~~~~~~ @@ -3540,6 +3583,9 @@ /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, @@ -3553,10 +3599,13 @@ 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/promod3-3.2.1+ds/modelling/pymod/export_gap.cc:17: + from /build/promod3-3.2.1+ds/modelling/pymod/export_score_container.cc:17: /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, @@ -3570,19 +3619,13 @@ 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/promod3-3.2.1+ds/modelling/pymod/export_rigid_blocks.cc:17: + from /build/promod3-3.2.1+ds/modelling/pymod/export_gap_extender.cc:17: /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("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -/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, @@ -3596,7 +3639,7 @@ 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/promod3-3.2.1+ds/modelling/pymod/export_scoring_weights.cc:17: + from /build/promod3-3.2.1+ds/modelling/pymod/export_gap.cc:17: /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( | ^~~~~~~~~~~~~~~~~~~~ @@ -3616,7 +3659,7 @@ 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/promod3-3.2.1+ds/modelling/pymod/export_motif_finder.cc:17: + from /build/promod3-3.2.1+ds/modelling/pymod/export_rigid_blocks.cc:17: /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( | ^~~~~~~~~~~~~~~~~~~~ @@ -3656,7 +3699,7 @@ 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/promod3-3.2.1+ds/modelling/pymod/export_loop_closure.cc:17: + from /build/promod3-3.2.1+ds/modelling/pymod/export_model.cc:17: /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( | ^~~~~~~~~~~~~~~~~~~~ @@ -3676,13 +3719,10 @@ 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/promod3-3.2.1+ds/modelling/pymod/export_monte_carlo.cc:17: + from /build/promod3-3.2.1+ds/modelling/pymod/export_loop_closure.cc:17: /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, @@ -3696,13 +3736,16 @@ 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/promod3-3.2.1+ds/modelling/pymod/export_loop_candidate.cc:17: + from /build/promod3-3.2.1+ds/modelling/pymod/export_monte_carlo.cc:17: /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, @@ -3716,7 +3759,7 @@ 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/promod3-3.2.1+ds/modelling/pymod/export_model.cc:17: + from /build/promod3-3.2.1+ds/modelling/pymod/export_loop_candidate.cc:17: /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( | ^~~~~~~~~~~~~~~~~~~~ @@ -3738,176 +3781,176 @@ make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' [ 90%] Built target _init make -f loop/data/CMakeFiles/generate_loop_data_ff_lookup_charmm.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_ff_lookup_charmm.dat.dir/depend -make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/loop/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/generate_loop_data_ff_lookup_charmm.dat.dir/DependInfo.cmake --color= make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler.dat.dir/depend -make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/loop/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/generate_loop_data_torsion_sampler.dat.dir/DependInfo.cmake --color= make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler_coil.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler_coil.dat.dir/depend make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler_extended.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler_extended.dat.dir/depend make -f 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scoring/data/CMakeFiles/generate_scoring_data_aa_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_aa_scorer.dat.dir/depend -make -f sidechain/data/CMakeFiles/generate_sidechain_data_bb_dep_lib.dat.dir/build.make sidechain/data/CMakeFiles/generate_sidechain_data_bb_dep_lib.dat.dir/depend -make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/scoring/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_aa_scorer.dat.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/sidechain/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/data/CMakeFiles/generate_sidechain_data_bb_dep_lib.dat.dir/DependInfo.cmake --color= -make -f loop/data/CMakeFiles/generate_loop_data_ff_lookup_charmm.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_ff_lookup_charmm.dat.dir/build -make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler_helical.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler_helical.dat.dir/build make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler.dat.dir/build -make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler_coil.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler_coil.dat.dir/build make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler_extended.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler_extended.dat.dir/build -make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler_helical.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler_helical.dat.dir/build -make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -make -f loop/data/CMakeFiles/generate_loop_data_frag_db.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_frag_db.dat.dir/build make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -make -f scoring/data/CMakeFiles/generate_scoring_data_aa_packing_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_aa_packing_scorer.dat.dir/build +make -f loop/data/CMakeFiles/generate_loop_data_ff_lookup_charmm.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_ff_lookup_charmm.dat.dir/build make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler.dat.dir/build +make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler_coil.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler_coil.dat.dir/build +make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler_extended.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler_extended.dat.dir/build make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +make -f loop/data/CMakeFiles/generate_loop_data_frag_db.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_frag_db.dat.dir/build make -f loop/data/CMakeFiles/generate_loop_data_structure_db.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_structure_db.dat.dir/build +make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +make -f scoring/data/CMakeFiles/generate_scoring_data_aa_packing_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_aa_packing_scorer.dat.dir/build +make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make -f scoring/data/CMakeFiles/generate_scoring_data_cb_packing_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_cb_packing_scorer.dat.dir/build +make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -[ 91%] Generating ../../stage/share/promod3/loop_data/torsion_sampler.dat make -f scoring/data/CMakeFiles/generate_scoring_data_cbeta_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_cbeta_scorer.dat.dir/build make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -[ 92%] Generating ../../stage/share/promod3/loop_data/ff_lookup_charmm.dat -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/\ /usr/bin/python3\ '/build/promod3-3.2.1+ds/loop/data/convert_binaries.py'\ '/build/promod3-3.2.1+ds/loop/data/portable_torsion_sampler.dat'\ '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data/torsion_sampler.dat'\ TorsionSampler -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/\ /usr/bin/python3\ '/build/promod3-3.2.1+ds/loop/data/convert_binaries.py'\ '/build/promod3-3.2.1+ds/loop/data/portable_ff_lookup_charmm.dat'\ '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data/ff_lookup_charmm.dat'\ ForcefieldLookup -[ 94%] Generating ../../stage/share/promod3/loop_data/torsion_sampler_extended.dat +make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make -f scoring/data/CMakeFiles/generate_scoring_data_reduced_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_reduced_scorer.dat.dir/build make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/\ /usr/bin/python3\ '/build/promod3-3.2.1+ds/loop/data/convert_binaries.py'\ '/build/promod3-3.2.1+ds/loop/data/portable_torsion_sampler_extended.dat'\ '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data/torsion_sampler_extended.dat'\ TorsionSampler -[ 94%] Generating ../../stage/share/promod3/loop_data/frag_db.dat -[ 94%] Generating ../../stage/share/promod3/loop_data/torsion_sampler_coil.dat -[ 94%] Generating ../../stage/share/promod3/loop_data/torsion_sampler_helical.dat -[ 94%] Generating ../../stage/share/promod3/scoring_data/aa_packing_scorer.dat -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/\ /usr/bin/python3\ '/build/promod3-3.2.1+ds/loop/data/convert_binaries.py'\ '/build/promod3-3.2.1+ds/loop/data/portable_torsion_sampler_coil.dat'\ '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data/torsion_sampler_coil.dat'\ TorsionSampler -[ 94%] Generating ../../stage/share/promod3/loop_data/structure_db.dat -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/\ /usr/bin/python3\ '/build/promod3-3.2.1+ds/scoring/data/convert_binaries.py'\ '/build/promod3-3.2.1+ds/scoring/data/portable_aa_packing_scorer.dat'\ '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data/aa_packing_scorer.dat'\ AllAtomPackingScorer -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/\ /usr/bin/python3\ '/build/promod3-3.2.1+ds/loop/data/convert_binaries.py'\ '/build/promod3-3.2.1+ds/loop/data/portable_torsion_sampler_helical.dat'\ '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data/torsion_sampler_helical.dat'\ TorsionSampler -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/\ /usr/bin/python3\ '/build/promod3-3.2.1+ds/loop/data/convert_binaries.py'\ '/build/promod3-3.2.1+ds/loop/data/portable_frag_db.dat'\ '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data/frag_db.dat'\ FragDB +make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make -f scoring/data/CMakeFiles/generate_scoring_data_hbond_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_hbond_scorer.dat.dir/build -[ 94%] Generating ../../stage/share/promod3/scoring_data/cb_packing_scorer.dat -make -f scoring/data/CMakeFiles/generate_scoring_data_ss_agreement_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_ss_agreement_scorer.dat.dir/build -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/\ /usr/bin/python3\ '/build/promod3-3.2.1+ds/loop/data/convert_binaries.py'\ '/build/promod3-3.2.1+ds/loop/data/portable_structure_db.dat'\ '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data/structure_db.dat'\ StructureDB -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/\ /usr/bin/python3\ '/build/promod3-3.2.1+ds/scoring/data/convert_binaries.py'\ '/build/promod3-3.2.1+ds/scoring/data/portable_cb_packing_scorer.dat'\ '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data/cb_packing_scorer.dat'\ CBPackingScorer make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -[ 95%] Generating ../../stage/share/promod3/scoring_data/cbeta_scorer.dat +make -f scoring/data/CMakeFiles/generate_scoring_data_ss_agreement_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_ss_agreement_scorer.dat.dir/build make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make -f scoring/data/CMakeFiles/generate_scoring_data_torsion_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_torsion_scorer.dat.dir/build -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/\ /usr/bin/python3\ '/build/promod3-3.2.1+ds/scoring/data/convert_binaries.py'\ '/build/promod3-3.2.1+ds/scoring/data/portable_cbeta_scorer.dat'\ '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data/cbeta_scorer.dat'\ CBetaScorer make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make -f scoring/data/CMakeFiles/generate_scoring_data_aa_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_aa_scorer.dat.dir/build +[ 90%] Generating ../../stage/share/promod3/loop_data/torsion_sampler_helical.dat +[ 91%] Generating ../../stage/share/promod3/loop_data/torsion_sampler.dat +[ 91%] Generating ../../stage/share/promod3/loop_data/structure_db.dat +[ 92%] Generating ../../stage/share/promod3/loop_data/ff_lookup_charmm.dat +[ 92%] Generating ../../stage/share/promod3/loop_data/torsion_sampler_coil.dat +[ 92%] Generating ../../stage/share/promod3/loop_data/frag_db.dat +[ 94%] Generating ../../stage/share/promod3/loop_data/torsion_sampler_extended.dat +[ 95%] Generating ../../stage/share/promod3/scoring_data/cbeta_scorer.dat +[ 95%] Generating ../../stage/share/promod3/scoring_data/aa_packing_scorer.dat +[ 95%] Generating ../../stage/share/promod3/scoring_data/cb_packing_scorer.dat [ 95%] Generating ../../stage/share/promod3/scoring_data/reduced_scorer.dat -[ 97%] Generating ../../stage/share/promod3/scoring_data/ss_agreement_scorer.dat -[ 97%] Generating ../../stage/share/promod3/scoring_data/hbond_scorer.dat +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/\ /usr/bin/python3\ '/build/promod3-3.2.1+ds/loop/data/convert_binaries.py'\ '/build/promod3-3.2.1+ds/loop/data/portable_torsion_sampler_helical.dat'\ '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data/torsion_sampler_helical.dat'\ TorsionSampler +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/\ /usr/bin/python3\ '/build/promod3-3.2.1+ds/loop/data/convert_binaries.py'\ '/build/promod3-3.2.1+ds/loop/data/portable_structure_db.dat'\ '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data/structure_db.dat'\ StructureDB +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/\ /usr/bin/python3\ '/build/promod3-3.2.1+ds/loop/data/convert_binaries.py'\ '/build/promod3-3.2.1+ds/loop/data/portable_torsion_sampler.dat'\ '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data/torsion_sampler.dat'\ TorsionSampler +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/\ /usr/bin/python3\ '/build/promod3-3.2.1+ds/loop/data/convert_binaries.py'\ '/build/promod3-3.2.1+ds/loop/data/portable_ff_lookup_charmm.dat'\ '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data/ff_lookup_charmm.dat'\ ForcefieldLookup +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/\ /usr/bin/python3\ '/build/promod3-3.2.1+ds/scoring/data/convert_binaries.py'\ '/build/promod3-3.2.1+ds/scoring/data/portable_cb_packing_scorer.dat'\ '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data/cb_packing_scorer.dat'\ CBPackingScorer +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/\ /usr/bin/python3\ '/build/promod3-3.2.1+ds/loop/data/convert_binaries.py'\ '/build/promod3-3.2.1+ds/loop/data/portable_torsion_sampler_extended.dat'\ '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data/torsion_sampler_extended.dat'\ TorsionSampler +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/\ /usr/bin/python3\ '/build/promod3-3.2.1+ds/scoring/data/convert_binaries.py'\ '/build/promod3-3.2.1+ds/scoring/data/portable_aa_packing_scorer.dat'\ '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data/aa_packing_scorer.dat'\ AllAtomPackingScorer +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/\ /usr/bin/python3\ '/build/promod3-3.2.1+ds/scoring/data/convert_binaries.py'\ '/build/promod3-3.2.1+ds/scoring/data/portable_cbeta_scorer.dat'\ '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data/cbeta_scorer.dat'\ CBetaScorer +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/\ /usr/bin/python3\ '/build/promod3-3.2.1+ds/loop/data/convert_binaries.py'\ '/build/promod3-3.2.1+ds/loop/data/portable_frag_db.dat'\ '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data/frag_db.dat'\ FragDB +[ 95%] Generating ../../stage/share/promod3/scoring_data/hbond_scorer.dat make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -make -f sidechain/data/CMakeFiles/generate_sidechain_data_bb_dep_lib.dat.dir/build.make sidechain/data/CMakeFiles/generate_sidechain_data_bb_dep_lib.dat.dir/build cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/\ /usr/bin/python3\ '/build/promod3-3.2.1+ds/scoring/data/convert_binaries.py'\ '/build/promod3-3.2.1+ds/scoring/data/portable_reduced_scorer.dat'\ '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data/reduced_scorer.dat'\ ReducedScorer -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/\ /usr/bin/python3\ '/build/promod3-3.2.1+ds/scoring/data/convert_binaries.py'\ '/build/promod3-3.2.1+ds/scoring/data/portable_ss_agreement_scorer.dat'\ '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data/ss_agreement_scorer.dat'\ SSAgreementScorer -make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/\ /usr/bin/python3\ '/build/promod3-3.2.1+ds/scoring/data/convert_binaries.py'\ '/build/promod3-3.2.1+ds/scoring/data/portable_hbond_scorer.dat'\ '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data/hbond_scorer.dat'\ HBondScorer -[ 97%] Generating ../../stage/share/promod3/scoring_data/torsion_scorer.dat +[ 95%] Generating ../../stage/share/promod3/scoring_data/torsion_scorer.dat +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/\ /usr/bin/python3\ '/build/promod3-3.2.1+ds/loop/data/convert_binaries.py'\ '/build/promod3-3.2.1+ds/loop/data/portable_torsion_sampler_coil.dat'\ '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data/torsion_sampler_coil.dat'\ TorsionSampler +[ 97%] Generating ../../stage/share/promod3/scoring_data/ss_agreement_scorer.dat cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/\ /usr/bin/python3\ '/build/promod3-3.2.1+ds/scoring/data/convert_binaries.py'\ '/build/promod3-3.2.1+ds/scoring/data/portable_torsion_scorer.dat'\ '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data/torsion_scorer.dat'\ TorsionScorer +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/\ /usr/bin/python3\ '/build/promod3-3.2.1+ds/scoring/data/convert_binaries.py'\ '/build/promod3-3.2.1+ds/scoring/data/portable_ss_agreement_scorer.dat'\ '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data/ss_agreement_scorer.dat'\ SSAgreementScorer [ 98%] Generating ../../stage/share/promod3/scoring_data/aa_scorer.dat cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/\ /usr/bin/python3\ '/build/promod3-3.2.1+ds/scoring/data/convert_binaries.py'\ '/build/promod3-3.2.1+ds/scoring/data/portable_aa_scorer.dat'\ '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data/aa_scorer.dat'\ AllAtomInteractionScorer -[100%] Generating ../../stage/share/promod3/sidechain_data/bb_dep_lib.dat -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/\ /usr/bin/python3\ '/build/promod3-3.2.1+ds/sidechain/data/convert_lib.py'\ '/build/promod3-3.2.1+ds/sidechain/data/portable_bb_dep_lib.dat'\ '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/share/promod3/sidechain_data/bb_dep_lib.dat'\ BBDepRotamerLib make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +[ 98%] Built target generate_scoring_data_torsion_scorer.dat +make -f sidechain/data/CMakeFiles/generate_sidechain_data_bb_dep_lib.dat.dir/build.make sidechain/data/CMakeFiles/generate_sidechain_data_bb_dep_lib.dat.dir/depend make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -[100%] Built target generate_loop_data_ff_lookup_charmm.dat -make -f sidechain/data/CMakeFiles/generate_sidechain_data_lib.dat.dir/build.make sidechain/data/CMakeFiles/generate_sidechain_data_lib.dat.dir/depend make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/sidechain/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/data/CMakeFiles/generate_sidechain_data_lib.dat.dir/DependInfo.cmake --color= -[100%] Built target generate_scoring_data_aa_packing_scorer.dat +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/sidechain/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/data/CMakeFiles/generate_sidechain_data_bb_dep_lib.dat.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -[100%] Built target generate_scoring_data_cb_packing_scorer.dat make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -make -f sidechain/data/CMakeFiles/generate_sidechain_data_lib.dat.dir/build.make sidechain/data/CMakeFiles/generate_sidechain_data_lib.dat.dir/build -make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -[100%] Built target generate_scoring_data_reduced_scorer.dat make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -[100%] Generating ../../stage/share/promod3/sidechain_data/lib.dat -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/\ /usr/bin/python3\ '/build/promod3-3.2.1+ds/sidechain/data/convert_lib.py'\ '/build/promod3-3.2.1+ds/sidechain/data/portable_lib.dat'\ '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/share/promod3/sidechain_data/lib.dat'\ RotamerLib -[100%] Built target generate_scoring_data_aa_scorer.dat +make -f sidechain/data/CMakeFiles/generate_sidechain_data_bb_dep_lib.dat.dir/build.make sidechain/data/CMakeFiles/generate_sidechain_data_bb_dep_lib.dat.dir/build +[ 98%] Built target generate_scoring_data_aa_packing_scorer.dat +make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +make -f sidechain/data/CMakeFiles/generate_sidechain_data_lib.dat.dir/build.make sidechain/data/CMakeFiles/generate_sidechain_data_lib.dat.dir/depend +make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/sidechain/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/data/CMakeFiles/generate_sidechain_data_lib.dat.dir/DependInfo.cmake --color= +[ 98%] Built target generate_scoring_data_aa_scorer.dat make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +[ 98%] Built target generate_scoring_data_cb_packing_scorer.dat +[ 98%] Built target generate_scoring_data_ss_agreement_scorer.dat +[100%] Generating ../../stage/share/promod3/sidechain_data/bb_dep_lib.dat +[100%] Built target generate_loop_data_ff_lookup_charmm.dat +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/\ /usr/bin/python3\ '/build/promod3-3.2.1+ds/sidechain/data/convert_lib.py'\ '/build/promod3-3.2.1+ds/sidechain/data/portable_bb_dep_lib.dat'\ '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/share/promod3/sidechain_data/bb_dep_lib.dat'\ BBDepRotamerLib [100%] Built target generate_scoring_data_hbond_scorer.dat -[100%] Built target generate_scoring_data_torsion_scorer.dat -make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -[100%] Built target generate_scoring_data_ss_agreement_scorer.dat make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +make -f sidechain/data/CMakeFiles/generate_sidechain_data_lib.dat.dir/build.make sidechain/data/CMakeFiles/generate_sidechain_data_lib.dat.dir/build +make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +[100%] Generating ../../stage/share/promod3/sidechain_data/lib.dat +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/\ /usr/bin/python3\ '/build/promod3-3.2.1+ds/sidechain/data/convert_lib.py'\ '/build/promod3-3.2.1+ds/sidechain/data/portable_lib.dat'\ '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/share/promod3/sidechain_data/lib.dat'\ RotamerLib make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +[100%] Built target generate_scoring_data_reduced_scorer.dat make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' [100%] Built target generate_scoring_data_cbeta_scorer.dat make -f scoring/data/CMakeFiles/scoring_data.dir/build.make scoring/data/CMakeFiles/scoring_data.dir/depend make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/scoring/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/scoring_data.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -[100%] Built target generate_loop_data_torsion_sampler_extended.dat -[100%] Built target generate_loop_data_torsion_sampler.dat -[100%] Built target generate_loop_data_torsion_sampler_coil.dat -make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make -f scoring/data/CMakeFiles/scoring_data.dir/build.make scoring/data/CMakeFiles/scoring_data.dir/build make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'scoring/data/CMakeFiles/scoring_data.dir/build'. make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' [100%] Built target scoring_data make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +[100%] Built target generate_loop_data_torsion_sampler_extended.dat +[100%] Built target generate_loop_data_torsion_sampler.dat +make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' [100%] Built target generate_loop_data_torsion_sampler_helical.dat +[100%] Built target generate_loop_data_torsion_sampler_coil.dat make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' [100%] Built target generate_sidechain_data_lib.dat make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' @@ -3938,7 +3981,7 @@ /usr/bin/cmake -E cmake_progress_start /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/promod3-3.2.1+ds/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/promod3-3.2.1+ds/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/promod3-3.2.1+ds -B/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 check @@ -3952,985 +3995,981 @@ make -f core/src/CMakeFiles/create_stage.dir/build.make core/src/CMakeFiles/create_stage.dir/depend make -f config/src/CMakeFiles/config_header.dir/build.make config/src/CMakeFiles/config_header.dir/depend make -f core/pymod/CMakeFiles/core_pymod.dir/build.make core/pymod/CMakeFiles/core_pymod.dir/depend -make -f loop/data/CMakeFiles/loop_data_dir.dir/build.make loop/data/CMakeFiles/loop_data_dir.dir/depend make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/actions /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/actions /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/actions/CMakeFiles/actions.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/core/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests/CMakeFiles/test_data_core.dir/DependInfo.cmake --color= +make -f loop/data/CMakeFiles/loop_data_dir.dir/build.make loop/data/CMakeFiles/loop_data_dir.dir/depend make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/core/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src/CMakeFiles/create_stage.dir/DependInfo.cmake --color= make -f modelling/pymod/CMakeFiles/modelling_pymod.dir/build.make modelling/pymod/CMakeFiles/modelling_pymod.dir/depend make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/config/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/config/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/config/src/CMakeFiles/config_header.dir/DependInfo.cmake --color= +make -f loop/pymod/CMakeFiles/loop_pymod.dir/build.make loop/pymod/CMakeFiles/loop_pymod.dir/depend +make -f scoring/pymod/CMakeFiles/scoring_pymod.dir/build.make scoring/pymod/CMakeFiles/scoring_pymod.dir/depend make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/core/pymod /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/pymod /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/pymod/CMakeFiles/core_pymod.dir/DependInfo.cmake --color= +make -f sidechain/pymod/CMakeFiles/sidechain_pymod.dir/build.make sidechain/pymod/CMakeFiles/sidechain_pymod.dir/depend make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/loop/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/loop_data_dir.dir/DependInfo.cmake --color= +make -f core/init/CMakeFiles/init___init__.py_pymod.dir/build.make core/init/CMakeFiles/init___init__.py_pymod.dir/depend +make -f scoring/data/CMakeFiles/scoring_data_dir.dir/build.make scoring/data/CMakeFiles/scoring_data_dir.dir/depend make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/modelling/pymod /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod/CMakeFiles/modelling_pymod.dir/DependInfo.cmake --color= -make -f loop/pymod/CMakeFiles/loop_pymod.dir/build.make loop/pymod/CMakeFiles/loop_pymod.dir/depend -make -f scoring/pymod/CMakeFiles/scoring_pymod.dir/build.make scoring/pymod/CMakeFiles/scoring_pymod.dir/depend make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +make -f sidechain/data/CMakeFiles/sidechain_data_dir.dir/build.make sidechain/data/CMakeFiles/sidechain_data_dir.dir/depend cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/loop/pymod /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/pymod /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/pymod/CMakeFiles/loop_pymod.dir/DependInfo.cmake --color= -make -f sidechain/pymod/CMakeFiles/sidechain_pymod.dir/build.make sidechain/pymod/CMakeFiles/sidechain_pymod.dir/depend make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/scoring/pymod /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/pymod /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/pymod/CMakeFiles/scoring_pymod.dir/DependInfo.cmake --color= +make -f modelling/tests/CMakeFiles/test_data_modelling.dir/build.make modelling/tests/CMakeFiles/test_data_modelling.dir/depend make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/sidechain/pymod /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/pymod /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/pymod/CMakeFiles/sidechain_pymod.dir/DependInfo.cmake --color= -make -f core/init/CMakeFiles/init___init__.py_pymod.dir/build.make core/init/CMakeFiles/init___init__.py_pymod.dir/depend make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/core/init /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/init /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/init/CMakeFiles/init___init__.py_pymod.dir/DependInfo.cmake --color= -make -f scoring/data/CMakeFiles/scoring_data_dir.dir/build.make scoring/data/CMakeFiles/scoring_data_dir.dir/depend +make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/scoring/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/scoring_data_dir.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/sidechain/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/data/CMakeFiles/sidechain_data_dir.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/modelling/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests/CMakeFiles/test_data_modelling.dir/DependInfo.cmake --color= +make -f scripts/CMakeFiles/subst_pm.dir/build.make scripts/CMakeFiles/subst_pm.dir/depend +make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/scripts /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scripts /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scripts/CMakeFiles/subst_pm.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +make -f actions/CMakeFiles/actions.dir/build.make actions/CMakeFiles/actions.dir/build +make -f config/src/CMakeFiles/config_header.dir/build.make config/src/CMakeFiles/config_header.dir/build +make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/actions/pm-build-model 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actions/CMakeFiles/actions.dir/build.make actions/CMakeFiles/actions.dir/build make -f core/tests/CMakeFiles/test_data_core.dir/build.make core/tests/CMakeFiles/test_data_core.dir/build -make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/scoring/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/scoring_data_dir.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/actions/pm-build-model /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/libexec/promod3/pm-build-model -make -f core/src/CMakeFiles/create_stage.dir/build.make core/src/CMakeFiles/create_stage.dir/build +make -f loop/data/CMakeFiles/loop_data_dir.dir/build.make loop/data/CMakeFiles/loop_data_dir.dir/build +make -f scoring/pymod/CMakeFiles/scoring_pymod.dir/build.make scoring/pymod/CMakeFiles/scoring_pymod.dir/build make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64 make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -make -f config/src/CMakeFiles/config_header.dir/build.make config/src/CMakeFiles/config_header.dir/build -make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/config/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/config/src/config.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/config.hh -make -f core/pymod/CMakeFiles/core_pymod.dir/build.make core/pymod/CMakeFiles/core_pymod.dir/build -make -f loop/data/CMakeFiles/loop_data_dir.dir/build.make loop/data/CMakeFiles/loop_data_dir.dir/build -make -f modelling/pymod/CMakeFiles/modelling_pymod.dir/build.make modelling/pymod/CMakeFiles/modelling_pymod.dir/build make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/pymod && /usr/bin/cmake -E copy_if_different 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/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/data && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/pymod/__init__.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/__init__.py -make -f loop/pymod/CMakeFiles/loop_pymod.dir/build.make loop/pymod/CMakeFiles/loop_pymod.dir/build +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/pymod/__init__.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/scoring/__init__.py make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/pymod/__init__.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/loop/__init__.py -make -f scoring/pymod/CMakeFiles/scoring_pymod.dir/build.make scoring/pymod/CMakeFiles/scoring_pymod.dir/build -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/actions/pm-build-rawmodel /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/libexec/promod3/pm-build-rawmodel -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/tests//test_helper.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core//test_helper.py +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/data && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data +make -f modelling/pymod/CMakeFiles/modelling_pymod.dir/build.make modelling/pymod/CMakeFiles/modelling_pymod.dir/build make -f sidechain/pymod/CMakeFiles/sidechain_pymod.dir/build.make sidechain/pymod/CMakeFiles/sidechain_pymod.dir/build +make -f core/init/CMakeFiles/init___init__.py_pymod.dir/build.make core/init/CMakeFiles/init___init__.py_pymod.dir/build +make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +make -f core/src/CMakeFiles/create_stage.dir/build.make core/src/CMakeFiles/create_stage.dir/build +make -f sidechain/data/CMakeFiles/sidechain_data_dir.dir/build.make sidechain/data/CMakeFiles/sidechain_data_dir.dir/build make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/pymod/__init__.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/scoring/__init__.py +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/pymod/__init__.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/__init__.py make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/pymod/__init__.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/sidechain/__init__.py +make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +make[4]: Nothing to be done for 'core/init/CMakeFiles/init___init__.py_pymod.dir/build'. make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -make -f core/init/CMakeFiles/init___init__.py_pymod.dir/build.make core/init/CMakeFiles/init___init__.py_pymod.dir/build -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/bin +make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64 +make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/data && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/share/promod3/sidechain_data +make -f modelling/tests/CMakeFiles/test_data_modelling.dir/build.make modelling/tests/CMakeFiles/test_data_modelling.dir/build +make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -make -f scoring/data/CMakeFiles/scoring_data_dir.dir/build.make scoring/data/CMakeFiles/scoring_data_dir.dir/build -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/pymod/_closegaps.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_closegaps.py +make -f scripts/CMakeFiles/subst_pm.dir/build.make scripts/CMakeFiles/subst_pm.dir/build +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/actions/pm-build-rawmodel /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/libexec/promod3/pm-build-rawmodel make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'core/init/CMakeFiles/init___init__.py_pymod.dir/build'. +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -DINPUT_FILE=/build/promod3-3.2.1+ds/scripts/pm.in -DOUT_FILE=pm -DOST_ROOT="/usr" -DLIBDIR=lib64 -DLIBEXECPATH=libexec/promod3 -DPYTHON_MODULE_PATH=python3.11/site-packages/ -DOST_PYMOD_PATH=/usr/lib/python3/dist-packages -DPython_EXECUTABLE=/usr/bin/python3 -P /build/promod3-3.2.1+ds/cmake_support/substitute.cmake +make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/tests//test_helper.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core//test_helper.py +make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/pymod/_closegaps.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_closegaps.py cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/pymod/helper.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/core/helper.py make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/bin +make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data +make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +[ 1%] Built target init___init__.py_pymod +make -f core/init/CMakeFiles/init_pymod.dir/build.make core/init/CMakeFiles/init_pymod.dir/depend +[ 1%] Built target config_header +[ 1%] Built target loop_pymod +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/pymod/_molprobity.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_molprobity.py make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/data && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/actions/pm-help /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/libexec/promod3/pm-help +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/core/init /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/init /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/init/CMakeFiles/init_pymod.dir/DependInfo.cmake --color= cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/actions/pm-help /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/libexec/promod3/pm-help cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/libexec/promod3 -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/pymod/_molprobity.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_molprobity.py -make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/pymod/pm3argparse.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/core/pm3argparse.py -[ 0%] Built target config_header -[ 1%] Built target init___init__.py_pymod -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/tests/data/broken_on_purpose.chemlib /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/broken_on_purpose.chemlib -make -f sidechain/data/CMakeFiles/sidechain_data_dir.dir/build.make sidechain/data/CMakeFiles/sidechain_data_dir.dir/depend -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests -make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' [ 1%] Built target loop_data_dir -make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +[ 1%] Built target sidechain_pymod +[ 1%] Built target scoring_data_dir +[ 1%] Built target scoring_pymod +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/1cjx-1.fasta /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/1cjx-1.fasta +[ 1%] Built target sidechain_data_dir +[ 1%] Built target subst_pm cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/pymod/_pipeline.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_pipeline.py +make -f scripts/CMakeFiles/promod3_scripts.dir/build.make scripts/CMakeFiles/promod3_scripts.dir/depend +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/sidechain/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/data/CMakeFiles/sidechain_data_dir.dir/DependInfo.cmake --color= -[ 1%] Built target loop_pymod +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/scripts /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scripts /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scripts/CMakeFiles/promod3_scripts.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +make -f core/init/CMakeFiles/init_pymod.dir/build.make core/init/CMakeFiles/init_pymod.dir/build cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/actions/pm-build-sidechains /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/libexec/promod3/pm-build-sidechains -make -f modelling/tests/CMakeFiles/test_data_modelling.dir/build.make modelling/tests/CMakeFiles/test_data_modelling.dir/depend -make -f scripts/CMakeFiles/subst_pm.dir/build.make scripts/CMakeFiles/subst_pm.dir/depend -make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/modelling/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests/CMakeFiles/test_data_modelling.dir/DependInfo.cmake --color= -[ 1%] Built target scoring_pymod -[ 1%] Built target sidechain_pymod -make -f core/init/CMakeFiles/init_pymod.dir/build.make core/init/CMakeFiles/init_pymod.dir/depend -make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/scripts /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scripts /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scripts/CMakeFiles/subst_pm.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/core/init /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/init /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/init/CMakeFiles/init_pymod.dir/DependInfo.cmake --color= -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/pymod/_ring_punches.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_ring_punches.py make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/tests/data/broken_on_purpose.chemlib /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/broken_on_purpose.chemlib +make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +make[4]: Nothing to be done for 'core/init/CMakeFiles/init_pymod.dir/build'. make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/pymod/_ring_punches.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_ring_punches.py [ 1%] Built target core_pymod +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/1cjx-1.pdb.gz /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/1cjx-1.pdb.gz +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl +[ 1%] Built target init_pymod make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -make -f modelling/tests/CMakeFiles/test_data_modelling.dir/build.make modelling/tests/CMakeFiles/test_data_modelling.dir/build -make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -make -f sidechain/data/CMakeFiles/sidechain_data_dir.dir/build.make sidechain/data/CMakeFiles/sidechain_data_dir.dir/build -[ 1%] Built target scoring_data_dir make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/pymod/_denovo.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_denovo.py -make -f scripts/CMakeFiles/subst_pm.dir/build.make scripts/CMakeFiles/subst_pm.dir/build +make -f scripts/CMakeFiles/promod3_scripts.dir/build.make scripts/CMakeFiles/promod3_scripts.dir/build make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/data && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/share/promod3/sidechain_data +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -E copy_if_different pm /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/bin/pm +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/pymod/_denovo.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_denovo.py [ 1%] Built target actions -make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -DINPUT_FILE=/build/promod3-3.2.1+ds/scripts/pm.in -DOUT_FILE=pm -DOST_ROOT="/usr" -DLIBDIR=lib64 -DLIBEXECPATH=libexec/promod3 -DPYTHON_MODULE_PATH=python3.11/site-packages/ -DOST_PYMOD_PATH=/usr/lib/python3/dist-packages -DPython_EXECUTABLE=/usr/bin/python3 -P /build/promod3-3.2.1+ds/cmake_support/substitute.cmake cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/tests/data/aln_tpl/1crn.fasta /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/1crn.fasta -make -f actions/tests/CMakeFiles/test_data_actions.dir/build.make actions/tests/CMakeFiles/test_data_actions.dir/depend [ 1%] Built target create_stage -make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/actions/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/actions/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/actions/tests/CMakeFiles/test_data_actions.dir/DependInfo.cmake --color= cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data -make -f core/init/CMakeFiles/init_pymod.dir/build.make core/init/CMakeFiles/init_pymod.dir/build -make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'core/init/CMakeFiles/init_pymod.dir/build'. -make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/pymod/_fragger_handle.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_fragger_handle.py +make -f actions/tests/CMakeFiles/test_data_actions.dir/build.make actions/tests/CMakeFiles/test_data_actions.dir/depend make -f core/src/CMakeFiles/promod3_core_headers.dir/build.make core/src/CMakeFiles/promod3_core_headers.dir/depend -make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/core/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src/CMakeFiles/promod3_core_headers.dir/DependInfo.cmake --color= make -f loop/src/CMakeFiles/promod3_loop_headers.dir/build.make loop/src/CMakeFiles/promod3_loop_headers.dir/depend +make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/actions/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/actions/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/actions/tests/CMakeFiles/test_data_actions.dir/DependInfo.cmake --color= make -f scoring/src/CMakeFiles/promod3_scoring_headers.dir/build.make scoring/src/CMakeFiles/promod3_scoring_headers.dir/depend -make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +make -f sidechain/src/CMakeFiles/promod3_sidechain_headers.dir/build.make sidechain/src/CMakeFiles/promod3_sidechain_headers.dir/depend +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scripts/pm /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/bin/pm +make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/core/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src/CMakeFiles/promod3_core_headers.dir/DependInfo.cmake --color= +make -f modelling/src/CMakeFiles/promod3_modelling_headers.dir/build.make modelling/src/CMakeFiles/promod3_modelling_headers.dir/depend make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/loop/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src/CMakeFiles/promod3_loop_headers.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/scoring/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src/CMakeFiles/promod3_scoring_headers.dir/DependInfo.cmake --color= -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl -[ 1%] Built target init_pymod -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/1cjx-1.fasta /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/1cjx-1.fasta -make -f sidechain/src/CMakeFiles/promod3_sidechain_headers.dir/build.make sidechain/src/CMakeFiles/promod3_sidechain_headers.dir/depend -make -f modelling/src/CMakeFiles/promod3_modelling_headers.dir/build.make modelling/src/CMakeFiles/promod3_modelling_headers.dir/depend make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/sidechain/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src/CMakeFiles/promod3_sidechain_headers.dir/DependInfo.cmake --color= -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/pymod/_reconstruct_sidechains.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_reconstruct_sidechains.py -[ 1%] Built target sidechain_data_dir -make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/scoring/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src/CMakeFiles/promod3_scoring_headers.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/modelling/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src/CMakeFiles/promod3_modelling_headers.dir/DependInfo.cmake --color= +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/pymod/_fragger_handle.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_fragger_handle.py +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/1crn.fasta /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/1crn.fasta make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make -f actions/tests/CMakeFiles/test_data_actions.dir/build.make actions/tests/CMakeFiles/test_data_actions.dir/build -make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/modelling/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src/CMakeFiles/promod3_modelling_headers.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/actions/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/actions -make -f loop/src/CMakeFiles/promod3_loop_headers.dir/build.make loop/src/CMakeFiles/promod3_loop_headers.dir/build +make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make -f core/src/CMakeFiles/promod3_core_headers.dir/build.make core/src/CMakeFiles/promod3_core_headers.dir/build +make -f loop/src/CMakeFiles/promod3_loop_headers.dir/build.make loop/src/CMakeFiles/promod3_loop_headers.dir/build make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./all_atom_env.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./all_atom_env.hh -make -f scoring/src/CMakeFiles/promod3_scoring_headers.dir/build.make scoring/src/CMakeFiles/promod3_scoring_headers.dir/build +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/actions/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/actions +make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./check_io.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./check_io.hh +make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./backbone_score_base.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./backbone_score_base.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/tests/data/aln_tpl/1crn_cut.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/1crn_cut.pdb -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./all_atom_env.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./all_atom_env.hh make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +make -f scoring/src/CMakeFiles/promod3_scoring_headers.dir/build.make scoring/src/CMakeFiles/promod3_scoring_headers.dir/build make -f sidechain/src/CMakeFiles/promod3_sidechain_headers.dir/build.make sidechain/src/CMakeFiles/promod3_sidechain_headers.dir/build -[ 1%] Built target subst_pm -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/pymod/_monte_carlo.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_monte_carlo.py -make -f scripts/CMakeFiles/promod3_scripts.dir/build.make scripts/CMakeFiles/promod3_scripts.dir/depend +make -f modelling/src/CMakeFiles/promod3_modelling_headers.dir/build.make modelling/src/CMakeFiles/promod3_modelling_headers.dir/build +make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./bb_dep_rotamer_lib.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./bb_dep_rotamer_lib.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./backbone_score_base.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./backbone_score_base.hh make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/scripts /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scripts /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scripts/CMakeFiles/promod3_scripts.dir/DependInfo.cmake --color= +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./extension_scheme.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./extension_scheme.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/tests/data/aln_tpl/1crn_cut.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/1crn_cut.pdb +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/pymod/_reconstruct_sidechains.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_reconstruct_sidechains.py +[ 1%] Built target promod3_scripts cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/actions/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/actions/data -make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -make -f modelling/src/CMakeFiles/promod3_modelling_headers.dir/build.make modelling/src/CMakeFiles/promod3_modelling_headers.dir/build -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/1cjx-1.pdb.gz /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/1cjx-1.pdb.gz +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./cluster.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./cluster.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./all_atom_positions.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./all_atom_positions.hh -make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./extension_scheme.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./extension_scheme.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./gap.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./gap.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./backbone_overall_scorer.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./backbone_overall_scorer.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./cluster.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./cluster.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./disulfid.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./disulfid.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/pymod/_mhandle_helper.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_mhandle_helper.py -make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/1CRN.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/1CRN.pdb cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl -make -f scripts/CMakeFiles/promod3_scripts.dir/build.make scripts/CMakeFiles/promod3_scripts.dir/build -make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -E copy_if_different pm /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/bin/pm +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/pymod/_monte_carlo.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_monte_carlo.py cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/actions/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/actions/tests/data/gly.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/actions/data/gly.pdb +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./dynamic_spatial_organizer.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./dynamic_spatial_organizer.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./gap_extender.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./gap_extender.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./amino_acid_atoms.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./amino_acid_atoms.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./scoring_object_loader.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./scoring_object_loader.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./dynamic_spatial_organizer.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./dynamic_spatial_organizer.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./gap.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./gap.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scripts/pm /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/bin/pm -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/tests/data/aln_tpl/2aoh-1_cut.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/2aoh-1_cut.pdb cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./frame.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./frame.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/pymod/_alignment_fiddling.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_alignment_fiddling.py -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/1crn.fasta /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/1crn.fasta -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./backbone.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./backbone.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/actions/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/actions/data -make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/pymod/_mhandle_helper.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_mhandle_helper.py +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/tests/data/aln_tpl/2aoh-1_cut.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/2aoh-1_cut.pdb +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./model.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./model.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./export_helper.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./export_helper.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./backbone.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./backbone.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./cbeta_env_listener.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./cbeta_env_listener.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./gap_extender.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./gap_extender.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/pymod/_raw_model.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_raw_model.py -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./bb_trace_param.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./bb_trace_param.hh -[ 1%] Built target promod3_scripts cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./rotamer_graph.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_graph.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./model.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./model.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/actions/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/actions/tests/data/seq.fasta /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/actions/data/seq.fasta -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/tests/data/aln_tpl/2aoh-1_cut_A.fasta /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/2aoh-1_cut_A.fasta -make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/1crn_build.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/1crn_build.pdb +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/pymod/_alignment_fiddling.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_alignment_fiddling.py +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./all_atom_relaxer.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./all_atom_relaxer.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./geom_base.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./geom_base.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/1CRN.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/1CRN.pdb +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./bb_trace_param.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./bb_trace_param.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./cb_packing_score.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./cb_packing_score.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./all_atom_relaxer.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./all_atom_relaxer.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./particle.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./particle.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./data_bag.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./data_bag.hh -[ 1%] Built target modelling_pymod cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/actions/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/actions/data -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./geom_stems.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./geom_stems.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./particle_scoring_base.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./particle_scoring_base.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./message.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./message.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./backbone_relaxer.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./backbone_relaxer.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/pymod/_raw_model.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_raw_model.py +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./data_bag.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./data_bag.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/tests/data/aln_tpl/2aoh-1_cut_A.fasta /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/2aoh-1_cut_A.fasta +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./geom_stems.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./geom_stems.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./particle_scoring_base.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./particle_scoring_base.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./cbeta_score.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./cbeta_score.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./dense_hash_table.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./dense_hash_table.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/actions/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/actions/tests/data/seq_ins.fasta /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/actions/data/seq_ins.fasta -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./particle_scoring.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./particle_scoring.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/tests/data/aln_tpl/2aoh-1_cut_B.fasta /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/2aoh-1_cut_B.fasta -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./portable_binary_data_sink.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./portable_binary_data_sink.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/1crn_cut.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/1crn_cut.pdb cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./ccd.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./ccd.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./dense_hash_table.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./dense_hash_table.hh +make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./particle_scoring.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./particle_scoring.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./message.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./message.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./reduced_env_listener.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./reduced_env_listener.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/1crn_build.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/1crn_build.pdb +make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./kic.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./kic.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./dense_map.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./dense_map.hh +[ 1%] Built target modelling_pymod +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./portable_binary_data_sink.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./portable_binary_data_sink.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./scwrl4_particle_scoring.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./scwrl4_particle_scoring.hh -make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./portable_binary_data_source.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./portable_binary_data_source.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./reduced_score.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./reduced_score.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./dense_map.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./dense_map.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./kic.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./kic.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/tests/data/aln_tpl/2jlp-1.aln /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/2jlp-1.aln +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/tests/data/aln_tpl/2aoh-1_cut_B.fasta /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/2aoh-1_cut_B.fasta [ 1%] Built target test_data_actions make -f actions/tests/CMakeFiles/test_actions.py_run.dir/build.make actions/tests/CMakeFiles/test_actions.py_run.dir/depend make -f actions/tests/CMakeFiles/test_action_build-model.py_run.dir/build.make actions/tests/CMakeFiles/test_action_build-model.py_run.dir/depend -make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/actions/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/actions/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/actions/tests/CMakeFiles/test_actions.py_run.dir/DependInfo.cmake --color= make -f actions/tests/CMakeFiles/test_action_build-rawmodel.py_run.dir/build.make actions/tests/CMakeFiles/test_action_build-rawmodel.py_run.dir/depend -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data make -f actions/tests/CMakeFiles/test_action_help.py_run.dir/build.make actions/tests/CMakeFiles/test_action_help.py_run.dir/depend -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./clash_env_listener.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./clash_env_listener.hh make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/actions/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/actions/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/actions/tests/CMakeFiles/test_action_build-rawmodel.py_run.dir/DependInfo.cmake --color= +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/actions/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/actions/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/actions/tests/CMakeFiles/test_actions.py_run.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/actions/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/actions/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/actions/tests/CMakeFiles/test_action_build-model.py_run.dir/DependInfo.cmake --color= -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./scwrl3_particle_scoring.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./scwrl3_particle_scoring.hh +make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/actions/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/actions/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/actions/tests/CMakeFiles/test_action_build-rawmodel.py_run.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/actions/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/actions/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/actions/tests/CMakeFiles/test_action_help.py_run.dir/DependInfo.cmake --color= -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./portable_binary_serializer.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./portable_binary_serializer.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/1crn_final.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/1crn_final.pdb +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./loop_candidate.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./loop_candidate.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./dense_map.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./dense_map.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./clash_env_listener.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./clash_env_listener.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./portable_binary_data_source.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./portable_binary_data_source.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./scwrl3_particle_scoring.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./scwrl3_particle_scoring.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +make -f actions/tests/CMakeFiles/test_action_build-rawmodel.py_run.dir/build.make actions/tests/CMakeFiles/test_action_build-rawmodel.py_run.dir/build make -f actions/tests/CMakeFiles/test_actions.py_run.dir/build.make actions/tests/CMakeFiles/test_actions.py_run.dir/build -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./loop_candidate.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./loop_candidate.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./clash_score.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./clash_score.hh -make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./density_creator.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./density_creator.hh make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make -f actions/tests/CMakeFiles/test_action_build-model.py_run.dir/build.make actions/tests/CMakeFiles/test_action_build-model.py_run.dir/build -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/1crn_cut.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/1crn_cut.pdb make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./runtime_profiling.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./runtime_profiling.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./monte_carlo.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo.hh -make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -make -f actions/tests/CMakeFiles/test_action_help.py_run.dir/build.make actions/tests/CMakeFiles/test_action_help.py_run.dir/build -[ 1%] running checks test_actions.py -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/tests/data/aln_tpl/2jlp-1.fasta /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/2jlp-1.fasta -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./vina_particle_scoring.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./vina_particle_scoring.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/actions && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/ /usr/bin/python3 /build/promod3-3.2.1+ds/actions/tests/test_actions.py" +make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -make -f actions/tests/CMakeFiles/test_action_build-rawmodel.py_run.dir/build.make actions/tests/CMakeFiles/test_action_build-rawmodel.py_run.dir/build -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./forcefield_lookup.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./forcefield_lookup.hh -[ 1%] running checks test_action_build-model.py +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data +make -f actions/tests/CMakeFiles/test_action_help.py_run.dir/build.make actions/tests/CMakeFiles/test_action_help.py_run.dir/build +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./density_creator.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./density_creator.hh make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./monte_carlo.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./clash_score.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./clash_score.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./portable_binary_serializer.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./portable_binary_serializer.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./vina_particle_scoring.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./vina_particle_scoring.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/tests/data/aln_tpl/2jlp-1.aln /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/2jlp-1.aln +[ 2%] running checks test_action_build-rawmodel.py +[ 2%] running checks test_action_build-model.py +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/actions && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/ /usr/bin/python3 /build/promod3-3.2.1+ds/actions/tests/test_action_build-rawmodel.py" cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/actions && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/ /usr/bin/python3 /build/promod3-3.2.1+ds/actions/tests/test_action_build-model.py" -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./density_score.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./density_score.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./superpose.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./superpose.hh -[ 2%] running checks test_action_help.py +[ 2%] running checks test_actions.py +[ 3%] running checks test_action_help.py +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/1crn_rec.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/1crn_rec.pdb +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./forcefield_lookup.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./forcefield_lookup.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./monte_carlo_closer.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo_closer.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl -[ 3%] running checks test_action_build-rawmodel.py cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/actions && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/ /usr/bin/python3 /build/promod3-3.2.1+ds/actions/tests/test_action_help.py" -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/actions && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/ /usr/bin/python3 /build/promod3-3.2.1+ds/actions/tests/test_action_build-rawmodel.py" +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/actions && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/ /usr/bin/python3 /build/promod3-3.2.1+ds/actions/tests/test_actions.py" +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./density_score.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./density_score.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./runtime_profiling.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./runtime_profiling.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./rotamer.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./frag_db.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./frag_db.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./rotamer.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./hbond_env_listener.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./hbond_env_listener.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/tests/data/aln_tpl/2jlp-1.json /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/2jlp-1.json -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/1crn_final.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/1crn_final.pdb -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./enumerator.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./enumerator.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./monte_carlo_cooler.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo_cooler.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./fragger.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./fragger.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./superpose.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./superpose.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./hbond_env_listener.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./hbond_env_listener.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./rotamer_cruncher.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_cruncher.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/tests/data/aln_tpl/2jlp-1.fasta /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/2jlp-1.fasta +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./fragger.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./fragger.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/1crn_sc.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/1crn_sc.pdb +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./monte_carlo_sampler.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo_sampler.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./enumerator.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./enumerator.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./hbond_score.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./hbond_score.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./rotamer_density.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_density.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./graph.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./graph.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./hydrogen_constructor.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./hydrogen_constructor.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./ss_agreement_score.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./ss_agreement_score.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./monte_carlo_sampler.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo_sampler.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/tests/data/aln_tpl/2jlp-1.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/2jlp-1.pdb -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/1crn_rec.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/1crn_rec.pdb -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./rotamer_density.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_density.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./ss_agreement_env_listener.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./ss_agreement_env_listener.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./hydrogen_rule_lookup.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./hydrogen_rule_lookup.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./monte_carlo_scorer.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo_scorer.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./tree.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./tree.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./graph.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./graph.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./ss_agreement_score.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./ss_agreement_score.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./rotamer_group.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_group.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./idx_handler.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./idx_handler.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./torsion_score.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./torsion_score.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./rotamer_id.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_id.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./loop_object_loader.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./loop_object_loader.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/tests/data/aln_tpl/2jlp-1.json /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/2jlp-1.json +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./hydrogen_rule_lookup.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./hydrogen_rule_lookup.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./rigid_blocks.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./rigid_blocks.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/1crn_sc_test.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/1crn_sc_test.pdb . ---------------------------------------------------------------------- Ran 1 test in 0.000s OK -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./pairwise_scoring_function.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./pairwise_scoring_function.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./mm_system_creator.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./mm_system_creator.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./tree.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./tree.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./ss_agreement_env_listener.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./ss_agreement_env_listener.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./rotamer_id.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_id.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./idx_handler.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./idx_handler.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data +make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./score_container.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./score_container.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./tetrahedral_polytope.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./tetrahedral_polytope.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/1crn_sc.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/1crn_sc.pdb +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./torsion_score.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./torsion_score.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./rotamer_lib.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_lib.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./score_container.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./score_container.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/tests/data/aln_tpl/5d52-1_cut.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/5d52-1_cut.pdb -make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./psipred_prediction.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./psipred_prediction.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/tests/data/aln_tpl/2jlp-1.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/2jlp-1.pdb +[ 3%] Built target test_actions.py_run +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./loop_object_loader.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./loop_object_loader.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./graph_minimizer.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./graph_minimizer.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./scoring_weights.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./scoring_weights.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/1CRNA.hhm /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/1CRNA.hhm +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./pairwise_scoring_function.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./pairwise_scoring_function.hh .. ---------------------------------------------------------------------- -Ran 2 tests in 0.126s +Ran 2 tests in 0.059s OK -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./scoring_weights.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./scoring_weights.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./pairwise_score.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./pairwise_score.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./graph_minimizer.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./graph_minimizer.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./rotamer_lib_entry.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_lib_entry.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./mm_system_creator.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./mm_system_creator.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl -[ 3%] Built target test_actions.py_run -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./stem_geom.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./stem_geom.hh -make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./sidechain_reconstructor.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./sidechain_reconstructor.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./rotamer_lib_entry.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_lib_entry.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/tests/data/aln_tpl/5d52-1_cut_A.fasta /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/5d52-1_cut_A.fasta -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/1crn_sc_test.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/1crn_sc_test.pdb -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./structure_db.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./structure_db.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./eigen_types.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./eigen_types.hh -[ 3%] Built target test_action_help.py_run -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./constraint_constructor.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./constraint_constructor.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./rotamer_lib_reader.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_lib_reader.hh make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./pairwise_score.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./pairwise_score.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./rotamer_lib_reader.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_lib_reader.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./psipred_prediction.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./psipred_prediction.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/tests/data/aln_tpl/5d52-1_cut.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/5d52-1_cut.pdb cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./sidechain_env_listener.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./sidechain_env_listener.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./torsion_sampler.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./torsion_sampler.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/tests/data/aln_tpl/5d52-1_cut_B.fasta /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/5d52-1_cut_B.fasta +[ 3%] Built target test_action_help.py_run +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/1eye.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/1eye.pdb +make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./sidechain_connector.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./sidechain_connector.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./all_atom_score_base.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_score_base.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./constraint_constructor.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./constraint_constructor.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./stem_geom.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./stem_geom.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./motif_finder.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./motif_finder.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl [ 3%] Built target promod3_core_headers make -f core/src/CMakeFiles/promod3_core.dir/build.make core/src/CMakeFiles/promod3_core.dir/depend make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/core/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src/CMakeFiles/promod3_core.dir/DependInfo.cmake --color= -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./all_atom_overall_scorer.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_overall_scorer.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./sidechain_object_loader.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./sidechain_object_loader.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./all_atom_score_base.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_score_base.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./structure_db.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./structure_db.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./robin_hood.h /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./robin_hood.h -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./ushort_vec.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./ushort_vec.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/1CRNA.hhm /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/1CRNA.hhm -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./all_atom_interaction_env_listener.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_interaction_env_listener.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./sidechain_atom_rule_lookup.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./sidechain_atom_rule_lookup.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/tests/data/aln_tpl/1crn.hhm /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/1crn.hhm +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/tests/data/aln_tpl/5d52-1_cut_A.fasta /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/5d52-1_cut_A.fasta cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./rotamer_constructor.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_constructor.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/1eye_rec.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/1eye_rec.pdb +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./all_atom_overall_scorer.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_overall_scorer.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./torsion_sampler.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./torsion_sampler.hh make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./all_atom_interaction_score.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_interaction_score.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./sidechain_atom_constructor.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./sidechain_atom_constructor.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./rotamer_lookup.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_lookup.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./all_atom_interaction_env_listener.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_interaction_env_listener.hh +[ 3%] Built target promod3_modelling_headers +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make -f core/src/CMakeFiles/promod3_core.dir/build.make core/src/CMakeFiles/promod3_core.dir/build -[ 3%] Built target promod3_modelling_headers +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./ushort_vec.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./ushort_vec.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/tests/data/aln_tpl/5d52-1_cut_B.fasta /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/5d52-1_cut_B.fasta +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./scwrl4_rotamer_constructor.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./scwrl4_rotamer_constructor.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./all_atom_interaction_score.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_interaction_score.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/1eye_sc_test.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/1eye_sc_test.pdb +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./sidechain_atom_rule_lookup.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./sidechain_atom_rule_lookup.hh make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'core/src/CMakeFiles/promod3_core.dir/build'. make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/tests/data/aln_tpl/1crn_corrupted.hhm /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/1crn_corrupted.hhm -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./structure_db_custom_types.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./structure_db_custom_types.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./scwrl3_rotamer_constructor.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./scwrl3_rotamer_constructor.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./all_atom_packing_score.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_packing_score.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/1eye.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/1eye.pdb -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./rotamer_lookup.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_lookup.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./sidechain_atom_constructor.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./sidechain_atom_constructor.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data [ 6%] Built target promod3_core -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl make -f core/pymod/CMakeFiles/_core.dir/build.make core/pymod/CMakeFiles/_core.dir/depend make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/core/pymod /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/pymod /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/pymod/CMakeFiles/_core.dir/DependInfo.cmake --color= +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./vina_rotamer_constructor.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./vina_rotamer_constructor.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/tests/data/aln_tpl/1crn.hhm /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/1crn.hhm +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./structure_db_custom_types.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./structure_db_custom_types.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./all_atom_clash_score.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_clash_score.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/1ITX-A-11_sidechain.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/1ITX-A-11_sidechain.pdb +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./subrotamer_optimizer.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./subrotamer_optimizer.hh make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./scwrl4_rotamer_constructor.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./scwrl4_rotamer_constructor.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./scwrl3_energy_functions.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./scwrl3_energy_functions.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/tests/data/aln_tpl/5ua4_B.fasta /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/5ua4_B.fasta +make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +make -f core/pymod/CMakeFiles/_core.dir/build.make core/pymod/CMakeFiles/_core.dir/build +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/tests/data/aln_tpl/1crn_corrupted.hhm /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/1crn_corrupted.hhm [ 6%] Built target promod3_loop_headers +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/1K5C-A-16_clash.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/1K5C-A-16_clash.pdb make -f loop/src/CMakeFiles/promod3_loop.dir/build.make loop/src/CMakeFiles/promod3_loop.dir/depend -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./scwrl3_energy_functions.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./scwrl3_energy_functions.hh +make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +[ 6%] Built target promod3_sidechain_headers make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/loop/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src/CMakeFiles/promod3_loop.dir/DependInfo.cmake --color= -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./scwrl3_rotamer_constructor.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./scwrl3_rotamer_constructor.hh -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/1eye_rec.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/1eye_rec.pdb cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl -make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -make -f core/pymod/CMakeFiles/_core.dir/build.make core/pymod/CMakeFiles/_core.dir/build -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./vina_rotamer_constructor.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./vina_rotamer_constructor.hh [ 6%] Built target promod3_scoring_headers -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/tests/data/aln_tpl/5ua4_B.hhm /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/5ua4_B.hhm -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'core/pymod/CMakeFiles/_core.dir/build'. make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./subrotamer_optimizer.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./subrotamer_optimizer.hh +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/tests/data/aln_tpl/5ua4_B.fasta /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/5ua4_B.fasta [ 8%] Built target _core -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/1eye_sc_test.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/1eye_sc_test.pdb -make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/fasta +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/1mcg.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/1mcg.pdb +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/tests/data/aln_tpl/5ua4_B.hhm /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/5ua4_B.hhm +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/2aoh-1_cut.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/2aoh-1_cut.pdb +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/fasta cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/tests/data/fasta/alignment.fas /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/fasta/alignment.fas -[ 8%] Built target promod3_sidechain_headers +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/fasta make -f loop/src/CMakeFiles/promod3_loop.dir/build.make loop/src/CMakeFiles/promod3_loop.dir/build -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/1ITX-A-11_sidechain.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/1ITX-A-11_sidechain.pdb +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/fasta +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/2aoh-1_cut_A.fasta /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/2aoh-1_cut_A.fasta cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/tests/data/fasta/1ake.fas /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/fasta/1ake.fas cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/fasta make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'loop/src/CMakeFiles/promod3_loop.dir/build'. make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/1K5C-A-16_clash.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/1K5C-A-16_clash.pdb -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/tests/data/fasta/1ake_1.fas /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/fasta/1ake_1.fas -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/fasta +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/2aoh-1_cut_B.fasta /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/2aoh-1_cut_B.fasta [ 17%] Built target promod3_loop make -f loop/pymod/CMakeFiles/_loop.dir/build.make loop/pymod/CMakeFiles/_loop.dir/depend make -f scoring/src/CMakeFiles/promod3_scoring.dir/build.make scoring/src/CMakeFiles/promod3_scoring.dir/depend +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/tests/data/fasta/1ake_1.fas /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/fasta/1ake_1.fas make -f sidechain/src/CMakeFiles/promod3_sidechain.dir/build.make sidechain/src/CMakeFiles/promod3_sidechain.dir/depend make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/loop/pymod /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/pymod /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/pymod/CMakeFiles/_loop.dir/DependInfo.cmake --color= -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/fasta -make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/sidechain/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src/CMakeFiles/promod3_sidechain.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/scoring/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src/CMakeFiles/promod3_scoring.dir/DependInfo.cmake --color= -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/1mcg.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/1mcg.pdb -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/tests/data/fasta/1ake_2trg.fas /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/fasta/1ake_2trg.fas +make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/sidechain/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src/CMakeFiles/promod3_sidechain.dir/DependInfo.cmake --color= cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/fasta -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/2aoh-1_cut.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/2aoh-1_cut.pdb -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/tests/data/fasta/1ake_3.fas /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/fasta/1ake_3.fas +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/2dbs.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/2dbs.pdb +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/tests/data/fasta/1ake_2trg.fas /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/fasta/1ake_2trg.fas +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/fasta cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/tests/data/fasta/1ake_3.fas /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/fasta/1ake_3.fas +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/2jlp-1.fasta /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/2jlp-1.fasta cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/fasta -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/2aoh-1_cut_A.fasta /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/2aoh-1_cut_A.fasta +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/tests/data/fasta/1ake.fas.gz /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/fasta/1ake.fas.gz +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/2jlp-1.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/2jlp-1.pdb make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make -f loop/pymod/CMakeFiles/_loop.dir/build.make loop/pymod/CMakeFiles/_loop.dir/build +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/fasta +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/tests/data/fasta/1ake_nel.fas /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/fasta/1ake_nel.fas make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make -f sidechain/src/CMakeFiles/promod3_sidechain.dir/build.make sidechain/src/CMakeFiles/promod3_sidechain.dir/build +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/2xim-1.fasta /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/2xim-1.fasta cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/fasta +make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +make -f scoring/src/CMakeFiles/promod3_scoring.dir/build.make scoring/src/CMakeFiles/promod3_scoring.dir/build cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/tests/data/fasta/1ake_nel.fas /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/fasta/1ake_nel.fas -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/2aoh-1_cut_B.fasta /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/2aoh-1_cut_B.fasta make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'loop/pymod/CMakeFiles/_loop.dir/build'. make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/tests/data/fasta/1ake_sw.fas /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/fasta/1ake_sw.fas +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/2xim-1.pdb.gz /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/2xim-1.pdb.gz +[ 22%] Built target _loop make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'sidechain/src/CMakeFiles/promod3_sidechain.dir/build'. make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/fasta make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -make -f scoring/src/CMakeFiles/promod3_scoring.dir/build.make scoring/src/CMakeFiles/promod3_scoring.dir/build cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data -[ 27%] Built target promod3_sidechain +[ 33%] Built target promod3_sidechain make -f sidechain/pymod/CMakeFiles/_sidechain.dir/build.make sidechain/pymod/CMakeFiles/_sidechain.dir/depend -make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/sidechain/pymod /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/pymod /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/pymod/CMakeFiles/_sidechain.dir/DependInfo.cmake --color= -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/tests/data/fasta/1ake_sw.fas /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/fasta/1ake_sw.fas -[ 33%] Built target _loop -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/2dbs.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/2dbs.pdb -make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data -make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'scoring/src/CMakeFiles/promod3_scoring.dir/build'. -make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' [ 33%] Built target test_data_core make -f core/tests/CMakeFiles/test_suite_core.dir/build.make core/tests/CMakeFiles/test_suite_core.dir/depend make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/core/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests/CMakeFiles/test_suite_core.dir/DependInfo.cmake --color= +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/sidechain/pymod /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/pymod /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/pymod/CMakeFiles/_sidechain.dir/DependInfo.cmake --color= make -f core/tests/CMakeFiles/test_setcompoundschemlib.py_run.dir/build.make core/tests/CMakeFiles/test_setcompoundschemlib.py_run.dir/depend -make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/core/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests/CMakeFiles/test_setcompoundschemlib.py_run.dir/DependInfo.cmake --color= make -f core/tests/CMakeFiles/test_helper.py_run.dir/build.make core/tests/CMakeFiles/test_helper.py_run.dir/depend make -f core/tests/CMakeFiles/test_pm3argparse.py_run.dir/build.make core/tests/CMakeFiles/test_pm3argparse.py_run.dir/depend make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/core/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests/CMakeFiles/test_setcompoundschemlib.py_run.dir/DependInfo.cmake --color= +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/core/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests/CMakeFiles/test_suite_core.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/core/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests/CMakeFiles/test_helper.py_run.dir/DependInfo.cmake --color= -[ 44%] Built target promod3_scoring make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/core/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests/CMakeFiles/test_pm3argparse.py_run.dir/DependInfo.cmake --color= -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/2jlp-1.fasta /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/2jlp-1.fasta -make -f scoring/pymod/CMakeFiles/_scoring.dir/build.make scoring/pymod/CMakeFiles/_scoring.dir/depend -make -f modelling/src/CMakeFiles/promod3_modelling.dir/build.make modelling/src/CMakeFiles/promod3_modelling.dir/depend -make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/scoring/pymod /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/pymod /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/pymod/CMakeFiles/_scoring.dir/DependInfo.cmake --color= +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/3b08-3.pdb.gz /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/3b08-3.pdb.gz make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/modelling/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src/CMakeFiles/promod3_modelling.dir/DependInfo.cmake --color= -make -f core/tests/CMakeFiles/test_suite_core.dir/build.make core/tests/CMakeFiles/test_suite_core.dir/build +make[4]: Nothing to be done for 'scoring/src/CMakeFiles/promod3_scoring.dir/build'. +make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -make -f core/tests/CMakeFiles/test_helper.py_run.dir/build.make core/tests/CMakeFiles/test_helper.py_run.dir/build make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +make -f core/tests/CMakeFiles/test_suite_core.dir/build.make core/tests/CMakeFiles/test_suite_core.dir/build make -f core/tests/CMakeFiles/test_setcompoundschemlib.py_run.dir/build.make core/tests/CMakeFiles/test_setcompoundschemlib.py_run.dir/build +make -f core/tests/CMakeFiles/test_pm3argparse.py_run.dir/build.make core/tests/CMakeFiles/test_pm3argparse.py_run.dir/build make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +make -f core/tests/CMakeFiles/test_helper.py_run.dir/build.make core/tests/CMakeFiles/test_helper.py_run.dir/build +make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -make -f core/tests/CMakeFiles/test_pm3argparse.py_run.dir/build.make core/tests/CMakeFiles/test_pm3argparse.py_run.dir/build make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data -[ 44%] Building CXX object core/tests/CMakeFiles/test_suite_core.dir/test_graph_minimizer.cc.o -[ 45%] Building CXX object core/tests/CMakeFiles/test_suite_core.dir/test_portable_binary.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT core/tests/CMakeFiles/test_suite_core.dir/test_graph_minimizer.cc.o -MF CMakeFiles/test_suite_core.dir/test_graph_minimizer.cc.o.d -o CMakeFiles/test_suite_core.dir/test_graph_minimizer.cc.o -c /build/promod3-3.2.1+ds/core/tests/test_graph_minimizer.cc -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT core/tests/CMakeFiles/test_suite_core.dir/test_portable_binary.cc.o -MF CMakeFiles/test_suite_core.dir/test_portable_binary.cc.o.d -o CMakeFiles/test_suite_core.dir/test_portable_binary.cc.o -c /build/promod3-3.2.1+ds/core/tests/test_portable_binary.cc +[ 44%] Built target promod3_scoring +make -f scoring/pymod/CMakeFiles/_scoring.dir/build.make scoring/pymod/CMakeFiles/_scoring.dir/depend +make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/scoring/pymod /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/pymod /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/pymod/CMakeFiles/_scoring.dir/DependInfo.cmake --color= +make -f modelling/src/CMakeFiles/promod3_modelling.dir/build.make modelling/src/CMakeFiles/promod3_modelling.dir/depend +[ 45%] running checks test_helper.py [ 45%] Building CXX object core/tests/CMakeFiles/test_suite_core.dir/test_check_io.cc.o -[ 46%] running checks test_helper.py -[ 47%] Building CXX object core/tests/CMakeFiles/test_suite_core.dir/tests.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/ /usr/bin/python3 /build/promod3-3.2.1+ds/core/tests/test_helper.py" -make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +[ 46%] running checks test_setcompoundschemlib.py +[ 47%] Building CXX object core/tests/CMakeFiles/test_suite_core.dir/test_portable_binary.cc.o +[ 47%] running checks test_pm3argparse.py cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT core/tests/CMakeFiles/test_suite_core.dir/test_check_io.cc.o -MF CMakeFiles/test_suite_core.dir/test_check_io.cc.o.d -o CMakeFiles/test_suite_core.dir/test_check_io.cc.o -c /build/promod3-3.2.1+ds/core/tests/test_check_io.cc -make -f sidechain/pymod/CMakeFiles/_sidechain.dir/build.make sidechain/pymod/CMakeFiles/_sidechain.dir/build -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT core/tests/CMakeFiles/test_suite_core.dir/tests.cc.o -MF CMakeFiles/test_suite_core.dir/tests.cc.o.d -o CMakeFiles/test_suite_core.dir/tests.cc.o -c /build/promod3-3.2.1+ds/core/tests/tests.cc -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/2jlp-1.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/2jlp-1.pdb -[ 48%] running checks test_setcompoundschemlib.py +[ 48%] Building CXX object core/tests/CMakeFiles/test_suite_core.dir/test_graph_minimizer.cc.o +[ 48%] Building CXX object core/tests/CMakeFiles/test_suite_core.dir/tests.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/ /usr/bin/python3 /build/promod3-3.2.1+ds/core/tests/test_helper.py" +make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/modelling/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src/CMakeFiles/promod3_modelling.dir/DependInfo.cmake --color= cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/ /usr/bin/python3 /build/promod3-3.2.1+ds/core/tests/test_setcompoundschemlib.py" -[ 48%] running checks test_pm3argparse.py +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT core/tests/CMakeFiles/test_suite_core.dir/test_portable_binary.cc.o -MF CMakeFiles/test_suite_core.dir/test_portable_binary.cc.o.d -o CMakeFiles/test_suite_core.dir/test_portable_binary.cc.o -c /build/promod3-3.2.1+ds/core/tests/test_portable_binary.cc +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT core/tests/CMakeFiles/test_suite_core.dir/test_graph_minimizer.cc.o -MF CMakeFiles/test_suite_core.dir/test_graph_minimizer.cc.o.d -o CMakeFiles/test_suite_core.dir/test_graph_minimizer.cc.o -c /build/promod3-3.2.1+ds/core/tests/test_graph_minimizer.cc cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/ /usr/bin/python3 /build/promod3-3.2.1+ds/core/tests/test_pm3argparse.py" +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT core/tests/CMakeFiles/test_suite_core.dir/tests.cc.o -MF CMakeFiles/test_suite_core.dir/tests.cc.o.d -o CMakeFiles/test_suite_core.dir/tests.cc.o -c /build/promod3-3.2.1+ds/core/tests/tests.cc +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/3b08-3.fasta /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/3b08-3.fasta +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/4nyk.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/4nyk.pdb +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make -f scoring/pymod/CMakeFiles/_scoring.dir/build.make scoring/pymod/CMakeFiles/_scoring.dir/build +make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +make -f sidechain/pymod/CMakeFiles/_sidechain.dir/build.make sidechain/pymod/CMakeFiles/_sidechain.dir/build +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/4R6K-A-13_sidechain.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/4R6K-A-13_sidechain.pdb cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'scoring/pymod/CMakeFiles/_scoring.dir/build'. make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make -f modelling/src/CMakeFiles/promod3_modelling.dir/build.make modelling/src/CMakeFiles/promod3_modelling.dir/build -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/2xim-1.fasta /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/2xim-1.fasta -[ 52%] Built target _scoring +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/4ksl-1.pdb.gz /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/4ksl-1.pdb.gz make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'sidechain/pymod/CMakeFiles/_sidechain.dir/build'. make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +[ 52%] Built target _scoring cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data +[ 59%] Built target _sidechain +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/4ksl-1.fasta /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/4ksl-1.fasta make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'modelling/src/CMakeFiles/promod3_modelling.dir/build'. make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -[ 59%] Built target _sidechain -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/2xim-1.pdb.gz /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/2xim-1.pdb.gz -[ 68%] Built target promod3_modelling cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data +[ 68%] Built target promod3_modelling make -f modelling/pymod/CMakeFiles/_modelling.dir/build.make modelling/pymod/CMakeFiles/_modelling.dir/depend make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/modelling/pymod /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod/CMakeFiles/_modelling.dir/DependInfo.cmake --color= -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/3b08-3.pdb.gz /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/3b08-3.pdb.gz -............ ----------------------------------------------------------------------- -Ran 12 tests in 0.005s +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/5d52-1.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/5d52-1.pdb +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/5d52-1_cut.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/5d52-1_cut.pdb +..........cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data +......................cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/5d52-1_cut_A.fasta /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/5d52-1_cut_A.fasta +........ +.---------------------------------------------------------------------- +Ran 2 tests in 0.090s OK -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data -.. +.......... ---------------------------------------------------------------------- -Ran 2 tests in 0.085s +Ran 12 tests in 0.004s OK -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/3b08-3.fasta /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/3b08-3.fasta +....cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data +.cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/5d52-1_cut_B.fasta /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/5d52-1_cut_B.fasta make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make -f modelling/pymod/CMakeFiles/_modelling.dir/build.make modelling/pymod/CMakeFiles/_modelling.dir/build make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data +[ 68%] Built target test_setcompoundschemlib.py_run +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/CA-3cm91E.fasta /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/CA-3cm91E.fasta [ 68%] Built target test_helper.py_run +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'modelling/pymod/CMakeFiles/_modelling.dir/build'. make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -[ 68%] Built target test_setcompoundschemlib.py_run -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/4nyk.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/4nyk.pdb +.cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/CA-3cm91E.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/CA-3cm91E.pdb .[ 75%] Built target _modelling make -f core/init/CMakeFiles/_init.dir/build.make core/init/CMakeFiles/_init.dir/depend make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/core/init /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/init /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/init/CMakeFiles/_init.dir/DependInfo.cmake --color= cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -make -f core/init/CMakeFiles/_init.dir/build.make core/init/CMakeFiles/_init.dir/build -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/4R6K-A-13_sidechain.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/4R6K-A-13_sidechain.pdb -make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +.make -f core/init/CMakeFiles/_init.dir/build.make core/init/CMakeFiles/_init.dir/build +.make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'core/init/CMakeFiles/_init.dir/build'. make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -....cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data -...........[ 75%] Built target _init -.......make -f loop/data/CMakeFiles/generate_loop_data_ff_lookup_charmm.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_ff_lookup_charmm.dat.dir/depend -.....make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler.dat.dir/depend +.cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/cbeta.fasta /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/cbeta.fasta +[ 75%] Built target _init +make -f loop/data/CMakeFiles/generate_loop_data_ff_lookup_charmm.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_ff_lookup_charmm.dat.dir/depend +make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler.dat.dir/depend +make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler_coil.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler_coil.dat.dir/depend +make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler_extended.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler_extended.dat.dir/depend make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/loop/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/generate_loop_data_ff_lookup_charmm.dat.dir/DependInfo.cmake --color= -...cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/4ksl-1.pdb.gz /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/4ksl-1.pdb.gz -...make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler_helical.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler_helical.dat.dir/depend +make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/loop/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/generate_loop_data_torsion_sampler.dat.dir/DependInfo.cmake --color= -make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler_coil.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler_coil.dat.dir/depend -...make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +make -f loop/data/CMakeFiles/generate_loop_data_frag_db.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_frag_db.dat.dir/depend +make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/loop/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/generate_loop_data_torsion_sampler_coil.dat.dir/DependInfo.cmake --color= -make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler_extended.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler_extended.dat.dir/depend -...make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +make -f loop/data/CMakeFiles/generate_loop_data_structure_db.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_structure_db.dat.dir/depend +make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/loop/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/generate_loop_data_torsion_sampler_extended.dat.dir/DependInfo.cmake --color= -make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler_helical.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler_helical.dat.dir/depend -make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -..make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/loop/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/generate_loop_data_torsion_sampler_helical.dat.dir/DependInfo.cmake --color= -make -f loop/data/CMakeFiles/generate_loop_data_ff_lookup_charmm.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_ff_lookup_charmm.dat.dir/build -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'loop/data/CMakeFiles/generate_loop_data_ff_lookup_charmm.dat.dir/build'. +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/loop/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/generate_loop_data_frag_db.dat.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/loop/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/generate_loop_data_structure_db.dat.dir/DependInfo.cmake --color= +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -.make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler_coil.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler_coil.dat.dir/build make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'loop/data/CMakeFiles/generate_loop_data_torsion_sampler_coil.dat.dir/build'. make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler.dat.dir/build +make -f loop/data/CMakeFiles/generate_loop_data_ff_lookup_charmm.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_ff_lookup_charmm.dat.dir/build +make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler_coil.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler_coil.dat.dir/build make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler_extended.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler_extended.dat.dir/build +make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler_helical.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler_helical.dat.dir/build make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'loop/data/CMakeFiles/generate_loop_data_torsion_sampler.dat.dir/build'. make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/4ksl-1.fasta /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/4ksl-1.fasta +make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +make[4]: Nothing to be done for 'loop/data/CMakeFiles/generate_loop_data_ff_lookup_charmm.dat.dir/build'. +make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +make[4]: Nothing to be done for 'loop/data/CMakeFiles/generate_loop_data_torsion_sampler_coil.dat.dir/build'. make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -[ 76%] Built target generate_loop_data_ff_lookup_charmm.dat -make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler_helical.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler_helical.dat.dir/build make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'loop/data/CMakeFiles/generate_loop_data_torsion_sampler_extended.dat.dir/build'. make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'loop/data/CMakeFiles/generate_loop_data_torsion_sampler_helical.dat.dir/build'. make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -make -f loop/data/CMakeFiles/generate_loop_data_frag_db.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_frag_db.dat.dir/depend -[ 76%] Built target generate_loop_data_torsion_sampler_coil.dat -make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/loop/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/generate_loop_data_frag_db.dat.dir/DependInfo.cmake --color= -make -f loop/data/CMakeFiles/generate_loop_data_structure_db.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_structure_db.dat.dir/depend -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data -[ 77%] Built target generate_loop_data_torsion_sampler_extended.dat -[ 78%] Built target generate_loop_data_torsion_sampler.dat +make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +make -f loop/data/CMakeFiles/generate_loop_data_frag_db.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_frag_db.dat.dir/build make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/loop/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/generate_loop_data_structure_db.dat.dir/DependInfo.cmake --color= +make[4]: Nothing to be done for 'loop/data/CMakeFiles/generate_loop_data_frag_db.dat.dir/build'. +make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +[ 76%] Built target generate_loop_data_torsion_sampler.dat +[ 76%] Built target generate_loop_data_torsion_sampler_coil.dat +[ 77%] Built target generate_loop_data_ff_lookup_charmm.dat +[ 78%] Built target generate_loop_data_torsion_sampler_extended.dat make -f scoring/data/CMakeFiles/generate_scoring_data_aa_packing_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_aa_packing_scorer.dat.dir/depend -make -f scoring/data/CMakeFiles/generate_scoring_data_cb_packing_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_cb_packing_scorer.dat.dir/depend +make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/scoring/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_aa_packing_scorer.dat.dir/DependInfo.cmake --color= [ 78%] Built target generate_loop_data_torsion_sampler_helical.dat +make -f loop/data/CMakeFiles/generate_loop_data_structure_db.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_structure_db.dat.dir/build +make -f scoring/data/CMakeFiles/generate_scoring_data_cb_packing_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_cb_packing_scorer.dat.dir/depend make -f scoring/data/CMakeFiles/generate_scoring_data_cbeta_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_cbeta_scorer.dat.dir/depend +make -f scoring/data/CMakeFiles/generate_scoring_data_reduced_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_reduced_scorer.dat.dir/depend +make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +make[4]: Nothing to be done for 'loop/data/CMakeFiles/generate_loop_data_structure_db.dat.dir/build'. +make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/scoring/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_cb_packing_scorer.dat.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/scoring/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_cbeta_scorer.dat.dir/DependInfo.cmake --color= -make -f scoring/data/CMakeFiles/generate_scoring_data_reduced_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_reduced_scorer.dat.dir/depend -make -f scoring/data/CMakeFiles/generate_scoring_data_hbond_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_hbond_scorer.dat.dir/depend make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/scoring/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_reduced_scorer.dat.dir/DependInfo.cmake --color= +make -f scoring/data/CMakeFiles/generate_scoring_data_hbond_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_hbond_scorer.dat.dir/depend +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/cbeta.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/cbeta.pdb make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/scoring/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_hbond_scorer.dat.dir/DependInfo.cmake --color= +[ 78%] Built target generate_loop_data_frag_db.dat make -f scoring/data/CMakeFiles/generate_scoring_data_ss_agreement_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_ss_agreement_scorer.dat.dir/depend -make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +.make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/scoring/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_ss_agreement_scorer.dat.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/5d52-1.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/5d52-1.pdb -make -f loop/data/CMakeFiles/generate_loop_data_frag_db.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_frag_db.dat.dir/build +[ 78%] Built target generate_loop_data_structure_db.dat make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +make -f scoring/data/CMakeFiles/generate_scoring_data_cb_packing_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_cb_packing_scorer.dat.dir/build make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +make -f scoring/data/CMakeFiles/generate_scoring_data_cbeta_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_cbeta_scorer.dat.dir/build make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'loop/data/CMakeFiles/generate_loop_data_frag_db.dat.dir/build'. -make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -.make -f loop/data/CMakeFiles/generate_loop_data_structure_db.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_structure_db.dat.dir/build +make[4]: Nothing to be done for 'scoring/data/CMakeFiles/generate_scoring_data_cb_packing_scorer.dat.dir/build'. make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +make -f scoring/data/CMakeFiles/generate_scoring_data_reduced_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_reduced_scorer.dat.dir/build +make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +make[4]: Nothing to be done for 'scoring/data/CMakeFiles/generate_scoring_data_cbeta_scorer.dat.dir/build'. make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'loop/data/CMakeFiles/generate_loop_data_structure_db.dat.dir/build'. +make[4]: Nothing to be done for 'scoring/data/CMakeFiles/generate_scoring_data_reduced_scorer.dat.dir/build'. +make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make -f scoring/data/CMakeFiles/generate_scoring_data_aa_packing_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_aa_packing_scorer.dat.dir/build +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data +make -f scoring/data/CMakeFiles/generate_scoring_data_torsion_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_torsion_scorer.dat.dir/depend +make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'scoring/data/CMakeFiles/generate_scoring_data_aa_packing_scorer.dat.dir/build'. make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -make -f scoring/data/CMakeFiles/generate_scoring_data_cb_packing_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_cb_packing_scorer.dat.dir/build -.make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'scoring/data/CMakeFiles/generate_scoring_data_cb_packing_scorer.dat.dir/build'. make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -make -f scoring/data/CMakeFiles/generate_scoring_data_cbeta_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_cbeta_scorer.dat.dir/build make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'scoring/data/CMakeFiles/generate_scoring_data_cbeta_scorer.dat.dir/build'. -make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -make -f scoring/data/CMakeFiles/generate_scoring_data_reduced_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_reduced_scorer.dat.dir/build +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/scoring/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_torsion_scorer.dat.dir/DependInfo.cmake --color= make -f scoring/data/CMakeFiles/generate_scoring_data_hbond_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_hbond_scorer.dat.dir/build make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'scoring/data/CMakeFiles/generate_scoring_data_reduced_scorer.dat.dir/build'. -make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'scoring/data/CMakeFiles/generate_scoring_data_hbond_scorer.dat.dir/build'. make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make -f scoring/data/CMakeFiles/generate_scoring_data_ss_agreement_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_ss_agreement_scorer.dat.dir/build make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'scoring/data/CMakeFiles/generate_scoring_data_ss_agreement_scorer.dat.dir/build'. make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data -..[ 78%] Built target generate_loop_data_structure_db.dat -[ 78%] Built target generate_loop_data_frag_db.dat -[ 78%] Built target generate_scoring_data_aa_packing_scorer.dat -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/5d52-1_cut.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/5d52-1_cut.pdb -make -f scoring/data/CMakeFiles/generate_scoring_data_torsion_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_torsion_scorer.dat.dir/depend [ 78%] Built target generate_scoring_data_cb_packing_scorer.dat +[ 79%] Built target generate_scoring_data_cbeta_scorer.dat +[ 79%] Built target generate_scoring_data_reduced_scorer.dat make -f scoring/data/CMakeFiles/generate_scoring_data_aa_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_aa_scorer.dat.dir/depend -[ 78%] Built target generate_scoring_data_reduced_scorer.dat -make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/scoring/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_torsion_scorer.dat.dir/DependInfo.cmake --color= +make -f sidechain/data/CMakeFiles/generate_sidechain_data_bb_dep_lib.dat.dir/build.make sidechain/data/CMakeFiles/generate_sidechain_data_bb_dep_lib.dat.dir/depend make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/scoring/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_aa_scorer.dat.dir/DependInfo.cmake --color= -make -f sidechain/data/CMakeFiles/generate_sidechain_data_bb_dep_lib.dat.dir/build.make sidechain/data/CMakeFiles/generate_sidechain_data_bb_dep_lib.dat.dir/depend -[ 79%] Built target generate_scoring_data_cbeta_scorer.dat make -f sidechain/data/CMakeFiles/generate_sidechain_data_lib.dat.dir/build.make sidechain/data/CMakeFiles/generate_sidechain_data_lib.dat.dir/depend make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/sidechain/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/data/CMakeFiles/generate_sidechain_data_bb_dep_lib.dat.dir/DependInfo.cmake --color= -[ 80%] Built target generate_scoring_data_ss_agreement_scorer.dat -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data -make -f loop/data/CMakeFiles/loop_data.dir/build.make loop/data/CMakeFiles/loop_data.dir/depend +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/compounds.chemlib /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/compounds.chemlib +make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/sidechain/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/data/CMakeFiles/generate_sidechain_data_lib.dat.dir/DependInfo.cmake --color= -[ 80%] Built target generate_scoring_data_hbond_scorer.dat -make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/loop/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/loop_data.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make -f scoring/data/CMakeFiles/generate_scoring_data_torsion_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_torsion_scorer.dat.dir/build -make -f scoring/data/CMakeFiles/generate_scoring_data_aa_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_aa_scorer.dat.dir/build -make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'scoring/data/CMakeFiles/generate_scoring_data_torsion_scorer.dat.dir/build'. make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -make -f sidechain/data/CMakeFiles/generate_sidechain_data_bb_dep_lib.dat.dir/build.make sidechain/data/CMakeFiles/generate_sidechain_data_bb_dep_lib.dat.dir/build +[ 80%] Built target generate_scoring_data_hbond_scorer.dat +[ 80%] Built target generate_scoring_data_ss_agreement_scorer.dat +make -f loop/data/CMakeFiles/loop_data.dir/build.make loop/data/CMakeFiles/loop_data.dir/depend +[ 80%] Built target generate_scoring_data_aa_packing_scorer.dat make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'scoring/data/CMakeFiles/generate_scoring_data_aa_scorer.dat.dir/build'. +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/loop/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/loop_data.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +make -f scoring/data/CMakeFiles/generate_scoring_data_aa_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_aa_scorer.dat.dir/build make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'sidechain/data/CMakeFiles/generate_sidechain_data_bb_dep_lib.dat.dir/build'. +make[4]: Nothing to be done for 'scoring/data/CMakeFiles/generate_scoring_data_aa_scorer.dat.dir/build'. make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -.cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/5d52-1_cut_A.fasta /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/5d52-1_cut_A.fasta make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make -f sidechain/data/CMakeFiles/generate_sidechain_data_lib.dat.dir/build.make sidechain/data/CMakeFiles/generate_sidechain_data_lib.dat.dir/build make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'sidechain/data/CMakeFiles/generate_sidechain_data_lib.dat.dir/build'. make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +[ 80%] Built target generate_scoring_data_torsion_scorer.dat +make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +make -f sidechain/data/CMakeFiles/generate_sidechain_data_bb_dep_lib.dat.dir/build.make sidechain/data/CMakeFiles/generate_sidechain_data_bb_dep_lib.dat.dir/build +make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +make[4]: Nothing to be done for 'sidechain/data/CMakeFiles/generate_sidechain_data_bb_dep_lib.dat.dir/build'. +make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -[ 81%] Built target generate_scoring_data_aa_scorer.dat make -f loop/data/CMakeFiles/loop_data.dir/build.make loop/data/CMakeFiles/loop_data.dir/build -[ 81%] Built target generate_scoring_data_torsion_scorer.dat -make -f scoring/data/CMakeFiles/scoring_data.dir/build.make scoring/data/CMakeFiles/scoring_data.dir/depend +[ 80%] Built target generate_sidechain_data_lib.dat make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'loop/data/CMakeFiles/loop_data.dir/build'. make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -[ 82%] Built target generate_sidechain_data_bb_dep_lib.dat -[ 82%] Built target generate_sidechain_data_lib.dat +[ 81%] Built target generate_scoring_data_aa_scorer.dat +.make -f scoring/data/CMakeFiles/scoring_data.dir/build.make scoring/data/CMakeFiles/scoring_data.dir/depend make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/scoring/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/scoring_data.dir/DependInfo.cmake --color= +[ 82%] Built target generate_sidechain_data_bb_dep_lib.dat make -f sidechain/data/CMakeFiles/sidechain_data.dir/build.make sidechain/data/CMakeFiles/sidechain_data.dir/depend -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/sidechain/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/data/CMakeFiles/sidechain_data.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -make -f scoring/data/CMakeFiles/scoring_data.dir/build.make scoring/data/CMakeFiles/scoring_data.dir/build -make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/5d52-1_cut_B.fasta /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/5d52-1_cut_B.fasta +[ 82%] Built target loop_data +make -f loop/tests/CMakeFiles/test_data_loop.dir/build.make loop/tests/CMakeFiles/test_data_loop.dir/depend make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'scoring/data/CMakeFiles/scoring_data.dir/build'. +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/loop/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests/CMakeFiles/test_data_loop.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make -f sidechain/data/CMakeFiles/sidechain_data.dir/build.make sidechain/data/CMakeFiles/sidechain_data.dir/build -[ 82%] Built target loop_data make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'sidechain/data/CMakeFiles/sidechain_data.dir/build'. make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data -make -f loop/tests/CMakeFiles/test_data_loop.dir/build.make loop/tests/CMakeFiles/test_data_loop.dir/depend -make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/loop/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests/CMakeFiles/test_data_loop.dir/DependInfo.cmake --color= -.cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/CA-3cm91E.fasta /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/CA-3cm91E.fasta -[ 82%] Built target sidechain_data -make -f sidechain/tests/CMakeFiles/test_data_sidechain.dir/build.make sidechain/tests/CMakeFiles/test_data_sidechain.dir/depend -[ 82%] Built target scoring_data make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make -f loop/tests/CMakeFiles/test_data_loop.dir/build.make loop/tests/CMakeFiles/test_data_loop.dir/build -make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/sidechain/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/tests/CMakeFiles/test_data_sidechain.dir/DependInfo.cmake --color= -make -f scoring/tests/CMakeFiles/test_data_scoring.dir/build.make scoring/tests/CMakeFiles/test_data_scoring.dir/depend +make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +make -f scoring/data/CMakeFiles/scoring_data.dir/build.make scoring/data/CMakeFiles/scoring_data.dir/build make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/loop make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/scoring/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/tests/CMakeFiles/test_data_scoring.dir/DependInfo.cmake --color= -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/loop/data +make[4]: Nothing to be done for 'scoring/data/CMakeFiles/scoring_data.dir/build'. make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +[ 82%] Built target scoring_data +make -f scoring/tests/CMakeFiles/test_data_scoring.dir/build.make scoring/tests/CMakeFiles/test_data_scoring.dir/depend +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/loop/data +[ 82%] Built target sidechain_data +make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/scoring/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/tests/CMakeFiles/test_data_scoring.dir/DependInfo.cmake --color= +make -f sidechain/tests/CMakeFiles/test_data_sidechain.dir/build.make sidechain/tests/CMakeFiles/test_data_sidechain.dir/depend +make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/sidechain/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/tests/CMakeFiles/test_data_sidechain.dir/DependInfo.cmake --color= +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/tests/data/1A88A.hhm /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/loop/data/1A88A.hhm make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make -f sidechain/tests/CMakeFiles/test_data_sidechain.dir/build.make sidechain/tests/CMakeFiles/test_data_sidechain.dir/build -make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/sidechain +make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make -f scoring/tests/CMakeFiles/test_data_scoring.dir/build.make scoring/tests/CMakeFiles/test_data_scoring.dir/build -.. ----------------------------------------------------------------------- -Ran 3 tests in 2.283s - -OK make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/sidechain +.make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/scoring -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/tests/data/1A88A.hhm /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/loop/data/1A88A.hhm -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/CA-3cm91E.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/CA-3cm91E.pdb -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/sidechain/data cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/loop/data +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/sidechain/data cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/scoring/data cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/tests/data/1A88A.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/loop/data/1A88A.pdb -.cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/del.fasta /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/del.fasta cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/tests/data/1CRNA.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/scoring/data/1CRNA.pdb cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/tests/data/all_sc.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/sidechain/data/all_sc.pdb cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/loop/data +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/scoring/data -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/cbeta.fasta /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/cbeta.fasta make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/tests/data/1A88A_with_gap.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/loop/data/1A88A_with_gap.pdb +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/ff_NAD.dat /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/ff_NAD.dat cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/tests/data/3DEFA.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/scoring/data/3DEFA.pdb [ 82%] Built target test_data_sidechain -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/loop/data make -f sidechain/tests/CMakeFiles/test_suite_sidechain.dir/build.make sidechain/tests/CMakeFiles/test_suite_sidechain.dir/depend -make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/sidechain/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/tests/CMakeFiles/test_suite_sidechain.dir/DependInfo.cmake --color= +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/loop/data +.cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/scoring/data -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data +make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/tests/data/1akyA.horiz /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/loop/data/1akyA.horiz -[ 82%] Built target test_action_build-rawmodel.py_run -.make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make -f sidechain/tests/CMakeFiles/test_suite_sidechain.dir/build.make sidechain/tests/CMakeFiles/test_suite_sidechain.dir/build +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/gly.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/gly.pdb make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/tests/data/clash_test.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/scoring/data/clash_test.pdb cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/loop/data -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/cbeta.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/cbeta.pdb +[ 82%] Building CXX object sidechain/tests/CMakeFiles/test_suite_sidechain.dir/tests.cc.o [ 82%] Building CXX object sidechain/tests/CMakeFiles/test_suite_sidechain.dir/test_frame_construction.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data [ 83%] Building CXX object sidechain/tests/CMakeFiles/test_suite_sidechain.dir/test_rotamers.cc.o -make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/tests && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT sidechain/tests/CMakeFiles/test_suite_sidechain.dir/test_frame_construction.cc.o -MF CMakeFiles/test_suite_sidechain.dir/test_frame_construction.cc.o.d -o CMakeFiles/test_suite_sidechain.dir/test_frame_construction.cc.o -c /build/promod3-3.2.1+ds/sidechain/tests/test_frame_construction.cc -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/tests/data/1CRN.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/loop/data/1CRN.pdb cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/tests && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT sidechain/tests/CMakeFiles/test_suite_sidechain.dir/test_rotamers.cc.o -MF CMakeFiles/test_suite_sidechain.dir/test_rotamers.cc.o.d -o CMakeFiles/test_suite_sidechain.dir/test_rotamers.cc.o -c /build/promod3-3.2.1+ds/sidechain/tests/test_rotamers.cc -[ 83%] Building CXX object sidechain/tests/CMakeFiles/test_suite_sidechain.dir/tests.cc.o +make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/tests && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT sidechain/tests/CMakeFiles/test_suite_sidechain.dir/tests.cc.o -MF CMakeFiles/test_suite_sidechain.dir/tests.cc.o.d -o CMakeFiles/test_suite_sidechain.dir/tests.cc.o -c /build/promod3-3.2.1+ds/sidechain/tests/tests.cc -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/loop/data -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/compounds.chemlib /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/compounds.chemlib +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/gly_on_top.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/gly_on_top.pdb [ 83%] Built target test_data_scoring -.make -f scoring/tests/CMakeFiles/test_suite_scoring.dir/build.make scoring/tests/CMakeFiles/test_suite_scoring.dir/depend +make -f scoring/tests/CMakeFiles/test_suite_scoring.dir/build.make scoring/tests/CMakeFiles/test_suite_scoring.dir/depend make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/scoring/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/tests/CMakeFiles/test_suite_scoring.dir/DependInfo.cmake --color= -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/tests/data/3DEFA.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/loop/data/3DEFA.pdb +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/tests/data/1CRN.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/loop/data/1CRN.pdb +.cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/loop/data make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make -f scoring/tests/CMakeFiles/test_suite_scoring.dir/build.make scoring/tests/CMakeFiles/test_suite_scoring.dir/build -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/loop/data +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/tests/data/3DEFA.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/loop/data/3DEFA.pdb +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/gly_almost_on_top.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/gly_almost_on_top.pdb make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/tests/data/4nyk.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/loop/data/4nyk.pdb [ 84%] Building CXX object scoring/tests/CMakeFiles/test_suite_scoring.dir/test_backbone_score_base.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/loop/data cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/tests && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT scoring/tests/CMakeFiles/test_suite_scoring.dir/test_backbone_score_base.cc.o -MF CMakeFiles/test_suite_scoring.dir/test_backbone_score_base.cc.o.d -o CMakeFiles/test_suite_scoring.dir/test_backbone_score_base.cc.o -c /build/promod3-3.2.1+ds/scoring/tests/test_backbone_score_base.cc [ 84%] Building CXX object scoring/tests/CMakeFiles/test_suite_scoring.dir/test_backbone_scorer.cc.o -.cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/tests && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT scoring/tests/CMakeFiles/test_suite_scoring.dir/test_backbone_scorer.cc.o -MF CMakeFiles/test_suite_scoring.dir/test_backbone_scorer.cc.o.d -o CMakeFiles/test_suite_scoring.dir/test_backbone_scorer.cc.o -c /build/promod3-3.2.1+ds/scoring/tests/test_backbone_scorer.cc -.[ 84%] Building CXX object scoring/tests/CMakeFiles/test_suite_scoring.dir/test_all_atom_scorer.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/tests && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT scoring/tests/CMakeFiles/test_suite_scoring.dir/test_backbone_scorer.cc.o -MF CMakeFiles/test_suite_scoring.dir/test_backbone_scorer.cc.o.d -o CMakeFiles/test_suite_scoring.dir/test_backbone_scorer.cc.o -c /build/promod3-3.2.1+ds/scoring/tests/test_backbone_scorer.cc +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data +[ 84%] Building CXX object scoring/tests/CMakeFiles/test_suite_scoring.dir/test_all_atom_scorer.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/tests && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT scoring/tests/CMakeFiles/test_suite_scoring.dir/test_all_atom_scorer.cc.o -MF CMakeFiles/test_suite_scoring.dir/test_all_atom_scorer.cc.o.d -o CMakeFiles/test_suite_scoring.dir/test_all_atom_scorer.cc.o -c /build/promod3-3.2.1+ds/scoring/tests/test_all_atom_scorer.cc -[ 86%] Building CXX object scoring/tests/CMakeFiles/test_suite_scoring.dir/tests.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/tests && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT scoring/tests/CMakeFiles/test_suite_scoring.dir/tests.cc.o -MF CMakeFiles/test_suite_scoring.dir/tests.cc.o.d -o CMakeFiles/test_suite_scoring.dir/tests.cc.o -c /build/promod3-3.2.1+ds/scoring/tests/tests.cc +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/tests/data/4nyk.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/loop/data/4nyk.pdb +..cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/gly_shifted_nter.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/gly_shifted_nter.pdb cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/loop/data -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/tests/data/all_aa.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/loop/data/all_aa.pdb cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/tests/data/all_aa.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/loop/data/all_aa.pdb +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/hetero-punched.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/hetero-punched.pdb cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/loop/data -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/del.fasta /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/del.fasta +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data +.. +---------------------------------------------------------------------- +Ran 3 tests in 1.873s + +OK cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/tests/data/all_aa_prot_polar_hisd.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/loop/data/all_aa_prot_polar_hisd.pdb +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/ins.fasta /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/ins.fasta cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/loop/data -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/ff_NAD.dat /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/ff_NAD.dat +make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/modelCApartial-5tgl1A.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/modelCApartial-5tgl1A.pdb cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/tests/data/all_aa_prot_polar_hise.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/loop/data/all_aa_prot_polar_hise.pdb +[ 84%] Built target test_action_build-rawmodel.py_run +[ 86%] Building CXX object scoring/tests/CMakeFiles/test_suite_scoring.dir/tests.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/tests && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT scoring/tests/CMakeFiles/test_suite_scoring.dir/tests.cc.o -MF CMakeFiles/test_suite_scoring.dir/tests.cc.o.d -o CMakeFiles/test_suite_scoring.dir/tests.cc.o -c /build/promod3-3.2.1+ds/scoring/tests/tests.cc cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/loop/data -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/gly.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/gly.pdb +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/neighbor-punched.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/neighbor-punched.pdb cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/tests/data/all_aa_prot_polar_hish.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/loop/data/all_aa_prot_polar_hish.pdb cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/loop/data -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/gly_on_top.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/gly_on_top.pdb +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/port_frag_db.dat /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/port_frag_db.dat cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/tests/data/all_aa_prot_ref.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/loop/data/all_aa_prot_ref.pdb -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/loop/data -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/gly_almost_on_top.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/gly_almost_on_top.pdb cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/tests/data/CHARMM27.dat /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/loop/data/CHARMM27.dat +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/port_str_db.dat /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/port_str_db.dat make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/gly_shifted_nter.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/gly_shifted_nter.pdb -[ 86%] Built target test_data_loop cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data +[ 86%] Built target test_data_loop make -f loop/tests/CMakeFiles/test_suite_loop.dir/build.make loop/tests/CMakeFiles/test_suite_loop.dir/depend +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/sep.fasta /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/sep.fasta make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/loop/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests/CMakeFiles/test_suite_loop.dir/DependInfo.cmake --color= -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/hetero-punched.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/hetero-punched.pdb -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make -f loop/tests/CMakeFiles/test_suite_loop.dir/build.make loop/tests/CMakeFiles/test_suite_loop.dir/build make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/ins.fasta /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/ins.fasta -[ 87%] Building CXX object loop/tests/CMakeFiles/test_suite_loop.dir/test_all_atom_positions.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT loop/tests/CMakeFiles/test_suite_loop.dir/test_all_atom_positions.cc.o -MF CMakeFiles/test_suite_loop.dir/test_all_atom_positions.cc.o.d -o CMakeFiles/test_suite_loop.dir/test_all_atom_positions.cc.o -c /build/promod3-3.2.1+ds/loop/tests/test_all_atom_positions.cc -[ 87%] Building CXX object loop/tests/CMakeFiles/test_suite_loop.dir/test_amino_acid_atoms.cc.o -[ 87%] Building CXX object loop/tests/CMakeFiles/test_suite_loop.dir/test_all_atom_env.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT loop/tests/CMakeFiles/test_suite_loop.dir/test_amino_acid_atoms.cc.o -MF CMakeFiles/test_suite_loop.dir/test_amino_acid_atoms.cc.o.d -o CMakeFiles/test_suite_loop.dir/test_amino_acid_atoms.cc.o -c /build/promod3-3.2.1+ds/loop/tests/test_amino_acid_atoms.cc -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT loop/tests/CMakeFiles/test_suite_loop.dir/test_all_atom_env.cc.o -MF CMakeFiles/test_suite_loop.dir/test_all_atom_env.cc.o.d -o CMakeFiles/test_suite_loop.dir/test_all_atom_env.cc.o -c /build/promod3-3.2.1+ds/loop/tests/test_all_atom_env.cc -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/modelCApartial-5tgl1A.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/modelCApartial-5tgl1A.pdb -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/neighbor-punched.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/neighbor-punched.pdb -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/port_frag_db.dat /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/port_frag_db.dat -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/port_str_db.dat /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/port_str_db.dat -.cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/sep.fasta /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/sep.fasta cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data +[ 86%] Building CXX object loop/tests/CMakeFiles/test_suite_loop.dir/test_all_atom_env.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT loop/tests/CMakeFiles/test_suite_loop.dir/test_all_atom_env.cc.o -MF CMakeFiles/test_suite_loop.dir/test_all_atom_env.cc.o.d -o CMakeFiles/test_suite_loop.dir/test_all_atom_env.cc.o -c /build/promod3-3.2.1+ds/loop/tests/test_all_atom_env.cc cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/sep.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/sep.pdb cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/seq.fasta /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/seq.fasta @@ -4938,193 +4977,200 @@ cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/smtl2bl4.1.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/smtl2bl4.1.pdb cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/ter.fasta /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/ter.fasta -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data +.cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/terminal_deletion_aln.fasta /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/terminal_deletion_aln.fasta cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/double_gap_aln.fasta /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/double_gap_aln.fasta make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -[ 87%] Built target test_data_modelling +[ 86%] Built target test_data_modelling make -f modelling/tests/CMakeFiles/test_suite_modelling.dir/build.make modelling/tests/CMakeFiles/test_suite_modelling.dir/depend make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/modelling/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests/CMakeFiles/test_suite_modelling.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make -f modelling/tests/CMakeFiles/test_suite_modelling.dir/build.make modelling/tests/CMakeFiles/test_suite_modelling.dir/build make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -[ 88%] Building CXX object modelling/tests/CMakeFiles/test_suite_modelling.dir/test_loop_candidates.cc.o +[ 87%] Building CXX object modelling/tests/CMakeFiles/test_suite_modelling.dir/test_loop_candidates.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT modelling/tests/CMakeFiles/test_suite_modelling.dir/test_loop_candidates.cc.o -MF CMakeFiles/test_suite_modelling.dir/test_loop_candidates.cc.o.d -o CMakeFiles/test_suite_modelling.dir/test_loop_candidates.cc.o -c /build/promod3-3.2.1+ds/modelling/tests/test_loop_candidates.cc -..[ 88%] Building CXX object loop/tests/CMakeFiles/test_suite_loop.dir/test_backbone.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT loop/tests/CMakeFiles/test_suite_loop.dir/test_backbone.cc.o -MF CMakeFiles/test_suite_loop.dir/test_backbone.cc.o.d -o CMakeFiles/test_suite_loop.dir/test_backbone.cc.o -c /build/promod3-3.2.1+ds/loop/tests/test_backbone.cc -.......... +[ 87%] Building CXX object modelling/tests/CMakeFiles/test_suite_modelling.dir/test_loop_closing.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT modelling/tests/CMakeFiles/test_suite_modelling.dir/test_loop_closing.cc.o -MF CMakeFiles/test_suite_modelling.dir/test_loop_closing.cc.o.d -o CMakeFiles/test_suite_modelling.dir/test_loop_closing.cc.o -c /build/promod3-3.2.1+ds/modelling/tests/test_loop_closing.cc +............ ---------------------------------------------------------------------- -Ran 66 tests in 4.045s +Ran 66 tests in 3.050s OK make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -[ 88%] Built target test_pm3argparse.py_run make -f modelling/tests/CMakeFiles/test_close_gaps.py_run.dir/build.make modelling/tests/CMakeFiles/test_close_gaps.py_run.dir/depend make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/modelling/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests/CMakeFiles/test_close_gaps.py_run.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -make -f modelling/tests/CMakeFiles/test_close_gaps.py_run.dir/build.make modelling/tests/CMakeFiles/test_close_gaps.py_run.dir/build -[ 89%] Building CXX object loop/tests/CMakeFiles/test_suite_loop.dir/test_forcefield.cc.o -make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT loop/tests/CMakeFiles/test_suite_loop.dir/test_forcefield.cc.o -MF CMakeFiles/test_suite_loop.dir/test_forcefield.cc.o.d -o CMakeFiles/test_suite_loop.dir/test_forcefield.cc.o -c /build/promod3-3.2.1+ds/loop/tests/test_forcefield.cc -[ 89%] running checks test_close_gaps.py -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/ /usr/bin/python3 /build/promod3-3.2.1+ds/modelling/tests/test_close_gaps.py" -[ 89%] Building CXX object modelling/tests/CMakeFiles/test_suite_modelling.dir/test_loop_closing.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT modelling/tests/CMakeFiles/test_suite_modelling.dir/test_loop_closing.cc.o -MF CMakeFiles/test_suite_modelling.dir/test_loop_closing.cc.o.d -o CMakeFiles/test_suite_modelling.dir/test_loop_closing.cc.o -c /build/promod3-3.2.1+ds/modelling/tests/test_loop_closing.cc -...[ 90%] Building CXX object modelling/tests/CMakeFiles/test_suite_modelling.dir/test_sidechain_reconstructor.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT modelling/tests/CMakeFiles/test_suite_modelling.dir/test_sidechain_reconstructor.cc.o -MF CMakeFiles/test_suite_modelling.dir/test_sidechain_reconstructor.cc.o.d -o CMakeFiles/test_suite_modelling.dir/test_sidechain_reconstructor.cc.o -c /build/promod3-3.2.1+ds/modelling/tests/test_sidechain_reconstructor.cc -[ 90%] Linking CXX executable ../../tests/core/test_suite_core -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_suite_core.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro CMakeFiles/test_suite_core.dir/test_check_io.cc.o CMakeFiles/test_suite_core.dir/test_portable_binary.cc.o CMakeFiles/test_suite_core.dir/test_graph_minimizer.cc.o CMakeFiles/test_suite_core.dir/tests.cc.o -o ../../tests/core/test_suite_core -L/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64 /usr/lib/x86_64-linux-gnu/libboost_unit_test_framework.so.1.74.0 ../../stage/lib64/libpromod3_core.so.3.2.1 /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.74.0 -.make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -.[ 90%] Built target test_suite_core +[ 87%] Built target test_pm3argparse.py_run make -f modelling/tests/CMakeFiles/test_gap_extension.py_run.dir/build.make modelling/tests/CMakeFiles/test_gap_extension.py_run.dir/depend make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/modelling/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests/CMakeFiles/test_gap_extension.py_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make -f modelling/tests/CMakeFiles/test_gap_extension.py_run.dir/build.make modelling/tests/CMakeFiles/test_gap_extension.py_run.dir/build make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -[ 91%] running checks test_gap_extension.py +make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +make -f modelling/tests/CMakeFiles/test_close_gaps.py_run.dir/build.make modelling/tests/CMakeFiles/test_close_gaps.py_run.dir/build +[ 88%] running checks test_gap_extension.py cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/ /usr/bin/python3 /build/promod3-3.2.1+ds/modelling/tests/test_gap_extension.py" +make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +[ 88%] running checks test_close_gaps.py +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/ /usr/bin/python3 /build/promod3-3.2.1+ds/modelling/tests/test_close_gaps.py" +[ 89%] Building CXX object modelling/tests/CMakeFiles/test_suite_modelling.dir/test_sidechain_reconstructor.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT modelling/tests/CMakeFiles/test_suite_modelling.dir/test_sidechain_reconstructor.cc.o -MF CMakeFiles/test_suite_modelling.dir/test_sidechain_reconstructor.cc.o.d -o CMakeFiles/test_suite_modelling.dir/test_sidechain_reconstructor.cc.o -c /build/promod3-3.2.1+ds/modelling/tests/test_sidechain_reconstructor.cc ...... ---------------------------------------------------------------------- -Ran 6 tests in 0.047s +Ran 6 tests in 0.050s OK make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -[ 91%] Built target test_gap_extension.py_run +[ 89%] Built target test_gap_extension.py_run make -f modelling/tests/CMakeFiles/test_modelling.py_run.dir/build.make modelling/tests/CMakeFiles/test_modelling.py_run.dir/depend make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/modelling/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests/CMakeFiles/test_modelling.py_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make -f modelling/tests/CMakeFiles/test_modelling.py_run.dir/build.make modelling/tests/CMakeFiles/test_modelling.py_run.dir/build make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -[ 91%] running checks test_modelling.py +[ 89%] running checks test_modelling.py cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/ /usr/bin/python3 /build/promod3-3.2.1+ds/modelling/tests/test_modelling.py" -............................ +......................... ---------------------------------------------------------------------- -Ran 25 tests in 0.310s +Ran 25 tests in 0.356s OK make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -[ 91%] Built target test_modelling.py_run +[ 89%] Built target test_modelling.py_run make -f modelling/tests/CMakeFiles/test_pipeline.py_run.dir/build.make modelling/tests/CMakeFiles/test_pipeline.py_run.dir/depend make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/modelling/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests/CMakeFiles/test_pipeline.py_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make -f modelling/tests/CMakeFiles/test_pipeline.py_run.dir/build.make modelling/tests/CMakeFiles/test_pipeline.py_run.dir/build make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -[ 91%] running checks test_pipeline.py +[ 89%] running checks test_pipeline.py cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/ /usr/bin/python3 /build/promod3-3.2.1+ds/modelling/tests/test_pipeline.py" -/build/promod3-3.2.1+ds/scoring/tests/test_all_atom_scorer.cc:73:33: warning: 'promod3::loop::AllAtomPositions scoring::{anonymous}::GenerateTestPos(const String&, uint, uint)' defined but not used [-Wunused-function] - 73 | promod3::loop::AllAtomPositions GenerateTestPos( - | ^~~~~~~~~~~~~~~ -.. ----------------------------------------------------------------------- -Ran 3 tests in 14.968s - -OK -.make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -[ 91%] Built target test_action_build-model.py_run -make -f modelling/tests/CMakeFiles/test_ring_punches.py_run.dir/build.make modelling/tests/CMakeFiles/test_ring_punches.py_run.dir/depend +.make -f modelling/tests/CMakeFiles/test_ring_punches.py_run.dir/build.make modelling/tests/CMakeFiles/test_ring_punches.py_run.dir/depend make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/modelling/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests/CMakeFiles/test_ring_punches.py_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make -f modelling/tests/CMakeFiles/test_ring_punches.py_run.dir/build.make modelling/tests/CMakeFiles/test_ring_punches.py_run.dir/build make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -[ 91%] running checks test_ring_punches.py +[ 89%] running checks test_ring_punches.py cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/ /usr/bin/python3 /build/promod3-3.2.1+ds/modelling/tests/test_ring_punches.py" -.. +... ---------------------------------------------------------------------- -Ran 2 tests in 0.353s +Ran 2 tests in 0.338s OK make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -[ 91%] Built target test_ring_punches.py_run +[ 89%] Built target test_ring_punches.py_run make -f modelling/tests/CMakeFiles/test_sidechain_reconstruction.py_run.dir/build.make modelling/tests/CMakeFiles/test_sidechain_reconstruction.py_run.dir/depend make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/modelling/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests/CMakeFiles/test_sidechain_reconstruction.py_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make -f modelling/tests/CMakeFiles/test_sidechain_reconstruction.py_run.dir/build.make modelling/tests/CMakeFiles/test_sidechain_reconstruction.py_run.dir/build make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -[ 92%] running checks test_sidechain_reconstruction.py +[ 90%] running checks test_sidechain_reconstruction.py cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/ /usr/bin/python3 /build/promod3-3.2.1+ds/modelling/tests/test_sidechain_reconstruction.py" +... +---------------------------------------------------------------------- +Ran 3 tests in 9.492s + +OK +[ 90%] Building CXX object modelling/tests/CMakeFiles/test_suite_modelling.dir/tests.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT modelling/tests/CMakeFiles/test_suite_modelling.dir/tests.cc.o -MF CMakeFiles/test_suite_modelling.dir/tests.cc.o.d -o CMakeFiles/test_suite_modelling.dir/tests.cc.o -c /build/promod3-3.2.1+ds/modelling/tests/tests.cc +make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +[ 90%] Built target test_action_build-model.py_run make -f modelling/tests/CMakeFiles/test_alignment_fiddling.py_run.dir/build.make modelling/tests/CMakeFiles/test_alignment_fiddling.py_run.dir/depend make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/modelling/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests/CMakeFiles/test_alignment_fiddling.py_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make -f modelling/tests/CMakeFiles/test_alignment_fiddling.py_run.dir/build.make modelling/tests/CMakeFiles/test_alignment_fiddling.py_run.dir/build make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -[ 92%] running checks test_alignment_fiddling.py +[ 90%] running checks test_alignment_fiddling.py cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/ /usr/bin/python3 /build/promod3-3.2.1+ds/modelling/tests/test_alignment_fiddling.py" ... ---------------------------------------------------------------------- -Ran 2 tests in 0.025s +Ran 2 tests in 0.028s OK make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -[ 92%] Built target test_alignment_fiddling.py_run +[ 90%] Built target test_alignment_fiddling.py_run +[ 91%] Building CXX object loop/tests/CMakeFiles/test_suite_loop.dir/test_all_atom_positions.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT loop/tests/CMakeFiles/test_suite_loop.dir/test_all_atom_positions.cc.o -MF CMakeFiles/test_suite_loop.dir/test_all_atom_positions.cc.o.d -o CMakeFiles/test_suite_loop.dir/test_all_atom_positions.cc.o -c /build/promod3-3.2.1+ds/loop/tests/test_all_atom_positions.cc +....[ 91%] Linking CXX executable ../../tests/core/test_suite_core +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_suite_core.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro CMakeFiles/test_suite_core.dir/test_check_io.cc.o CMakeFiles/test_suite_core.dir/test_portable_binary.cc.o CMakeFiles/test_suite_core.dir/test_graph_minimizer.cc.o CMakeFiles/test_suite_core.dir/tests.cc.o -o ../../tests/core/test_suite_core -L/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64 /usr/lib/x86_64-linux-gnu/libboost_unit_test_framework.so.1.74.0 ../../stage/lib64/libpromod3_core.so.3.2.1 /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.74.0 +..make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +[ 91%] Built target test_suite_core make -f core/tests/CMakeFiles/test_suite_core_run.dir/build.make core/tests/CMakeFiles/test_suite_core_run.dir/depend make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/core/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests/CMakeFiles/test_suite_core_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make -f core/tests/CMakeFiles/test_suite_core_run.dir/build.make core/tests/CMakeFiles/test_suite_core_run.dir/build make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -[ 92%] running checks for module core +[ 91%] Building CXX object loop/tests/CMakeFiles/test_suite_loop.dir/test_amino_acid_atoms.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT loop/tests/CMakeFiles/test_suite_loop.dir/test_amino_acid_atoms.cc.o -MF CMakeFiles/test_suite_loop.dir/test_amino_acid_atoms.cc.o.d -o CMakeFiles/test_suite_loop.dir/test_amino_acid_atoms.cc.o -c /build/promod3-3.2.1+ds/loop/tests/test_amino_acid_atoms.cc +[ 91%] running checks for module core cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core && PROMOD3_ROOT=/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/test_suite_core -Running 4 test cases... +.Running 4 test cases... *** No errors detected make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -[ 92%] Built target test_suite_core_run -[ 92%] Building CXX object loop/tests/CMakeFiles/test_suite_loop.dir/test_hydrogens.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT loop/tests/CMakeFiles/test_suite_loop.dir/test_hydrogens.cc.o -MF CMakeFiles/test_suite_loop.dir/test_hydrogens.cc.o.d -o CMakeFiles/test_suite_loop.dir/test_hydrogens.cc.o -c /build/promod3-3.2.1+ds/loop/tests/test_hydrogens.cc -..[ 93%] Building CXX object loop/tests/CMakeFiles/test_suite_loop.dir/test_idx_handler.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT loop/tests/CMakeFiles/test_suite_loop.dir/test_idx_handler.cc.o -MF CMakeFiles/test_suite_loop.dir/test_idx_handler.cc.o.d -o CMakeFiles/test_suite_loop.dir/test_idx_handler.cc.o -c /build/promod3-3.2.1+ds/loop/tests/test_idx_handler.cc -... +[ 91%] Built target test_suite_core_run +[ 91%] Building CXX object loop/tests/CMakeFiles/test_suite_loop.dir/test_backbone.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT loop/tests/CMakeFiles/test_suite_loop.dir/test_backbone.cc.o -MF CMakeFiles/test_suite_loop.dir/test_backbone.cc.o.d -o CMakeFiles/test_suite_loop.dir/test_backbone.cc.o -c /build/promod3-3.2.1+ds/loop/tests/test_backbone.cc +/build/promod3-3.2.1+ds/scoring/tests/test_all_atom_scorer.cc:73:33: warning: 'promod3::loop::AllAtomPositions scoring::{anonymous}::GenerateTestPos(const String&, uint, uint)' defined but not used [-Wunused-function] + 73 | promod3::loop::AllAtomPositions GenerateTestPos( + | ^~~~~~~~~~~~~~~ +.. ---------------------------------------------------------------------- -Ran 2 tests in 6.064s +Ran 2 tests in 6.214s OK make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -[ 93%] Built target test_sidechain_reconstruction.py_run +[ 91%] Built target test_sidechain_reconstruction.py_run +[ 92%] Building CXX object loop/tests/CMakeFiles/test_suite_loop.dir/test_forcefield.cc.o +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT loop/tests/CMakeFiles/test_suite_loop.dir/test_forcefield.cc.o -MF CMakeFiles/test_suite_loop.dir/test_forcefield.cc.o.d -o CMakeFiles/test_suite_loop.dir/test_forcefield.cc.o 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loop/tests/CMakeFiles/test_suite_loop.dir/test_torsion_sampler.cc.o -MF CMakeFiles/test_suite_loop.dir/test_torsion_sampler.cc.o.d -o CMakeFiles/test_suite_loop.dir/test_torsion_sampler.cc.o -c /build/promod3-3.2.1+ds/loop/tests/test_torsion_sampler.cc -[ 95%] Building CXX object loop/tests/CMakeFiles/test_suite_loop.dir/test_structuredb.cc.o -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT loop/tests/CMakeFiles/test_suite_loop.dir/test_structuredb.cc.o -MF CMakeFiles/test_suite_loop.dir/test_structuredb.cc.o.d -o 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-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT loop/tests/CMakeFiles/test_suite_loop.dir/tests.cc.o -MF CMakeFiles/test_suite_loop.dir/tests.cc.o.d -o CMakeFiles/test_suite_loop.dir/tests.cc.o -c /build/promod3-3.2.1+ds/loop/tests/tests.cc +.[ 96%] Linking CXX executable ../../tests/scoring/test_suite_scoring cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_suite_scoring.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro CMakeFiles/test_suite_scoring.dir/test_backbone_score_base.cc.o CMakeFiles/test_suite_scoring.dir/test_backbone_scorer.cc.o CMakeFiles/test_suite_scoring.dir/test_all_atom_scorer.cc.o CMakeFiles/test_suite_scoring.dir/tests.cc.o -o ../../tests/scoring/test_suite_scoring -L/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64 /usr/lib/x86_64-linux-gnu/libboost_unit_test_framework.so.1.74.0 ../../stage/lib64/libpromod3_scoring.so.3.2.1 ../../stage/lib64/libpromod3_loop.so.3.2.1 ../../stage/lib64/libpromod3_core.so.3.2.1 /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.74.0 +[ 96%] Linking CXX executable ../../tests/modelling/test_suite_modelling +cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_suite_modelling.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro CMakeFiles/test_suite_modelling.dir/test_loop_candidates.cc.o CMakeFiles/test_suite_modelling.dir/test_loop_closing.cc.o CMakeFiles/test_suite_modelling.dir/test_sidechain_reconstructor.cc.o CMakeFiles/test_suite_modelling.dir/tests.cc.o -o ../../tests/modelling/test_suite_modelling -L/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64 /usr/lib/x86_64-linux-gnu/libboost_unit_test_framework.so.1.74.0 ../../stage/lib64/libpromod3_modelling.so.3.2.1 ../../stage/lib64/libpromod3_scoring.so.3.2.1 ../../stage/lib64/libpromod3_sidechain.so.3.2.1 ../../stage/lib64/libpromod3_loop.so.3.2.1 ../../stage/lib64/libpromod3_core.so.3.2.1 /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.74.0 make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' [ 96%] Built target test_suite_scoring make -f scoring/tests/CMakeFiles/test_suite_scoring_run.dir/build.make scoring/tests/CMakeFiles/test_suite_scoring_run.dir/depend @@ -5135,14 +5181,6 @@ make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' [ 97%] running checks for module scoring cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/scoring && PROMOD3_ROOT=/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/scoring/test_suite_scoring -Running 20 test cases... - -*** No errors detected -make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -[ 97%] Built target test_suite_scoring_run -[ 97%] Linking CXX executable ../../tests/modelling/test_suite_modelling -cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_suite_modelling.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro CMakeFiles/test_suite_modelling.dir/test_loop_candidates.cc.o CMakeFiles/test_suite_modelling.dir/test_loop_closing.cc.o CMakeFiles/test_suite_modelling.dir/test_sidechain_reconstructor.cc.o CMakeFiles/test_suite_modelling.dir/tests.cc.o -o ../../tests/modelling/test_suite_modelling -L/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64 /usr/lib/x86_64-linux-gnu/libboost_unit_test_framework.so.1.74.0 ../../stage/lib64/libpromod3_modelling.so.3.2.1 ../../stage/lib64/libpromod3_scoring.so.3.2.1 ../../stage/lib64/libpromod3_sidechain.so.3.2.1 ../../stage/lib64/libpromod3_loop.so.3.2.1 ../../stage/lib64/libpromod3_core.so.3.2.1 /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.74.0 make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' [ 97%] Built target test_suite_modelling make -f modelling/tests/CMakeFiles/test_suite_modelling_run.dir/build.make modelling/tests/CMakeFiles/test_suite_modelling_run.dir/depend @@ -5153,21 +5191,19 @@ make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' [ 98%] running checks for module modelling cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling && PROMOD3_ROOT=/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/test_suite_modelling +...Running 20 test cases... + +*** No errors detected +make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +[ 98%] Built target test_suite_scoring_run Running 7 test cases... *** No errors detected make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' [ 98%] Built target test_suite_modelling_run -..............[100%] Linking CXX executable ../../tests/loop/test_suite_loop +...[100%] Linking CXX executable ../../tests/loop/test_suite_loop cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_suite_loop.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro CMakeFiles/test_suite_loop.dir/test_all_atom_env.cc.o CMakeFiles/test_suite_loop.dir/test_all_atom_positions.cc.o CMakeFiles/test_suite_loop.dir/test_amino_acid_atoms.cc.o CMakeFiles/test_suite_loop.dir/test_backbone.cc.o CMakeFiles/test_suite_loop.dir/test_forcefield.cc.o CMakeFiles/test_suite_loop.dir/test_hydrogens.cc.o CMakeFiles/test_suite_loop.dir/test_idx_handler.cc.o CMakeFiles/test_suite_loop.dir/test_mm_system_creator.cc.o CMakeFiles/test_suite_loop.dir/test_psipred_prediction.cc.o CMakeFiles/test_suite_loop.dir/test_sidechain_construction.cc.o CMakeFiles/test_suite_loop.dir/test_torsion_sampler.cc.o CMakeFiles/test_suite_loop.dir/test_structuredb.cc.o CMakeFiles/test_suite_loop.dir/tests.cc.o -o ../../tests/loop/test_suite_loop -L/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64 /usr/lib/x86_64-linux-gnu/libboost_unit_test_framework.so.1.74.0 ../../stage/lib64/libpromod3_loop.so.3.2.1 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.74.0 ../../stage/lib64/libpromod3_core.so.3.2.1 /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.74.0 -. ----------------------------------------------------------------------- -Ran 33 tests in 48.530s - -OK -make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' -[100%] Built target test_close_gaps.py_run make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' [100%] Built target test_suite_loop make -f loop/tests/CMakeFiles/test_suite_loop_run.dir/build.make loop/tests/CMakeFiles/test_suite_loop_run.dir/depend @@ -5178,6 +5214,13 @@ make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' [100%] running checks for module loop cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/loop && PROMOD3_ROOT=/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/loop/test_suite_loop +............ +---------------------------------------------------------------------- +Ran 33 tests in 50.756s + +OK +make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' +[100%] Built target test_close_gaps.py_run Running 68 test cases... *** No errors detected @@ -5185,7 +5228,7 @@ [100%] Built target test_suite_loop_run ........... ---------------------------------------------------------------------- -Ran 15 tests in 96.877s +Ran 15 tests in 86.480s OK OpenMM CPU platform not available. Skipping almost_on_top check. @@ -5219,7 +5262,7 @@ debian/rules override_dh_auto_install make[1]: Entering directory '/build/promod3-3.2.1+ds' dh_auto_install - cd obj-x86_64-linux-gnu && make -j16 install DESTDIR=/build/promod3-3.2.1\+ds/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd obj-x86_64-linux-gnu && make -j15 install DESTDIR=/build/promod3-3.2.1\+ds/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/promod3-3.2.1+ds -B/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -5460,16 +5503,16 @@ dpkg-gencontrol: warning: Provides field of package python3-promod3: substitution variable ${python3:Provides} used, but is not defined dh_md5sums dh_builddeb -dpkg-deb: building package 'libpromod3-sidechain-dev' in '../libpromod3-sidechain-dev_3.2.1+ds-6_amd64.deb'. -dpkg-deb: building package 'libpromod3-loop3.2' in '../libpromod3-loop3.2_3.2.1+ds-6_amd64.deb'. dpkg-deb: building package 'libpromod3-core-dev' in '../libpromod3-core-dev_3.2.1+ds-6_amd64.deb'. -dpkg-deb: building package 'python3-promod3-dbgsym' in '../python3-promod3-dbgsym_3.2.1+ds-6_amd64.deb'. -dpkg-deb: building package 'libpromod3-modelling3.2-dbgsym' in '../libpromod3-modelling3.2-dbgsym_3.2.1+ds-6_amd64.deb'. dpkg-deb: building package 'libpromod3-core3.2-dbgsym' in '../libpromod3-core3.2-dbgsym_3.2.1+ds-6_amd64.deb'. -dpkg-deb: building package 'promod3-data' in '../promod3-data_3.2.1+ds-6_all.deb'. -dpkg-deb: building package 'libpromod3-sidechain3.2-dbgsym' in '../libpromod3-sidechain3.2-dbgsym_3.2.1+ds-6_amd64.deb'. -dpkg-deb: building package 'libpromod3-scoring3.2' in '../libpromod3-scoring3.2_3.2.1+ds-6_amd64.deb'. +dpkg-deb: building package 'libpromod3-loop3.2' in '../libpromod3-loop3.2_3.2.1+ds-6_amd64.deb'. dpkg-deb: building package 'libpromod3-modelling-dev' in '../libpromod3-modelling-dev_3.2.1+ds-6_amd64.deb'. +dpkg-deb: building package 'libpromod3-modelling3.2-dbgsym' in '../libpromod3-modelling3.2-dbgsym_3.2.1+ds-6_amd64.deb'. +dpkg-deb: building package 'libpromod3-scoring3.2' in '../libpromod3-scoring3.2_3.2.1+ds-6_amd64.deb'. +dpkg-deb: building package 'libpromod3-sidechain-dev' in '../libpromod3-sidechain-dev_3.2.1+ds-6_amd64.deb'. +dpkg-deb: building package 'libpromod3-sidechain3.2-dbgsym' in '../libpromod3-sidechain3.2-dbgsym_3.2.1+ds-6_amd64.deb'. +dpkg-deb: building package 'promod3-data' in '../promod3-data_3.2.1+ds-6_all.deb'. +dpkg-deb: building package 'python3-promod3-dbgsym' in '../python3-promod3-dbgsym_3.2.1+ds-6_amd64.deb'. dpkg-deb: building package 'libpromod3-core3.2' in '../libpromod3-core3.2_3.2.1+ds-6_amd64.deb'. dpkg-deb: building package 'libpromod3-sidechain3.2' in '../libpromod3-sidechain3.2_3.2.1+ds-6_amd64.deb'. dpkg-deb: building package 'libpromod3-modelling3.2' in '../libpromod3-modelling3.2_3.2.1+ds-6_amd64.deb'. @@ -5486,12 +5529,14 @@ 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/3094074/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3094074/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/273034 and its subdirectories -I: Current time: Sun Jul 7 08:05:31 -12 2024 -I: pbuilder-time-stamp: 1720382731 +I: removing directory /srv/workspace/pbuilder/3094074 and its subdirectories +I: Current time: Tue Jun 6 03:56:40 +14 2023 +I: pbuilder-time-stamp: 1685973400