Diff of the two buildlogs: -- --- b1/build.log 2023-06-09 12:49:46.212818594 +0000 +++ b2/build.log 2023-06-09 14:07:41.948451301 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Jun 8 21:39:41 -12 2023 -I: pbuilder-time-stamp: 1686303581 +I: Current time: Sat Jun 10 03:17:07 +14 2023 +I: pbuilder-time-stamp: 1686316627 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 [./relion_3.1.3.orig.tar.gz] I: copying [./relion_3.1.3-3.debian.tar.xz] I: Extracting source -gpgv: Signature made Mon Dec 5 23:51:10 2022 -12 +gpgv: Signature made Wed Dec 7 01:51:10 2022 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -29,135 +29,167 @@ dpkg-source: info: applying typos.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/22283/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/29454/tmp/hooks/D01_modify_environment starting +debug: Running on jtx1a. +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 10 03:17 /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/29454/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/29454/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='armhf' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' - DISTRIBUTION='bookworm' - HOME='/root' - HOST_ARCH='armhf' + 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]="arm-unknown-linux-gnueabihf") + 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=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4 ' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='a6f9d58d3fc840ec8a97fe872dec8bd4' - 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='22283' - PS1='# ' - PS2='> ' + INVOCATION_ID=42950684cc0245fead75437ef15b60b4 + LANG=C + LANGUAGE=it_CH:it + LC_ALL=C + MACHTYPE=arm-unknown-linux-gnueabihf + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnueabihf + 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=29454 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.BuJ5alNF/pbuilderrc_Mqhz --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.BuJ5alNF/b1 --logfile b1/build.log relion_3.1.3-3.dsc' - SUDO_GID='113' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:3142/' + 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.BuJ5alNF/pbuilderrc_gpXf --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.BuJ5alNF/b2 --logfile b2/build.log --extrapackages usrmerge relion_3.1.3-3.dsc' + SUDO_GID=114 + SUDO_UID=108 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:3142/ I: uname -a - Linux cbxi4a 5.10.0-23-armmp #1 SMP Debian 5.10.179-1 (2023-05-12) armv7l GNU/Linux + Linux i-capture-the-hostname 5.10.0-23-arm64 #1 SMP Debian 5.10.179-1 (2023-05-12) aarch64 GNU/Linux I: ls -l /bin total 5072 - -rwxr-xr-x 1 root root 838488 Apr 23 09:24 bash - -rwxr-xr-x 3 root root 67144 Sep 18 2022 bunzip2 - -rwxr-xr-x 3 root root 67144 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 67144 Sep 18 2022 bzip2 - -rwxr-xr-x 1 root root 67112 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 67632 Sep 20 2022 cat - -rwxr-xr-x 1 root root 67676 Sep 20 2022 chgrp - -rwxr-xr-x 1 root root 67644 Sep 20 2022 chmod - -rwxr-xr-x 1 root root 67684 Sep 20 2022 chown - -rwxr-xr-x 1 root root 133532 Sep 20 2022 cp - -rwxr-xr-x 1 root root 132868 Jan 5 01:20 dash - -rwxr-xr-x 1 root root 133220 Sep 20 2022 date - -rwxr-xr-x 1 root root 67732 Sep 20 2022 dd - -rwxr-xr-x 1 root root 68104 Sep 20 2022 df - -rwxr-xr-x 1 root root 133632 Sep 20 2022 dir - -rwxr-xr-x 1 root root 59128 Mar 22 21:02 dmesg - lrwxrwxrwx 1 root root 8 Dec 19 01:33 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Dec 19 01:33 domainname -> hostname - -rwxr-xr-x 1 root root 67560 Sep 20 2022 echo - -rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep - -rwxr-xr-x 1 root root 67548 Sep 20 2022 false - -rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep - -rwxr-xr-x 1 root root 55748 Mar 22 21:02 findmnt - -rwsr-xr-x 1 root root 26208 Mar 22 20:15 fusermount - -rwxr-xr-x 1 root root 128608 Jan 24 02:43 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 64220 Apr 9 2022 gzip - -rwxr-xr-x 1 root root 67032 Dec 19 01:33 hostname - -rwxr-xr-x 1 root root 67720 Sep 20 2022 ln - -rwxr-xr-x 1 root root 35132 Mar 22 21:51 login - -rwxr-xr-x 1 root root 133632 Sep 20 2022 ls - -rwxr-xr-x 1 root root 136808 Mar 22 21:02 lsblk - -rwxr-xr-x 1 root root 67800 Sep 20 2022 mkdir - -rwxr-xr-x 1 root root 67764 Sep 20 2022 mknod - -rwxr-xr-x 1 root root 67596 Sep 20 2022 mktemp - -rwxr-xr-x 1 root root 38504 Mar 22 21:02 more - -rwsr-xr-x 1 root root 38496 Mar 22 21:02 mount - -rwxr-xr-x 1 root root 9824 Mar 22 21:02 mountpoint - -rwxr-xr-x 1 root root 133532 Sep 20 2022 mv - lrwxrwxrwx 1 root root 8 Dec 19 01:33 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 2 18:25 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 67608 Sep 20 2022 pwd - lrwxrwxrwx 1 root root 4 Apr 23 09:24 rbash -> bash - -rwxr-xr-x 1 root root 67600 Sep 20 2022 readlink - -rwxr-xr-x 1 root root 67672 Sep 20 2022 rm - -rwxr-xr-x 1 root root 67600 Sep 20 2022 rmdir - -rwxr-xr-x 1 root root 67400 Nov 2 2022 run-parts - -rwxr-xr-x 1 root root 133372 Jan 5 07:55 sed - lrwxrwxrwx 1 root root 4 Jan 5 01:20 sh -> dash - -rwxr-xr-x 1 root root 67584 Sep 20 2022 sleep - -rwxr-xr-x 1 root root 67644 Sep 20 2022 stty - -rwsr-xr-x 1 root root 50800 Mar 22 21:02 su - -rwxr-xr-x 1 root root 67584 Sep 20 2022 sync - -rwxr-xr-x 1 root root 336764 Apr 6 02:25 tar - -rwxr-xr-x 1 root root 67144 Nov 2 2022 tempfile - -rwxr-xr-x 1 root root 133224 Sep 20 2022 touch - -rwxr-xr-x 1 root root 67548 Sep 20 2022 true - -rwxr-xr-x 1 root root 9768 Mar 22 20:15 ulockmgr_server - -rwsr-xr-x 1 root root 22108 Mar 22 21:02 umount - -rwxr-xr-x 1 root root 67572 Sep 20 2022 uname - -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress - -rwxr-xr-x 1 root root 133632 Sep 20 2022 vdir - -rwxr-xr-x 1 root root 42608 Mar 22 21:02 wdctl - lrwxrwxrwx 1 root root 8 Dec 19 01:33 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/22283/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 838488 Apr 24 11:24 bash + -rwxr-xr-x 3 root root 67144 Sep 19 2022 bunzip2 + -rwxr-xr-x 3 root root 67144 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 67144 Sep 19 2022 bzip2 + -rwxr-xr-x 1 root root 67112 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 67632 Sep 21 2022 cat + -rwxr-xr-x 1 root root 67676 Sep 21 2022 chgrp + -rwxr-xr-x 1 root root 67644 Sep 21 2022 chmod + -rwxr-xr-x 1 root root 67684 Sep 21 2022 chown + -rwxr-xr-x 1 root root 133532 Sep 21 2022 cp + -rwxr-xr-x 1 root root 132868 Jan 6 03:20 dash + -rwxr-xr-x 1 root root 133220 Sep 21 2022 date + -rwxr-xr-x 1 root root 67732 Sep 21 2022 dd + -rwxr-xr-x 1 root root 68104 Sep 21 2022 df + -rwxr-xr-x 1 root root 133632 Sep 21 2022 dir + -rwxr-xr-x 1 root root 59128 Mar 23 23:02 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 67560 Sep 21 2022 echo + -rwxr-xr-x 1 root root 41 Jan 25 04:43 egrep + -rwxr-xr-x 1 root root 67548 Sep 21 2022 false + -rwxr-xr-x 1 root root 41 Jan 25 04:43 fgrep + -rwxr-xr-x 1 root root 55748 Mar 23 23:02 findmnt + -rwsr-xr-x 1 root root 26208 Mar 23 22:15 fusermount + -rwxr-xr-x 1 root root 128608 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 64220 Apr 10 2022 gzip + -rwxr-xr-x 1 root root 67032 Dec 20 03:33 hostname + -rwxr-xr-x 1 root root 67720 Sep 21 2022 ln + -rwxr-xr-x 1 root root 35132 Mar 23 23:51 login + -rwxr-xr-x 1 root root 133632 Sep 21 2022 ls + -rwxr-xr-x 1 root root 136808 Mar 23 23:02 lsblk + -rwxr-xr-x 1 root root 67800 Sep 21 2022 mkdir + -rwxr-xr-x 1 root root 67764 Sep 21 2022 mknod + -rwxr-xr-x 1 root root 67596 Sep 21 2022 mktemp + -rwxr-xr-x 1 root root 38504 Mar 23 23:02 more + -rwsr-xr-x 1 root root 38496 Mar 23 23:02 mount + -rwxr-xr-x 1 root root 9824 Mar 23 23:02 mountpoint + -rwxr-xr-x 1 root root 133532 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 67608 Sep 21 2022 pwd + lrwxrwxrwx 1 root root 4 Apr 24 11:24 rbash -> bash + -rwxr-xr-x 1 root root 67600 Sep 21 2022 readlink + -rwxr-xr-x 1 root root 67672 Sep 21 2022 rm + -rwxr-xr-x 1 root root 67600 Sep 21 2022 rmdir + -rwxr-xr-x 1 root root 67400 Nov 3 2022 run-parts + -rwxr-xr-x 1 root root 133372 Jan 6 09:55 sed + lrwxrwxrwx 1 root root 9 Jun 10 03:17 sh -> /bin/bash + -rwxr-xr-x 1 root root 67584 Sep 21 2022 sleep + -rwxr-xr-x 1 root root 67644 Sep 21 2022 stty + -rwsr-xr-x 1 root root 50800 Mar 23 23:02 su + -rwxr-xr-x 1 root root 67584 Sep 21 2022 sync + -rwxr-xr-x 1 root root 336764 Apr 7 04:25 tar + -rwxr-xr-x 1 root root 67144 Nov 3 2022 tempfile + -rwxr-xr-x 1 root root 133224 Sep 21 2022 touch + -rwxr-xr-x 1 root root 67548 Sep 21 2022 true + -rwxr-xr-x 1 root root 9768 Mar 23 22:15 ulockmgr_server + -rwsr-xr-x 1 root root 22108 Mar 23 23:02 umount + -rwxr-xr-x 1 root root 67572 Sep 21 2022 uname + -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress + -rwxr-xr-x 1 root root 133632 Sep 21 2022 vdir + -rwxr-xr-x 1 root root 42608 Mar 23 23:02 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/29454/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -378,7 +410,7 @@ Get: 171 http://deb.debian.org/debian bookworm/main armhf libtiff6 armhf 4.5.0-6 [295 kB] Get: 172 http://deb.debian.org/debian bookworm/main armhf libtiffxx6 armhf 4.5.0-6 [144 kB] Get: 173 http://deb.debian.org/debian bookworm/main armhf libtiff-dev armhf 4.5.0-6 [434 kB] -Fetched 92.6 MB in 10s (8820 kB/s) +Fetched 92.6 MB in 19s (5001 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libproc2-0:armhf. (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 ... 19324 files and directories currently installed.) @@ -1087,8 +1119,19 @@ 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/relion-3.1.3/ && 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 > ../relion_3.1.3-3_source.changes +I: user script /srv/workspace/pbuilder/29454/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/29454/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/relion-3.1.3/ && 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 > ../relion_3.1.3-3_source.changes dpkg-buildpackage: info: source package relion dpkg-buildpackage: info: source version 3.1.3-3 dpkg-buildpackage: info: source distribution unstable @@ -1219,7 +1262,7 @@ make[1]: Leaving directory '/build/relion-3.1.3' debian/rules override_dh_auto_build make[1]: Entering directory '/build/relion-3.1.3' -/usr/bin/make -j3 -C build +/usr/bin/make -j4 -C build make[2]: Entering directory '/build/relion-3.1.3/build' /usr/bin/cmake -S/build/relion-3.1.3 -B/build/relion-3.1.3/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/relion-3.1.3/build/CMakeFiles /build/relion-3.1.3/build//CMakeFiles/progress.marks @@ -1237,30 +1280,85 @@ /usr/bin/cmake -E copy /build/relion-3.1.3/scripts/star_printtable /build/relion-3.1.3/build/bin/relion_star_printtable make[4]: Leaving directory '/build/relion-3.1.3/build' /usr/bin/make -f src/apps/CMakeFiles/relion_lib.dir/build.make src/apps/CMakeFiles/relion_lib.dir/build -/usr/bin/cmake -E copy /build/relion-3.1.3/scripts/star_plottable /build/relion-3.1.3/build/bin/relion_star_plottable -/usr/bin/cmake -E copy /build/relion-3.1.3/scripts/star_loopheader /build/relion-3.1.3/build/bin/relion_star_loopheader make[4]: Entering directory '/build/relion-3.1.3/build' +/usr/bin/cmake -E copy /build/relion-3.1.3/scripts/star_plottable /build/relion-3.1.3/build/bin/relion_star_plottable +[ 0%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/__/macros.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/__/macros.cpp.o -MF CMakeFiles/relion_lib.dir/__/__/macros.cpp.o.d -o CMakeFiles/relion_lib.dir/__/__/macros.cpp.o -c /build/relion-3.1.3/build/macros.cpp [ 1%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/CPlot2D.cpp.o -/usr/bin/cmake -E copy /build/relion-3.1.3/scripts/star_datablock_stack /build/relion-3.1.3/build/bin/relion_star_datablock_stack cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/CPlot2D.cpp.o -MF CMakeFiles/relion_lib.dir/__/CPlot2D.cpp.o.d -o CMakeFiles/relion_lib.dir/__/CPlot2D.cpp.o -c /build/relion-3.1.3/src/CPlot2D.cpp -[ 1%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/__/macros.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/__/macros.cpp.o -MF CMakeFiles/relion_lib.dir/__/__/macros.cpp.o.d -o CMakeFiles/relion_lib.dir/__/__/macros.cpp.o -c /build/relion-3.1.3/build/macros.cpp +/usr/bin/cmake -E copy /build/relion-3.1.3/scripts/star_loopheader /build/relion-3.1.3/build/bin/relion_star_loopheader +[ 1%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/args.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/args.cpp.o -MF CMakeFiles/relion_lib.dir/__/args.cpp.o.d -o CMakeFiles/relion_lib.dir/__/args.cpp.o -c /build/relion-3.1.3/src/args.cpp +/usr/bin/cmake -E copy /build/relion-3.1.3/scripts/star_datablock_stack /build/relion-3.1.3/build/bin/relion_star_datablock_stack /usr/bin/cmake -E copy /build/relion-3.1.3/scripts/star_datablock_singlefiles /build/relion-3.1.3/build/bin/relion_star_datablock_singlefiles /usr/bin/cmake -E copy /build/relion-3.1.3/scripts/star_datablock_ctfdat /build/relion-3.1.3/build/bin/relion_star_datablock_ctfdat /usr/bin/cmake -E copy /build/relion-3.1.3/scripts/qsub.csh /build/relion-3.1.3/build/bin/relion_qsub.csh make[4]: Leaving directory '/build/relion-3.1.3/build' [ 1%] Built target copy_scripts -[ 1%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/args.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/args.cpp.o -MF CMakeFiles/relion_lib.dir/__/args.cpp.o.d -o CMakeFiles/relion_lib.dir/__/args.cpp.o -c /build/relion-3.1.3/src/args.cpp [ 1%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/assembly.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/assembly.cpp.o -MF CMakeFiles/relion_lib.dir/__/assembly.cpp.o.d -o CMakeFiles/relion_lib.dir/__/assembly.cpp.o -c /build/relion-3.1.3/src/assembly.cpp -In file included from /usr/include/c++/12/vector:70, - from /build/relion-3.1.3/src/CPlot2D.h:30, - from /build/relion-3.1.3/src/CPlot2D.cpp:27: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const CDataPoint&}; _Tp = CDataPoint; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ +[ 2%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/autopicker.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/autopicker.cpp.o -MF CMakeFiles/relion_lib.dir/__/autopicker.cpp.o.d -o CMakeFiles/relion_lib.dir/__/autopicker.cpp.o -c /build/relion-3.1.3/src/autopicker.cpp +In file included from /build/relion-3.1.3/src/image.h:455, + from /build/relion-3.1.3/src/autopicker.h:10, + from /build/relion-3.1.3/src/autopicker.cpp:20: +/build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': +/build/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 43 | uint32 width, length; // apparent dimensions in the file + | ^~~~~ +In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31, + from /build/relion-3.1.3/src/image.h:57: +/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here + 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 43 | uint32 width, length; // apparent dimensions in the file + | ^~~~~~ +/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here + 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; + | ^~~~~~~~~~~~ +/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; + | ^~~~~~~~~~~~~ +/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; + | ^~~~~~~~~~~~~~ +/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 185 | uint32 cur_width, cur_length; + | ^~~~~~~~~ +/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here + 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 185 | uint32 cur_width, cur_length; + | ^~~~~~~~~~ +/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here + 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 186 | uint16 cur_sampleFormat, cur_bitsPerSample; + | ^~~~~~~~~~~~~~~~ +/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 186 | uint16 cur_sampleFormat, cur_bitsPerSample; + | ^~~~~~~~~~~~~~~~~ +/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ In file included from /usr/include/c++/12/vector:70, from /build/relion-3.1.3/src/assembly.h:15, from /build/relion-3.1.3/src/assembly.cpp:8: @@ -1268,8 +1366,6 @@ /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const CDataSet&}; _Tp = CDataSet; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Atom; _Alloc = std::allocator]', inlined from 'long int Residue::addAtom(std::string, double, double, double, double, double)' at /build/relion-3.1.3/src/assembly.cpp:36:17: @@ -1282,18 +1378,6 @@ 113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -In file included from /usr/include/c++/12/vector:64: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator]', - inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /build/relion-3.1.3/src/CPlot2D.h:168:33, - inlined from 'void CPlot2D::AddDataSet(std::vector, std::vector)' at /build/relion-3.1.3/src/CPlot2D.cpp:503:29: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataSet; _Alloc = std::allocator]', - inlined from 'void CPlot2D::AddDataSet(std::vector, std::vector)' at /build/relion-3.1.3/src/CPlot2D.cpp:505:25: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*; bool _TrivialValueTypes = false]', inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*; _Tp = Atom]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, @@ -1302,17 +1386,15 @@ /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator]', - inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /build/relion-3.1.3/src/CPlot2D.h:168:33, - inlined from 'void CPlot2D::AddDataSet(int, double*, double*)' at /build/relion-3.1.3/src/CPlot2D.cpp:478:29: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataSet; _Alloc = std::allocator]', - inlined from 'void CPlot2D::AddDataSet(int, double*, double*)' at /build/relion-3.1.3/src/CPlot2D.cpp:480:25: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:70, + from /build/relion-3.1.3/src/CPlot2D.h:30, + from /build/relion-3.1.3/src/CPlot2D.cpp:27: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const CDataPoint&}; _Tp = CDataPoint; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const CDataSet&}; _Tp = CDataSet; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*; bool _TrivialValueTypes = false]', inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*; _Tp = Atom]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, @@ -1350,6 +1432,69 @@ /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*; bool _TrivialValueTypes = false]', + inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, + inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*; _Tp = Atom]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, + inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Atom; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:601:31, + inlined from 'Residue::Residue(const Residue&)' at /build/relion-3.1.3/src/assembly.h:73:7, + inlined from 'void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = Residue; _Args = {const Residue&}; _Tp = Residue]' at /usr/include/c++/12/bits/new_allocator.h:175:4, + inlined from 'static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = Residue; _Args = {const Residue&}; _Tp = Residue]' at /usr/include/c++/12/bits/alloc_traits.h:516:17, + inlined from 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const Residue&}; _Tp = Residue; _Alloc = std::allocator]' at /usr/include/c++/12/bits/vector.tcc:462:28: +/usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 137 | { return std::__do_uninit_copy(__first, __last, __result); } + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:64: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator]', + inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /build/relion-3.1.3/src/CPlot2D.h:168:33, + inlined from 'void CPlot2D::AddDataSet(std::vector, std::vector)' at /build/relion-3.1.3/src/CPlot2D.cpp:503:29: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataSet; _Alloc = std::allocator]', + inlined from 'void CPlot2D::AddDataSet(std::vector, std::vector)' at /build/relion-3.1.3/src/CPlot2D.cpp:505:25: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +[ 2%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/autopicker_mpi.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/autopicker_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/autopicker_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/autopicker_mpi.cpp.o -c /build/relion-3.1.3/src/autopicker_mpi.cpp +In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*; bool _TrivialValueTypes = false]', + inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, + inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*; _Tp = Atom]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, + inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Atom; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:601:31, + inlined from 'Residue::Residue(const Residue&)' at /build/relion-3.1.3/src/assembly.h:73:7, + inlined from 'void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = Residue; _Args = {const Residue&}; _Tp = Residue]' at /usr/include/c++/12/bits/new_allocator.h:175:4, + inlined from 'static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = Residue; _Args = {const Residue&}; _Tp = Residue]' at /usr/include/c++/12/bits/alloc_traits.h:516:17, + inlined from 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Residue; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1281:30, + inlined from 'void Assembly::sortResidues()' at /build/relion-3.1.3/src/assembly.cpp:487:26: +/usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 137 | { return std::__do_uninit_copy(__first, __last, __result); } + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*; bool _TrivialValueTypes = false]', + inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, + inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*; _Tp = Atom]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, + inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Atom; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:601:31, + inlined from 'Residue::Residue(const Residue&)' at /build/relion-3.1.3/src/assembly.h:73:7, + inlined from 'void std::_Construct(_Tp*, _Args&& ...) [with _Tp = Residue; _Args = {Residue&}]' at /usr/include/c++/12/bits/stl_construct.h:119:7, + inlined from '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = Residue*; _ForwardIterator = Residue*]' at /usr/include/c++/12/bits/stl_uninitialized.h:120:21, + inlined from 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = Residue*; _ForwardIterator = Residue*; bool _TrivialValueTypes = false]' at /usr/include/c++/12/bits/stl_uninitialized.h:137:32, + inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = Residue*; _ForwardIterator = Residue*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, + inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = Residue*; _ForwardIterator = Residue*; _Tp = Residue]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, + inlined from 'std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = Residue; _Alloc = std::allocator]' at /usr/include/c++/12/bits/vector.tcc:251:35, + inlined from 'void Assembly::sortResidues()' at /build/relion-3.1.3/src/assembly.cpp:489:30: +/usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 137 | { return std::__do_uninit_copy(__first, __last, __result); } + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator]', + inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /build/relion-3.1.3/src/CPlot2D.h:168:33, + inlined from 'void CPlot2D::AddDataSet(int, double*, double*)' at /build/relion-3.1.3/src/CPlot2D.cpp:478:29: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataSet; _Alloc = std::allocator]', + inlined from 'void CPlot2D::AddDataSet(int, double*, double*)' at /build/relion-3.1.3/src/CPlot2D.cpp:480:25: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator]', inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /build/relion-3.1.3/src/CPlot2D.h:168:33, inlined from 'void CPlot2D::AddDataSet(std::vector)' at /build/relion-3.1.3/src/CPlot2D.cpp:523:29: @@ -1361,8 +1506,6 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 2%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/autopicker.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/autopicker.cpp.o -MF CMakeFiles/relion_lib.dir/__/autopicker.cpp.o.d -o CMakeFiles/relion_lib.dir/__/autopicker.cpp.o -c /build/relion-3.1.3/src/autopicker.cpp In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*; bool _TrivialValueTypes = false]', inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*; _Tp = Atom]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, @@ -1370,7 +1513,20 @@ inlined from 'Residue::Residue(const Residue&)' at /build/relion-3.1.3/src/assembly.h:73:7, inlined from 'void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = Residue; _Args = {const Residue&}; _Tp = Residue]' at /usr/include/c++/12/bits/new_allocator.h:175:4, inlined from 'static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = Residue; _Args = {const Residue&}; _Tp = Residue]' at /usr/include/c++/12/bits/alloc_traits.h:516:17, - inlined from 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const Residue&}; _Tp = Residue; _Alloc = std::allocator]' at /usr/include/c++/12/bits/vector.tcc:462:28: + inlined from 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Residue; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1281:30, + inlined from 'long int Molecule::addResidue(Residue&)' at /build/relion-3.1.3/src/assembly.cpp:57:20: +/usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 137 | { return std::__do_uninit_copy(__first, __last, __result); } + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*; bool _TrivialValueTypes = false]', + inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, + inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*; _Tp = Atom]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, + inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Atom; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:601:31, + inlined from 'Residue::Residue(const Residue&)' at /build/relion-3.1.3/src/assembly.h:73:7, + inlined from 'void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = Residue; _Args = {const Residue&}; _Tp = Residue]' at /usr/include/c++/12/bits/new_allocator.h:175:4, + inlined from 'static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = Residue; _Args = {const Residue&}; _Tp = Residue]' at /usr/include/c++/12/bits/alloc_traits.h:516:17, + inlined from 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Residue; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1281:30, + inlined from 'long int Molecule::addResidue(std::string, int)' at /build/relion-3.1.3/src/assembly.cpp:65:20: /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -1422,57 +1578,6 @@ inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*; _Tp = Atom]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Atom; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:601:31, inlined from 'Residue::Residue(const Residue&)' at /build/relion-3.1.3/src/assembly.h:73:7, - inlined from 'void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = Residue; _Args = {const Residue&}; _Tp = Residue]' at /usr/include/c++/12/bits/new_allocator.h:175:4, - inlined from 'static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = Residue; _Args = {const Residue&}; _Tp = Residue]' at /usr/include/c++/12/bits/alloc_traits.h:516:17, - inlined from 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Residue; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1281:30, - inlined from 'void Assembly::sortResidues()' at /build/relion-3.1.3/src/assembly.cpp:487:26: -/usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 137 | { return std::__do_uninit_copy(__first, __last, __result); } - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*; bool _TrivialValueTypes = false]', - inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, - inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*; _Tp = Atom]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, - inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Atom; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:601:31, - inlined from 'Residue::Residue(const Residue&)' at /build/relion-3.1.3/src/assembly.h:73:7, - inlined from 'void std::_Construct(_Tp*, _Args&& ...) [with _Tp = Residue; _Args = {Residue&}]' at /usr/include/c++/12/bits/stl_construct.h:119:7, - inlined from '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = Residue*; _ForwardIterator = Residue*]' at /usr/include/c++/12/bits/stl_uninitialized.h:120:21, - inlined from 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = Residue*; _ForwardIterator = Residue*; bool _TrivialValueTypes = false]' at /usr/include/c++/12/bits/stl_uninitialized.h:137:32, - inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = Residue*; _ForwardIterator = Residue*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, - inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = Residue*; _ForwardIterator = Residue*; _Tp = Residue]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, - inlined from 'std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = Residue; _Alloc = std::allocator]' at /usr/include/c++/12/bits/vector.tcc:251:35, - inlined from 'void Assembly::sortResidues()' at /build/relion-3.1.3/src/assembly.cpp:489:30: -/usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 137 | { return std::__do_uninit_copy(__first, __last, __result); } - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*; bool _TrivialValueTypes = false]', - inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, - inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*; _Tp = Atom]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, - inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Atom; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:601:31, - inlined from 'Residue::Residue(const Residue&)' at /build/relion-3.1.3/src/assembly.h:73:7, - inlined from 'void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = Residue; _Args = {const Residue&}; _Tp = Residue]' at /usr/include/c++/12/bits/new_allocator.h:175:4, - inlined from 'static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = Residue; _Args = {const Residue&}; _Tp = Residue]' at /usr/include/c++/12/bits/alloc_traits.h:516:17, - inlined from 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Residue; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1281:30, - inlined from 'long int Molecule::addResidue(Residue&)' at /build/relion-3.1.3/src/assembly.cpp:57:20: -/usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 137 | { return std::__do_uninit_copy(__first, __last, __result); } - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*; bool _TrivialValueTypes = false]', - inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, - inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*; _Tp = Atom]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, - inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Atom; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:601:31, - inlined from 'Residue::Residue(const Residue&)' at /build/relion-3.1.3/src/assembly.h:73:7, - inlined from 'void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = Residue; _Args = {const Residue&}; _Tp = Residue]' at /usr/include/c++/12/bits/new_allocator.h:175:4, - inlined from 'static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = Residue; _Args = {const Residue&}; _Tp = Residue]' at /usr/include/c++/12/bits/alloc_traits.h:516:17, - inlined from 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Residue; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1281:30, - inlined from 'long int Molecule::addResidue(std::string, int)' at /build/relion-3.1.3/src/assembly.cpp:65:20: -/usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 137 | { return std::__do_uninit_copy(__first, __last, __result); } - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*; bool _TrivialValueTypes = false]', - inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, - inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*; _Tp = Atom]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, - inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Atom; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:601:31, - inlined from 'Residue::Residue(const Residue&)' at /build/relion-3.1.3/src/assembly.h:73:7, inlined from 'void std::_Construct(_Tp*, _Args&& ...) [with _Tp = Residue; _Args = {const Residue&}]' at /usr/include/c++/12/bits/stl_construct.h:119:7, inlined from '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Residue*]' at /usr/include/c++/12/bits/stl_uninitialized.h:120:21, inlined from 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Residue*; bool _TrivialValueTypes = false]' at /usr/include/c++/12/bits/stl_uninitialized.h:137:32, @@ -1505,11 +1610,10 @@ /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 2%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/autopicker_mpi.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/autopicker_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/autopicker_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/autopicker_mpi.cpp.o -c /build/relion-3.1.3/src/autopicker_mpi.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/autopicker.h:10, - from /build/relion-3.1.3/src/autopicker.cpp:20: + from /build/relion-3.1.3/src/autopicker_mpi.h:12, + from /build/relion-3.1.3/src/autopicker_mpi.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -1634,73 +1738,31 @@ /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/relion-3.1.3/src/image.h:455, - from /build/relion-3.1.3/src/autopicker.h:10, - from /build/relion-3.1.3/src/autopicker_mpi.h:12, - from /build/relion-3.1.3/src/autopicker_mpi.cpp:21: -/build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': -/build/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] - 43 | uint32 width, length; // apparent dimensions in the file - | ^~~~~ -In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31, - from /build/relion-3.1.3/src/image.h:57: -/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here - 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/relion-3.1.3/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations] - 43 | uint32 width, length; // apparent dimensions in the file - | ^~~~~~ -/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here - 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; - | ^~~~~~~~~~~~ -/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; - | ^~~~~~~~~~~~~ -/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; - | ^~~~~~~~~~~~~~ -/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] - 185 | uint32 cur_width, cur_length; - | ^~~~~~~~~ -/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here - 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] - 185 | uint32 cur_width, cur_length; - | ^~~~~~~~~~ -/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here - 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 186 | uint16 cur_sampleFormat, cur_bitsPerSample; - | ^~~~~~~~~~~~~~~~ -/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 186 | uint16 cur_sampleFormat, cur_bitsPerSample; - | ^~~~~~~~~~~~~~~~~ -/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ +In file included from /usr/include/c++/12/bits/stl_algo.h:60, + from /usr/include/c++/12/algorithm:61, + from /build/relion-3.1.3/src/funcs.h:55, + from /build/relion-3.1.3/src/image.h:58: +/usr/include/c++/12/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = ccfPixel; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, + | ^~~~~~~~~~~~~ [ 3%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/backprojector.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/backprojector.cpp.o -MF CMakeFiles/relion_lib.dir/__/backprojector.cpp.o.d -o CMakeFiles/relion_lib.dir/__/backprojector.cpp.o -c /build/relion-3.1.3/src/backprojector.cpp +/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1802 | __insertion_sort(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1908 | __introsort_loop(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 3%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/complex.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/complex.cpp.o -MF CMakeFiles/relion_lib.dir/__/complex.cpp.o.d -o CMakeFiles/relion_lib.dir/__/complex.cpp.o -c /build/relion-3.1.3/src/complex.cpp -[ 3%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ctf.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/ctf.cpp.o -MF CMakeFiles/relion_lib.dir/__/ctf.cpp.o.d -o CMakeFiles/relion_lib.dir/__/ctf.cpp.o -c /build/relion-3.1.3/src/ctf.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/projector.h:25, from /build/relion-3.1.3/src/backprojector.h:33, @@ -1762,6 +1824,14 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +[ 3%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ctf.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/ctf.cpp.o -MF CMakeFiles/relion_lib.dir/__/ctf.cpp.o.d -o CMakeFiles/relion_lib.dir/__/ctf.cpp.o -c /build/relion-3.1.3/src/ctf.cpp +/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_less_iter]': +/usr/include/c++/12/bits/stl_algo.h:1782:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1782 | __unguarded_linear_insert(_RandomAccessIterator __last, + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +[ 4%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ctffind_runner.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/ctffind_runner.cpp.o -MF CMakeFiles/relion_lib.dir/__/ctffind_runner.cpp.o.d -o CMakeFiles/relion_lib.dir/__/ctffind_runner.cpp.o -c /build/relion-3.1.3/src/ctffind_runner.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-3.1.3/src/ctf.h:50, @@ -1823,29 +1893,6 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -In file included from /usr/include/c++/12/bits/stl_algo.h:60, - from /usr/include/c++/12/algorithm:61, - from /build/relion-3.1.3/src/funcs.h:55, - from /build/relion-3.1.3/src/image.h:58: -/usr/include/c++/12/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = ccfPixel; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, - | ^~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1802 | __insertion_sort(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1908 | __introsort_loop(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 4%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ctffind_runner.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/ctffind_runner.cpp.o -MF CMakeFiles/relion_lib.dir/__/ctffind_runner.cpp.o.d -o CMakeFiles/relion_lib.dir/__/ctffind_runner.cpp.o -c /build/relion-3.1.3/src/ctffind_runner.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/ctffind_runner.h:31, from /build/relion-3.1.3/src/ctffind_runner.cpp:20: @@ -1906,10 +1953,8 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_less_iter]': -/usr/include/c++/12/bits/stl_algo.h:1782:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1782 | __unguarded_linear_insert(_RandomAccessIterator __last, - | ^~~~~~~~~~~~~~~~~~~~~~~~~ +[ 4%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ctffind_runner_mpi.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/ctffind_runner_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/ctffind_runner_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/ctffind_runner_mpi.cpp.o -c /build/relion-3.1.3/src/ctffind_runner_mpi.cpp In file included from /usr/include/c++/12/vector:70, from /build/relion-3.1.3/src/funcs.h:56: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': @@ -1944,56 +1989,6 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const ccfPeak&}; _Tp = ccfPeak; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = ccfPeak; _Alloc = std::allocator]': -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const Peak&}; _Tp = Peak; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Peak; _Alloc = std::allocator]', - inlined from 'void AutoPicker::prunePeakClusters(std::vector&, int, float)' at /build/relion-3.1.3/src/autopicker.cpp:3616:20: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Peak; _Alloc = std::allocator]', - inlined from 'void AutoPicker::prunePeakClusters(std::vector&, int, float)' at /build/relion-3.1.3/src/autopicker.cpp:3629:23: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Peak; _Alloc = std::allocator]', - inlined from 'void AutoPicker::prunePeakClusters(std::vector&, int, float)' at /build/relion-3.1.3/src/autopicker.cpp:3654:26: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Peak; _Alloc = std::allocator]', - inlined from 'void AutoPicker::removeTooCloselyNeighbouringPeaks(std::vector&, int, float)' at /build/relion-3.1.3/src/autopicker.cpp:3698:26: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Peak; _Alloc = std::allocator]', - inlined from 'void AutoPicker::peakSearch(const MultidimArray&, const MultidimArray&, const MultidimArray&, const MultidimArray&, int, int, std::vector&, float)' at /build/relion-3.1.3/src/autopicker.cpp:3599:20: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {ccfPixel}; _Tp = ccfPixel; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 -[ 4%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ctffind_runner_mpi.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/ctffind_runner_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/ctffind_runner_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/ctffind_runner_mpi.cpp.o -c /build/relion-3.1.3/src/ctffind_runner_mpi.cpp -/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1802 | __insertion_sort(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/ctffind_runner.h:31, from /build/relion-3.1.3/src/ctffind_runner_mpi.h:25, @@ -2055,20 +2050,55 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const ccfPeak&}; _Tp = ccfPeak; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = ccfPeak; _Alloc = std::allocator]': +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const Peak&}; _Tp = Peak; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Peak; _Alloc = std::allocator]', + inlined from 'void AutoPicker::prunePeakClusters(std::vector&, int, float)' at /build/relion-3.1.3/src/autopicker.cpp:3616:20: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Peak; _Alloc = std::allocator]', + inlined from 'void AutoPicker::prunePeakClusters(std::vector&, int, float)' at /build/relion-3.1.3/src/autopicker.cpp:3629:23: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Peak; _Alloc = std::allocator]', + inlined from 'void AutoPicker::prunePeakClusters(std::vector&, int, float)' at /build/relion-3.1.3/src/autopicker.cpp:3654:26: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Peak; _Alloc = std::allocator]', + inlined from 'void AutoPicker::removeTooCloselyNeighbouringPeaks(std::vector&, int, float)' at /build/relion-3.1.3/src/autopicker.cpp:3698:26: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Peak; _Alloc = std::allocator]', + inlined from 'void AutoPicker::peakSearch(const MultidimArray&, const MultidimArray&, const MultidimArray&, const MultidimArray&, int, int, std::vector&, float)' at /build/relion-3.1.3/src/autopicker.cpp:3599:20: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ [ 4%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/error.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/error.cpp.o -MF CMakeFiles/relion_lib.dir/__/error.cpp.o.d -o CMakeFiles/relion_lib.dir/__/error.cpp.o -c /build/relion-3.1.3/src/error.cpp +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {ccfPixel}; _Tp = ccfPixel; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 [ 5%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/euler.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/euler.cpp.o -MF CMakeFiles/relion_lib.dir/__/euler.cpp.o.d -o CMakeFiles/relion_lib.dir/__/euler.cpp.o -c /build/relion-3.1.3/src/euler.cpp -In file included from /usr/include/c++/12/vector:63: -/usr/include/c++/12/bits/stl_uninitialized.h: In function '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = ccfPeak*]': -/usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 [ 5%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/exp_model.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/exp_model.cpp.o -MF CMakeFiles/relion_lib.dir/__/exp_model.cpp.o.d -o CMakeFiles/relion_lib.dir/__/exp_model.cpp.o -c /build/relion-3.1.3/src/exp_model.cpp -[ 6%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/fftw.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/fftw.cpp.o -MF CMakeFiles/relion_lib.dir/__/fftw.cpp.o.d -o CMakeFiles/relion_lib.dir/__/fftw.cpp.o -c /build/relion-3.1.3/src/fftw.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/exp_model.h:24, from /build/relion-3.1.3/src/exp_model.cpp:20: @@ -2129,6 +2159,21 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1802 | __insertion_sort(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +In file included from /usr/include/c++/12/vector:63: +/usr/include/c++/12/bits/stl_uninitialized.h: In function '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = ccfPeak*]': +/usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +[ 6%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/fftw.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/fftw.cpp.o -MF CMakeFiles/relion_lib.dir/__/fftw.cpp.o.d -o CMakeFiles/relion_lib.dir/__/fftw.cpp.o -c /build/relion-3.1.3/src/fftw.cpp +[ 6%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/filename.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/filename.cpp.o -MF CMakeFiles/relion_lib.dir/__/filename.cpp.o.d -o CMakeFiles/relion_lib.dir/__/filename.cpp.o -c /build/relion-3.1.3/src/filename.cpp In file included from /usr/include/c++/12/vector:70, from /build/relion-3.1.3/src/funcs.h:56, from /build/relion-3.1.3/src/multidim_array.h:52, @@ -2193,10 +2238,73 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 6%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/flex_analyser.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/flex_analyser.cpp.o -MF CMakeFiles/relion_lib.dir/__/flex_analyser.cpp.o.d -o CMakeFiles/relion_lib.dir/__/flex_analyser.cpp.o -c /build/relion-3.1.3/src/flex_analyser.cpp /usr/include/c++/12/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = ccfPeak; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ +In file included from /build/relion-3.1.3/src/image.h:455, + from /build/relion-3.1.3/src/exp_model.h:24, + from /build/relion-3.1.3/src/flex_analyser.h:24, + from /build/relion-3.1.3/src/flex_analyser.cpp:21: +/build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': +/build/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 43 | uint32 width, length; // apparent dimensions in the file + | ^~~~~ +In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31, + from /build/relion-3.1.3/src/image.h:57: +/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here + 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 43 | uint32 width, length; // apparent dimensions in the file + | ^~~~~~ +/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here + 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; + | ^~~~~~~~~~~~ +/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; + | ^~~~~~~~~~~~~ +/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; + | ^~~~~~~~~~~~~~ +/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 185 | uint32 cur_width, cur_length; + | ^~~~~~~~~ +/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here + 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 185 | uint32 cur_width, cur_length; + | ^~~~~~~~~~ +/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here + 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 186 | uint16 cur_sampleFormat, cur_bitsPerSample; + | ^~~~~~~~~~~~~~~~ +/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 186 | uint16 cur_sampleFormat, cur_bitsPerSample; + | ^~~~~~~~~~~~~~~~~ +/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ /usr/include/c++/12/bits/stl_algo.h: In function 'void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/12/bits/stl_algo.h:1625:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1625 | __heap_select(_RandomAccessIterator __first, @@ -2287,8 +2395,8 @@ /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 6%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/filename.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/filename.cpp.o -MF CMakeFiles/relion_lib.dir/__/filename.cpp.o.d -o CMakeFiles/relion_lib.dir/__/filename.cpp.o -c /build/relion-3.1.3/src/filename.cpp +[ 7%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/funcs.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/funcs.cpp.o -MF CMakeFiles/relion_lib.dir/__/funcs.cpp.o.d -o CMakeFiles/relion_lib.dir/__/funcs.cpp.o -c /build/relion-3.1.3/src/funcs.cpp In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18, inlined from 'void AutoPicker::extractHelicalTubes(std::vector&, std::vector >&, std::vector >&, std::vector >&, double, double, double, double, float)' at /build/relion-3.1.3/src/autopicker.cpp:1809:11: @@ -2369,69 +2477,6 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 6%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/flex_analyser.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/flex_analyser.cpp.o -MF CMakeFiles/relion_lib.dir/__/flex_analyser.cpp.o.d -o CMakeFiles/relion_lib.dir/__/flex_analyser.cpp.o -c /build/relion-3.1.3/src/flex_analyser.cpp -In file included from /build/relion-3.1.3/src/image.h:455, - from /build/relion-3.1.3/src/exp_model.h:24, - from /build/relion-3.1.3/src/flex_analyser.h:24, - from /build/relion-3.1.3/src/flex_analyser.cpp:21: -/build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': -/build/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] - 43 | uint32 width, length; // apparent dimensions in the file - | ^~~~~ -In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31, - from /build/relion-3.1.3/src/image.h:57: -/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here - 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/relion-3.1.3/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations] - 43 | uint32 width, length; // apparent dimensions in the file - | ^~~~~~ -/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here - 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; - | ^~~~~~~~~~~~ -/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; - | ^~~~~~~~~~~~~ -/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; - | ^~~~~~~~~~~~~~ -/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] - 185 | uint32 cur_width, cur_length; - | ^~~~~~~~~ -/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here - 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] - 185 | uint32 cur_width, cur_length; - | ^~~~~~~~~~ -/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here - 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 186 | uint16 cur_sampleFormat, cur_bitsPerSample; - | ^~~~~~~~~~~~~~~~ -/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 186 | uint16 cur_sampleFormat, cur_bitsPerSample; - | ^~~~~~~~~~~~~~~~~ -/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ In file included from /usr/include/c++/12/bits/stl_algo.h:60, from /usr/include/c++/12/algorithm:61, from /build/relion-3.1.3/src/funcs.h:55, @@ -2455,8 +2500,6 @@ /usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 7%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/funcs.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/funcs.cpp.o -MF CMakeFiles/relion_lib.dir/__/funcs.cpp.o.d -o CMakeFiles/relion_lib.dir/__/funcs.cpp.o -c /build/relion-3.1.3/src/funcs.cpp [ 7%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/healpix_sampling.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/healpix_sampling.cpp.o -MF CMakeFiles/relion_lib.dir/__/healpix_sampling.cpp.o.d -o CMakeFiles/relion_lib.dir/__/healpix_sampling.cpp.o -c /build/relion-3.1.3/src/healpix_sampling.cpp In file included from /usr/include/c++/12/vector:70, @@ -2467,10 +2510,6 @@ | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const CDataSet&}; _Tp = CDataSet; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 -[ 7%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/helix.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/helix.cpp.o -MF CMakeFiles/relion_lib.dir/__/helix.cpp.o.d -o CMakeFiles/relion_lib.dir/__/helix.cpp.o -c /build/relion-3.1.3/src/helix.cpp -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/helix.h:30, from /build/relion-3.1.3/src/healpix_sampling.h:31, @@ -2532,6 +2571,10 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 +[ 7%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/helix.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/helix.cpp.o -MF CMakeFiles/relion_lib.dir/__/helix.cpp.o.d -o CMakeFiles/relion_lib.dir/__/helix.cpp.o -c /build/relion-3.1.3/src/helix.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/helix.h:30, from /build/relion-3.1.3/src/helix.cpp:22: @@ -2808,16 +2851,8 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/algorithm:61, - from /build/relion-3.1.3/src/funcs.h:55, - from /build/relion-3.1.3/src/multidim_array.h:52, - from /build/relion-3.1.3/src/helix.h:26: -/usr/include/c++/12/bits/stl_algo.h: In function '_RandomAccessIterator std::_V2::__rotate(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, std::random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >]': -/usr/include/c++/12/bits/stl_algo.h:1281:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1281 | __rotate(_RandomAccessIterator __first, - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_algo.h:1281:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/12/bits/stl_algo.h:1281:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +[ 8%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/helix_inimodel2d.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/helix_inimodel2d.cpp.o -MF CMakeFiles/relion_lib.dir/__/helix_inimodel2d.cpp.o.d -o CMakeFiles/relion_lib.dir/__/helix_inimodel2d.cpp.o -c /build/relion-3.1.3/src/helix_inimodel2d.cpp In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void HealpixSampling::selectOrientationsWithNonZeroPriorProbability(double, double, double, double, double, double, std::vector&, std::vector&, std::vector&, std::vector&, bool, double, double, double)' at /build/relion-3.1.3/src/healpix_sampling.cpp:846:31: @@ -2847,6 +2882,76 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/algorithm:61, + from /build/relion-3.1.3/src/funcs.h:55, + from /build/relion-3.1.3/src/multidim_array.h:52, + from /build/relion-3.1.3/src/helix.h:26: +/usr/include/c++/12/bits/stl_algo.h: In function '_RandomAccessIterator std::_V2::__rotate(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, std::random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >]': +/usr/include/c++/12/bits/stl_algo.h:1281:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1281 | __rotate(_RandomAccessIterator __first, + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_algo.h:1281:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/12/bits/stl_algo.h:1281:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +In file included from /build/relion-3.1.3/src/image.h:455, + from /build/relion-3.1.3/src/helix_inimodel2d.h:29, + from /build/relion-3.1.3/src/helix_inimodel2d.cpp:22: +/build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': +/build/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 43 | uint32 width, length; // apparent dimensions in the file + | ^~~~~ +In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31, + from /build/relion-3.1.3/src/image.h:57: +/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here + 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 43 | uint32 width, length; // apparent dimensions in the file + | ^~~~~~ +/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here + 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; + | ^~~~~~~~~~~~ +/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; + | ^~~~~~~~~~~~~ +/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; + | ^~~~~~~~~~~~~~ +/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 185 | uint32 cur_width, cur_length; + | ^~~~~~~~~ +/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here + 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 185 | uint32 cur_width, cur_length; + | ^~~~~~~~~~ +/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here + 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 186 | uint16 cur_sampleFormat, cur_bitsPerSample; + | ^~~~~~~~~~~~~~~~ +/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 186 | uint16 cur_sampleFormat, cur_bitsPerSample; + | ^~~~~~~~~~~~~~~~~ +/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void FlexAnalyser::make3DModelsAlongPrincipalComponents(std::vector > >&, std::vector > >&, std::vector >&)' at /build/relion-3.1.3/src/flex_analyser.cpp:564:21: @@ -2873,68 +2978,6 @@ /usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1854 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_algo.h: In function '_OutputIterator std::__move_merge(_InputIterator, _InputIterator, _InputIterator, _InputIterator, _OutputIterator, _Compare) [with _InputIterator = HelicalSegmentPriorInfoEntry*; _OutputIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/12/bits/stl_algo.h:2615:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2615 | __move_merge(_InputIterator __first1, _InputIterator __last1, - | ^~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_algo.h: In function '_OutputIterator std::__move_merge(_InputIterator, _InputIterator, _InputIterator, _InputIterator, _OutputIterator, _Compare) [with _InputIterator = __gnu_cxx::__normal_iterator >; _OutputIterator = HelicalSegmentPriorInfoEntry*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/12/bits/stl_algo.h:2615:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/12/bits/stl_algo.h:2615:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/12/bits/stl_algo.h:2615:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/12/bits/stl_algo.h:2615:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1802 | __insertion_sort(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__merge_sort_with_buffer(_RandomAccessIterator, _RandomAccessIterator, _Pointer, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Pointer = HelicalSegmentPriorInfoEntry*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/12/bits/stl_algo.h:2682:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2682 | __merge_sort_with_buffer(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_algo.h:2682:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -In function 'void std::__chunk_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Distance, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', - inlined from 'void std::__merge_sort_with_buffer(_RandomAccessIterator, _RandomAccessIterator, _Pointer, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Pointer = HelicalSegmentPriorInfoEntry*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2693:34: -/usr/include/c++/12/bits/stl_algo.h:2672:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2672 | std::__insertion_sort(__first, __first + __chunk_size, __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_algo.h:2675:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2675 | std::__insertion_sort(__first, __last, __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_algo.h:2675:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -In function 'void std::__merge_sort_loop(_RandomAccessIterator1, _RandomAccessIterator1, _RandomAccessIterator2, _Distance, _Compare) [with _RandomAccessIterator1 = __gnu_cxx::__normal_iterator >; _RandomAccessIterator2 = HelicalSegmentPriorInfoEntry*; _Distance = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', - inlined from 'void std::__merge_sort_with_buffer(_RandomAccessIterator, _RandomAccessIterator, _Pointer, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Pointer = HelicalSegmentPriorInfoEntry*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2697:26: -/usr/include/c++/12/bits/stl_algo.h:2650:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2650 | __result = std::__move_merge(__first, __first + __step_size, - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 2651 | __first + __step_size, - | ~~~~~~~~~~~~~~~~~~~~~~ - 2652 | __first + __two_step, - | ~~~~~~~~~~~~~~~~~~~~~ - 2653 | __result, __comp); - | ~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_algo.h:2650:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/12/bits/stl_algo.h:2658:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2658 | std::__move_merge(__first, __first + __step_size, - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 2659 | __first + __step_size, __last, __result, __comp); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_algo.h:2658:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -In function 'void std::__merge_sort_loop(_RandomAccessIterator1, _RandomAccessIterator1, _RandomAccessIterator2, _Distance, _Compare) [with _RandomAccessIterator1 = HelicalSegmentPriorInfoEntry*; _RandomAccessIterator2 = __gnu_cxx::__normal_iterator >; _Distance = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', - inlined from 'void std::__merge_sort_with_buffer(_RandomAccessIterator, _RandomAccessIterator, _Pointer, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Pointer = HelicalSegmentPriorInfoEntry*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2700:26: -/usr/include/c++/12/bits/stl_algo.h:2650:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2650 | __result = std::__move_merge(__first, __first + __step_size, - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 2651 | __first + __step_size, - | ~~~~~~~~~~~~~~~~~~~~~~ - 2652 | __first + __two_step, - | ~~~~~~~~~~~~~~~~~~~~~ - 2653 | __result, __comp); - | ~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_algo.h:2658:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2658 | std::__move_merge(__first, __first + __step_size, - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 2659 | __first + __step_size, __last, __result, __comp); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator]', inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /build/relion-3.1.3/src/CPlot2D.h:168:33, inlined from 'void FlexAnalyser::makePCAhistograms(std::vector > >&, std::vector >&, std::vector >&)' at /build/relion-3.1.3/src/flex_analyser.cpp:471:23: @@ -3020,6 +3063,15 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_algo.h: In function '_OutputIterator std::__move_merge(_InputIterator, _InputIterator, _InputIterator, _InputIterator, _OutputIterator, _Compare) [with _InputIterator = HelicalSegmentPriorInfoEntry*; _OutputIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/12/bits/stl_algo.h:2615:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2615 | __move_merge(_InputIterator __first1, _InputIterator __last1, + | ^~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_algo.h: In function '_OutputIterator std::__move_merge(_InputIterator, _InputIterator, _InputIterator, _InputIterator, _OutputIterator, _Compare) [with _InputIterator = __gnu_cxx::__normal_iterator >; _OutputIterator = HelicalSegmentPriorInfoEntry*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/12/bits/stl_algo.h:2615:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/12/bits/stl_algo.h:2615:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/12/bits/stl_algo.h:2615:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/12/bits/stl_algo.h:2615:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void HealpixSampling::removeSymmetryEquivalentPoints(double)' at /build/relion-3.1.3/src/healpix_sampling.cpp:2205:38: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 @@ -3030,6 +3082,59 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1802 | __insertion_sort(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__merge_sort_with_buffer(_RandomAccessIterator, _RandomAccessIterator, _Pointer, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Pointer = HelicalSegmentPriorInfoEntry*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/12/bits/stl_algo.h:2682:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2682 | __merge_sort_with_buffer(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_algo.h:2682:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +In function 'void std::__chunk_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Distance, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', + inlined from 'void std::__merge_sort_with_buffer(_RandomAccessIterator, _RandomAccessIterator, _Pointer, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Pointer = HelicalSegmentPriorInfoEntry*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2693:34: +/usr/include/c++/12/bits/stl_algo.h:2672:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2672 | std::__insertion_sort(__first, __first + __chunk_size, __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_algo.h:2675:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2675 | std::__insertion_sort(__first, __last, __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_algo.h:2675:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +In function 'void std::__merge_sort_loop(_RandomAccessIterator1, _RandomAccessIterator1, _RandomAccessIterator2, _Distance, _Compare) [with _RandomAccessIterator1 = __gnu_cxx::__normal_iterator >; _RandomAccessIterator2 = HelicalSegmentPriorInfoEntry*; _Distance = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', + inlined from 'void std::__merge_sort_with_buffer(_RandomAccessIterator, _RandomAccessIterator, _Pointer, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Pointer = HelicalSegmentPriorInfoEntry*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2697:26: +/usr/include/c++/12/bits/stl_algo.h:2650:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2650 | __result = std::__move_merge(__first, __first + __step_size, + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 2651 | __first + __step_size, + | ~~~~~~~~~~~~~~~~~~~~~~ + 2652 | __first + __two_step, + | ~~~~~~~~~~~~~~~~~~~~~ + 2653 | __result, __comp); + | ~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_algo.h:2650:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/12/bits/stl_algo.h:2658:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2658 | std::__move_merge(__first, __first + __step_size, + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 2659 | __first + __step_size, __last, __result, __comp); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_algo.h:2658:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +In function 'void std::__merge_sort_loop(_RandomAccessIterator1, _RandomAccessIterator1, _RandomAccessIterator2, _Distance, _Compare) [with _RandomAccessIterator1 = HelicalSegmentPriorInfoEntry*; _RandomAccessIterator2 = __gnu_cxx::__normal_iterator >; _Distance = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', + inlined from 'void std::__merge_sort_with_buffer(_RandomAccessIterator, _RandomAccessIterator, _Pointer, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Pointer = HelicalSegmentPriorInfoEntry*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2700:26: +/usr/include/c++/12/bits/stl_algo.h:2650:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2650 | __result = std::__move_merge(__first, __first + __step_size, + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 2651 | __first + __step_size, + | ~~~~~~~~~~~~~~~~~~~~~~ + 2652 | __first + __two_step, + | ~~~~~~~~~~~~~~~~~~~~~ + 2653 | __result, __comp); + | ~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_algo.h:2658:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2658 | std::__move_merge(__first, __first + __step_size, + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 2659 | __first + __step_size, __last, __result, __comp); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void HealpixSampling::setOrientations(int, double)' at /build/relion-3.1.3/src/healpix_sampling.cpp:501:24: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 @@ -3057,8 +3162,22 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 8%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/helix_inimodel2d.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/helix_inimodel2d.cpp.o -MF CMakeFiles/relion_lib.dir/__/helix_inimodel2d.cpp.o.d -o CMakeFiles/relion_lib.dir/__/helix_inimodel2d.cpp.o -c /build/relion-3.1.3/src/helix_inimodel2d.cpp +In file included from /usr/include/c++/12/vector:70, + from /build/relion-3.1.3/src/time.h:31, + from /build/relion-3.1.3/src/helix_inimodel2d.h:26: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:64: +/usr/include/c++/12/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ [ 8%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/image.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/image.cpp.o -MF CMakeFiles/relion_lib.dir/__/image.cpp.o.d -o CMakeFiles/relion_lib.dir/__/image.cpp.o -c /build/relion-3.1.3/src/image.cpp In file included from /build/relion-3.1.3/src/image.h:455, @@ -3120,66 +3239,6 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -In file included from /build/relion-3.1.3/src/image.h:455, - from /build/relion-3.1.3/src/helix_inimodel2d.h:29, - from /build/relion-3.1.3/src/helix_inimodel2d.cpp:22: -/build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': -/build/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] - 43 | uint32 width, length; // apparent dimensions in the file - | ^~~~~ -In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31, - from /build/relion-3.1.3/src/image.h:57: -/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here - 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/relion-3.1.3/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations] - 43 | uint32 width, length; // apparent dimensions in the file - | ^~~~~~ -/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here - 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; - | ^~~~~~~~~~~~ -/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; - | ^~~~~~~~~~~~~ -/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; - | ^~~~~~~~~~~~~~ -/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] - 185 | uint32 cur_width, cur_length; - | ^~~~~~~~~ -/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here - 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] - 185 | uint32 cur_width, cur_length; - | ^~~~~~~~~~ -/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here - 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 186 | uint16 cur_sampleFormat, cur_bitsPerSample; - | ^~~~~~~~~~~~~~~~ -/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 186 | uint16 cur_sampleFormat, cur_bitsPerSample; - | ^~~~~~~~~~~~~~~~~ -/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ In file included from /usr/include/c++/12/vector:70, from /build/relion-3.1.3/src/funcs.h:56, from /build/relion-3.1.3/src/image.h:58: @@ -3187,6 +3246,35 @@ /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +[ 9%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/local_symmetry.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/local_symmetry.cpp.o -MF CMakeFiles/relion_lib.dir/__/local_symmetry.cpp.o.d -o CMakeFiles/relion_lib.dir/__/local_symmetry.cpp.o -c /build/relion-3.1.3/src/local_symmetry.cpp +In file included from /usr/include/c++/12/vector:70, + from /build/relion-3.1.3/src/funcs.h:56: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'void HelixAligner::readImages()' at /build/relion-3.1.3/src/helix_inimodel2d.cpp:337:21: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'void HelixAligner::readImages()' at /build/relion-3.1.3/src/helix_inimodel2d.cpp:338:22: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'void HelixAligner::readImages()' at /build/relion-3.1.3/src/helix_inimodel2d.cpp:363:33: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'void HelixAligner::readImages()' at /build/relion-3.1.3/src/helix_inimodel2d.cpp:372:34: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = fit_point3D; _Alloc = std::allocator]', inlined from 'void subtractBackgroundRamp(Image&, int, bool, double, double, double)' at /build/relion-3.1.3/src/image.cpp:307:24: @@ -3198,12 +3286,6 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:70, - from /build/relion-3.1.3/src/funcs.h:56: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void HermiteInterpolateOne3DHelicalFilament(MetaDataTable&, MetaDataTable&, int&, int, double, double, double, int, double, double, double, bool)' at /build/relion-3.1.3/src/helix.cpp:4957:21: @@ -3220,8 +3302,12 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 9%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/local_symmetry.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/local_symmetry.cpp.o -MF CMakeFiles/relion_lib.dir/__/local_symmetry.cpp.o.d -o CMakeFiles/relion_lib.dir/__/local_symmetry.cpp.o -c /build/relion-3.1.3/src/local_symmetry.cpp +In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'void HelixAlignerModel::initialise(int, int, int)' at /build/relion-3.1.3/src/helix_inimodel2d.cpp:37:16: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void combineParticlePriorsWithKaiLocalCTF(FileName&, FileName&, FileName&)' at /build/relion-3.1.3/src/helix.cpp:2051:61: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 @@ -3297,18 +3383,6 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:70, - from /build/relion-3.1.3/src/time.h:31, - from /build/relion-3.1.3/src/helix_inimodel2d.h:26: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:64: -/usr/include/c++/12/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/local_symmetry.h:30, from /build/relion-3.1.3/src/local_symmetry.cpp:21: @@ -3394,6 +3468,8 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +[ 9%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/local_symmetry_mpi.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/local_symmetry_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/local_symmetry_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/local_symmetry_mpi.cpp.o -c /build/relion-3.1.3/src/local_symmetry_mpi.cpp /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {HelicalSymmetryItem}; _Tp = HelicalSymmetryItem; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: @@ -3404,42 +3480,76 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ +In file included from /build/relion-3.1.3/src/image.h:455, + from /build/relion-3.1.3/src/local_symmetry.h:30, + from /build/relion-3.1.3/src/local_symmetry_mpi.h:5, + from /build/relion-3.1.3/src/local_symmetry_mpi.cpp:1: +/build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': +/build/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 43 | uint32 width, length; // apparent dimensions in the file + | ^~~~~ +In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31, + from /build/relion-3.1.3/src/image.h:57: +/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here + 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 43 | uint32 width, length; // apparent dimensions in the file + | ^~~~~~ +/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here + 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; + | ^~~~~~~~~~~~ +/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; + | ^~~~~~~~~~~~~ +/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; + | ^~~~~~~~~~~~~~ +/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 185 | uint32 cur_width, cur_length; + | ^~~~~~~~~ +/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here + 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 185 | uint32 cur_width, cur_length; + | ^~~~~~~~~~ +/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here + 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 186 | uint16 cur_sampleFormat, cur_bitsPerSample; + | ^~~~~~~~~~~~~~~~ +/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 186 | uint16 cur_sampleFormat, cur_bitsPerSample; + | ^~~~~~~~~~~~~~~~~ +/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ In file included from /usr/include/c++/12/bits/stl_algo.h:61: /usr/include/c++/12/bits/stl_tempbuf.h: In constructor 'std::_Temporary_buffer<_ForwardIterator, _Tp>::_Temporary_buffer(_ForwardIterator, size_type) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = HelicalSegmentPriorInfoEntry]': /usr/include/c++/12/bits/stl_tempbuf.h:258:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 258 | _Temporary_buffer<_ForwardIterator, _Tp>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void HelixAligner::readImages()' at /build/relion-3.1.3/src/helix_inimodel2d.cpp:337:21: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void HelixAligner::readImages()' at /build/relion-3.1.3/src/helix_inimodel2d.cpp:338:22: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void HelixAligner::readImages()' at /build/relion-3.1.3/src/helix_inimodel2d.cpp:363:33: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'void HelixAligner::readImages()' at /build/relion-3.1.3/src/helix_inimodel2d.cpp:372:34: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'void HelixAlignerModel::initialise(int, int, int)' at /build/relion-3.1.3/src/helix_inimodel2d.cpp:37:16: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 9%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/mask.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/mask.cpp.o -MF CMakeFiles/relion_lib.dir/__/mask.cpp.o.d -o CMakeFiles/relion_lib.dir/__/mask.cpp.o -c /build/relion-3.1.3/src/mask.cpp +[ 10%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/matrix1d.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/matrix1d.cpp.o -MF CMakeFiles/relion_lib.dir/__/matrix1d.cpp.o.d -o CMakeFiles/relion_lib.dir/__/matrix1d.cpp.o -c /build/relion-3.1.3/src/matrix1d.cpp In file included from /usr/include/c++/12/vector:70, from /build/relion-3.1.3/src/args.h:52, from /build/relion-3.1.3/src/local_symmetry.h:24: @@ -3447,6 +3557,8 @@ /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +[ 10%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/matrix2d.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/matrix2d.cpp.o -MF CMakeFiles/relion_lib.dir/__/matrix2d.cpp.o.d -o CMakeFiles/relion_lib.dir/__/matrix2d.cpp.o -c /build/relion-3.1.3/src/matrix2d.cpp In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void Interpolate3DCurves(FileName&, FileName&, int, double, double, double, int, bool)' at /build/relion-3.1.3/src/helix.cpp:5283:20: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 @@ -3489,8 +3601,10 @@ | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 -[ 9%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/local_symmetry_mpi.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/local_symmetry_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/local_symmetry_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/local_symmetry_mpi.cpp.o -c /build/relion-3.1.3/src/local_symmetry_mpi.cpp +[ 11%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/memory.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/memory.cpp.o -MF CMakeFiles/relion_lib.dir/__/memory.cpp.o.d -o CMakeFiles/relion_lib.dir/__/memory.cpp.o -c /build/relion-3.1.3/src/memory.cpp +[ 11%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/metadata_container.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/metadata_container.cpp.o -MF CMakeFiles/relion_lib.dir/__/metadata_container.cpp.o.d -o CMakeFiles/relion_lib.dir/__/metadata_container.cpp.o -c /build/relion-3.1.3/src/metadata_container.cpp /usr/include/c++/12/bits/stl_algo.h: In function '_BidirectionalIterator1 std::__rotate_adaptive(_BidirectionalIterator1, _BidirectionalIterator1, _BidirectionalIterator1, _Distance, _Distance, _BidirectionalIterator2, _Distance) [with _BidirectionalIterator1 = __gnu_cxx::__normal_iterator >; _BidirectionalIterator2 = HelicalSegmentPriorInfoEntry*; _Distance = int]': /usr/include/c++/12/bits/stl_algo.h:2352:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2352 | __rotate_adaptive(_BidirectionalIterator1 __first, @@ -3932,67 +4046,10 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5002 | _DistanceType(__buf.size()), __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/relion-3.1.3/src/image.h:455, - from /build/relion-3.1.3/src/local_symmetry.h:30, - from /build/relion-3.1.3/src/local_symmetry_mpi.h:5, - from /build/relion-3.1.3/src/local_symmetry_mpi.cpp:1: -/build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': -/build/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] - 43 | uint32 width, length; // apparent dimensions in the file - | ^~~~~ -In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31, - from /build/relion-3.1.3/src/image.h:57: -/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here - 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/relion-3.1.3/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations] - 43 | uint32 width, length; // apparent dimensions in the file - | ^~~~~~ -/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here - 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; - | ^~~~~~~~~~~~ -/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; - | ^~~~~~~~~~~~~ -/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; - | ^~~~~~~~~~~~~~ -/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] - 185 | uint32 cur_width, cur_length; - | ^~~~~~~~~ -/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here - 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] - 185 | uint32 cur_width, cur_length; - | ^~~~~~~~~~ -/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here - 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 186 | uint16 cur_sampleFormat, cur_bitsPerSample; - | ^~~~~~~~~~~~~~~~ -/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 186 | uint16 cur_sampleFormat, cur_bitsPerSample; - | ^~~~~~~~~~~~~~~~~ -/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ +[ 11%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/metadata_label.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/metadata_label.cpp.o -MF CMakeFiles/relion_lib.dir/__/metadata_label.cpp.o.d -o CMakeFiles/relion_lib.dir/__/metadata_label.cpp.o -c /build/relion-3.1.3/src/metadata_label.cpp +[ 12%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/metadata_table.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/metadata_table.cpp.o -MF CMakeFiles/relion_lib.dir/__/metadata_table.cpp.o.d -o CMakeFiles/relion_lib.dir/__/metadata_table.cpp.o -c /build/relion-3.1.3/src/metadata_table.cpp In file included from /usr/include/c++/12/vector:63: /usr/include/c++/12/bits/stl_uninitialized.h: In function '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*]': /usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 @@ -4031,8 +4088,66 @@ /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 9%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/mask.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/mask.cpp.o -MF CMakeFiles/relion_lib.dir/__/mask.cpp.o.d -o CMakeFiles/relion_lib.dir/__/mask.cpp.o -c /build/relion-3.1.3/src/mask.cpp +In file included from /usr/include/c++/12/bits/stl_algo.h:60, + from /usr/include/c++/12/algorithm:61, + from /build/relion-3.1.3/src/funcs.h:55, + from /build/relion-3.1.3/src/metadata_table.h:43, + from /build/relion-3.1.3/src/metadata_table.cpp:45: +/usr/include/c++/12/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, + | ^~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Distance = int; _Tp = pair; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 +/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1802 | __insertion_sort(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1908 | __introsort_loop(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 + 1908 | __introsort_loop(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 +/usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 + 1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 + 1802 | __insertion_sort(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 +[ 12%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/micrograph_model.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/micrograph_model.cpp.o -MF CMakeFiles/relion_lib.dir/__/micrograph_model.cpp.o.d -o CMakeFiles/relion_lib.dir/__/micrograph_model.cpp.o -c /build/relion-3.1.3/src/micrograph_model.cpp +In file included from /usr/include/c++/12/vector:70, + from /build/relion-3.1.3/src/metadata_table.h:33: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const CDataPoint&}; _Tp = CDataPoint; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const CDataSet&}; _Tp = CDataSet; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 +In file included from /usr/include/c++/12/vector:64: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator]', + inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /build/relion-3.1.3/src/CPlot2D.h:168:33, + inlined from 'void MetaDataTable::addToCPlot2D(CPlot2D*, EMDLabel, EMDLabel, double, double, double, double, std::string)' at /build/relion-3.1.3/src/metadata_table.cpp:1528:23: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataSet; _Alloc = std::allocator]', + inlined from 'void CPlot2D::AddDataSet(CDataSet)' at /build/relion-3.1.3/src/CPlot2D.h:1198:26, + inlined from 'void MetaDataTable::addToCPlot2D(CPlot2D*, EMDLabel, EMDLabel, double, double, double, double, std::string)' at /build/relion-3.1.3/src/metadata_table.cpp:1532:20: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void getLocalSearchOperatorSamplings(const Matrix1D&, const Matrix1D&, std::vector >&, double, double, bool, bool)' at /build/relion-3.1.3/src/local_symmetry.cpp:1550:18: @@ -4097,65 +4212,10 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 10%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/matrix1d.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/matrix1d.cpp.o -MF CMakeFiles/relion_lib.dir/__/matrix1d.cpp.o.d -o CMakeFiles/relion_lib.dir/__/matrix1d.cpp.o -c /build/relion-3.1.3/src/matrix1d.cpp -[ 10%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/matrix2d.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/matrix2d.cpp.o -MF CMakeFiles/relion_lib.dir/__/matrix2d.cpp.o.d -o CMakeFiles/relion_lib.dir/__/matrix2d.cpp.o -c /build/relion-3.1.3/src/matrix2d.cpp -[ 11%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/memory.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/memory.cpp.o -MF CMakeFiles/relion_lib.dir/__/memory.cpp.o.d -o CMakeFiles/relion_lib.dir/__/memory.cpp.o -c /build/relion-3.1.3/src/memory.cpp -[ 11%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/metadata_container.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/metadata_container.cpp.o -MF CMakeFiles/relion_lib.dir/__/metadata_container.cpp.o.d -o CMakeFiles/relion_lib.dir/__/metadata_container.cpp.o -c /build/relion-3.1.3/src/metadata_container.cpp -[ 11%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/metadata_label.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/metadata_label.cpp.o -MF CMakeFiles/relion_lib.dir/__/metadata_label.cpp.o.d -o CMakeFiles/relion_lib.dir/__/metadata_label.cpp.o -c /build/relion-3.1.3/src/metadata_label.cpp -[ 12%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/metadata_table.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/metadata_table.cpp.o -MF CMakeFiles/relion_lib.dir/__/metadata_table.cpp.o.d -o CMakeFiles/relion_lib.dir/__/metadata_table.cpp.o -c /build/relion-3.1.3/src/metadata_table.cpp -In file included from /usr/include/c++/12/bits/stl_algo.h:60, - from /usr/include/c++/12/algorithm:61, - from /build/relion-3.1.3/src/funcs.h:55, - from /build/relion-3.1.3/src/metadata_table.h:43, - from /build/relion-3.1.3/src/metadata_table.cpp:45: -/usr/include/c++/12/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, - | ^~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Distance = int; _Tp = pair; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 -/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1802 | __insertion_sort(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1908 | __introsort_loop(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 - 1908 | __introsort_loop(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 -/usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 - 1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 - 1802 | __insertion_sort(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 -[ 12%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/micrograph_model.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/micrograph_model.cpp.o -MF CMakeFiles/relion_lib.dir/__/micrograph_model.cpp.o.d -o CMakeFiles/relion_lib.dir/__/micrograph_model.cpp.o -c /build/relion-3.1.3/src/micrograph_model.cpp -In file included from /usr/include/c++/12/vector:70, - from /build/relion-3.1.3/src/metadata_table.h:33: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const CDataPoint&}; _Tp = CDataPoint; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const CDataSet&}; _Tp = CDataSet; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/micrograph_model.cpp:23: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': @@ -4215,23 +4275,6 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -In file included from /usr/include/c++/12/vector:64: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator]', - inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /build/relion-3.1.3/src/CPlot2D.h:168:33, - inlined from 'void MetaDataTable::addToCPlot2D(CPlot2D*, EMDLabel, EMDLabel, double, double, double, double, std::string)' at /build/relion-3.1.3/src/metadata_table.cpp:1528:23: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataSet; _Alloc = std::allocator]', - inlined from 'void CPlot2D::AddDataSet(CDataSet)' at /build/relion-3.1.3/src/CPlot2D.h:1198:26, - inlined from 'void MetaDataTable::addToCPlot2D(CPlot2D*, EMDLabel, EMDLabel, double, double, double, double, std::string)' at /build/relion-3.1.3/src/metadata_table.cpp:1532:20: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 523 | vector<_Tp, _Alloc>:: @@ -4356,8 +4399,7 @@ In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/projector.h:25, from /build/relion-3.1.3/src/ml_model.h:23, - from /build/relion-3.1.3/src/ml_optimiser.h:35, - from /build/relion-3.1.3/src/ml_optimiser.cpp:44: + from /build/relion-3.1.3/src/ml_model.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -4391,10 +4433,35 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 185 | uint32 cur_width, cur_length; + | ^~~~~~~~~ +/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here + 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 185 | uint32 cur_width, cur_length; + | ^~~~~~~~~~ +/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here + 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 186 | uint16 cur_sampleFormat, cur_bitsPerSample; + | ^~~~~~~~~~~~~~~~ +/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 186 | uint16 cur_sampleFormat, cur_bitsPerSample; + | ^~~~~~~~~~~~~~~~~ +/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/projector.h:25, from /build/relion-3.1.3/src/ml_model.h:23, - from /build/relion-3.1.3/src/ml_model.cpp:21: + from /build/relion-3.1.3/src/ml_optimiser.h:35, + from /build/relion-3.1.3/src/ml_optimiser.cpp:44: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -4452,6 +4519,47 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +[ 13%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ml_optimiser_mpi.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/ml_optimiser_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/ml_optimiser_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/ml_optimiser_mpi.cpp.o -c /build/relion-3.1.3/src/ml_optimiser_mpi.cpp +In file included from /build/relion-3.1.3/src/image.h:455, + from /build/relion-3.1.3/src/projector.h:25, + from /build/relion-3.1.3/src/ml_model.h:23, + from /build/relion-3.1.3/src/ml_optimiser.h:35, + from /build/relion-3.1.3/src/ml_optimiser_mpi.h:24, + from /build/relion-3.1.3/src/ml_optimiser_mpi.cpp:20: +/build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': +/build/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 43 | uint32 width, length; // apparent dimensions in the file + | ^~~~~ +In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31, + from /build/relion-3.1.3/src/image.h:57: +/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here + 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 43 | uint32 width, length; // apparent dimensions in the file + | ^~~~~~ +/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here + 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; + | ^~~~~~~~~~~~ +/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; + | ^~~~~~~~~~~~~ +/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; + | ^~~~~~~~~~~~~~ +/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ @@ -4523,21 +4631,6 @@ 113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 -In file included from /usr/include/c++/12/vector:70, - from /build/relion-3.1.3/src/ml_optimiser.h:33: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 - 523 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:64: -/usr/include/c++/12/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 1032 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void MlModel::initialiseBodies(FileName, FileName, bool, int)' at /build/relion-3.1.3/src/ml_model.cpp:1085:21: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 @@ -4558,6 +4651,21 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:70, + from /build/relion-3.1.3/src/ml_optimiser.h:33: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 + 523 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:64: +/usr/include/c++/12/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 1032 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void MlModel::initialise(bool)' at /build/relion-3.1.3/src/ml_model.cpp:45:26: /usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 @@ -4613,108 +4721,10 @@ /usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1032 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 13%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ml_optimiser_mpi.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/ml_optimiser_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/ml_optimiser_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/ml_optimiser_mpi.cpp.o -c /build/relion-3.1.3/src/ml_optimiser_mpi.cpp -In file included from /build/relion-3.1.3/src/image.h:455, - from /build/relion-3.1.3/src/projector.h:25, - from /build/relion-3.1.3/src/ml_model.h:23, - from /build/relion-3.1.3/src/ml_optimiser.h:35, - from /build/relion-3.1.3/src/ml_optimiser_mpi.h:24, - from /build/relion-3.1.3/src/ml_optimiser_mpi.cpp:20: -/build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': -/build/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] - 43 | uint32 width, length; // apparent dimensions in the file - | ^~~~~ -In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31, - from /build/relion-3.1.3/src/image.h:57: -/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here - 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/relion-3.1.3/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations] - 43 | uint32 width, length; // apparent dimensions in the file - | ^~~~~~ -/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here - 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; - | ^~~~~~~~~~~~ -/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; - | ^~~~~~~~~~~~~ -/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; - | ^~~~~~~~~~~~~~ -/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] - 185 | uint32 cur_width, cur_length; - | ^~~~~~~~~ -/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here - 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] - 185 | uint32 cur_width, cur_length; - | ^~~~~~~~~~ -/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here - 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 186 | uint16 cur_sampleFormat, cur_bitsPerSample; - | ^~~~~~~~~~~~~~~~ -/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 186 | uint16 cur_sampleFormat, cur_bitsPerSample; - | ^~~~~~~~~~~~~~~~~ -/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void MlOptimiser::initialiseGeneral(int)' at /build/relion-3.1.3/src/ml_optimiser.cpp:1933:33: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void MlOptimiser::initialiseGeneral(int)' at /build/relion-3.1.3/src/ml_optimiser.cpp:1934:34: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void MlOptimiser::initialiseGeneral(int)' at /build/relion-3.1.3/src/ml_optimiser.cpp:1938:32: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void MlOptimiser::convertAllSquaredDifferencesToWeights(long int, int, int, int, int, int, int, int, int, int, int, int, int, MultidimArray&, MultidimArray&, std::vector >&, std::vector >&, std::vector >&, std::vector >&, std::vector >&, std::vector&, std::vector&, std::vector >&, std::vector >&)' at /build/relion-3.1.3/src/ml_optimiser.cpp:6682:23: -/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 1032 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void MlOptimiser::convertAllSquaredDifferencesToWeights(long int, int, int, int, int, int, int, int, int, int, int, int, int, MultidimArray&, MultidimArray&, std::vector >&, std::vector >&, std::vector >&, std::vector >&, std::vector >&, std::vector&, std::vector&, std::vector >&, std::vector >&)' at /build/relion-3.1.3/src/ml_optimiser.cpp:7049:31: -/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 1032 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void MlOptimiser::expectationSomeParticles(long int, long int)' at /build/relion-3.1.3/src/ml_optimiser.cpp:3402:33: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void MlOptimiser::getAllSquaredDifferences(long int, int, int, int, int, int, int, int, int, int, int, int, int, std::vector >&, std::vector >&, std::vector > >&, std::vector >&, MultidimArray&, MultidimArray&, std::vector&, std::vector&, std::vector >&, std::vector >&, std::vector > > >&, std::vector >&, std::vector >&, std::vector >&)' at /build/relion-3.1.3/src/ml_optimiser.cpp:6108:22: -/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 1032 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 14%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/motioncorr_runner.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/motioncorr_runner.cpp.o -MF CMakeFiles/relion_lib.dir/__/motioncorr_runner.cpp.o.d -o CMakeFiles/relion_lib.dir/__/motioncorr_runner.cpp.o -c /build/relion-3.1.3/src/motioncorr_runner.cpp +[ 14%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/motioncorr_runner_mpi.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/motioncorr_runner_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/motioncorr_runner_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/motioncorr_runner_mpi.cpp.o -c /build/relion-3.1.3/src/motioncorr_runner_mpi.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/motioncorr_runner.h:32, from /build/relion-3.1.3/src/motioncorr_runner.cpp:22: @@ -4775,101 +4785,6 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void MlOptimiser::storeWeightedSums(long int, int, int, int, int, int, int, int, int, int, int, int, std::vector >&, std::vector >&, std::vector > >&, std::vector > >&, std::vector >&, std::vector >&, std::vector >&, std::vector >&, MultidimArray&, MultidimArray&, std::vector >&, std::vector >&, std::vector >&, std::vector&, std::vector&, std::vector >&, std::vector >&, std::vector > > >&, std::vector > > >&, std::vector >&, std::vector >&, std::vector >&)' at /build/relion-3.1.3/src/ml_optimiser.cpp:7233:23: -/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 1032 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void MlOptimiser::storeWeightedSums(long int, int, int, int, int, int, int, int, int, int, int, int, std::vector >&, std::vector >&, std::vector > >&, std::vector > >&, std::vector >&, std::vector >&, std::vector >&, std::vector >&, MultidimArray&, MultidimArray&, std::vector >&, std::vector >&, std::vector >&, std::vector&, std::vector&, std::vector >&, std::vector >&, std::vector > > >&, std::vector > > >&, std::vector >&, std::vector >&, std::vector >&)' at /build/relion-3.1.3/src/ml_optimiser.cpp:7315:23: -/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 1032 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void MlOptimiser::storeWeightedSums(long int, int, int, int, int, int, int, int, int, int, int, int, std::vector >&, std::vector >&, std::vector > >&, std::vector > >&, std::vector >&, std::vector >&, std::vector >&, std::vector >&, MultidimArray&, MultidimArray&, std::vector >&, std::vector >&, std::vector >&, std::vector&, std::vector&, std::vector >&, std::vector >&, std::vector > > >&, std::vector > > >&, std::vector >&, std::vector >&, std::vector >&)' at /build/relion-3.1.3/src/ml_optimiser.cpp:7317:27: -/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 1032 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void MlOptimiser::expectationOneParticle(long int, int)' at /build/relion-3.1.3/src/ml_optimiser.cpp:3741:32: -/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 1032 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:70, - from /build/relion-3.1.3/src/motioncorr_runner.h:25: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const CDataPoint&}; _Tp = CDataPoint; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const CDataSet&}; _Tp = CDataSet; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 -In file included from /usr/include/c++/12/vector:64: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator]', - inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /build/relion-3.1.3/src/CPlot2D.h:168:33, - inlined from 'void MotioncorrRunner::plotShifts(FileName, Micrograph&)' at /build/relion-3.1.3/src/motioncorr_runner.cpp:737:24: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataSet; _Alloc = std::allocator]', - inlined from 'void CPlot2D::AddDataSet(CDataSet)' at /build/relion-3.1.3/src/CPlot2D.h:1198:26, - inlined from 'void MotioncorrRunner::plotShifts(FileName, Micrograph&)' at /build/relion-3.1.3/src/motioncorr_runner.cpp:740:20: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator]', - inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /build/relion-3.1.3/src/CPlot2D.h:168:33, - inlined from 'void MotioncorrRunner::plotShifts(FileName, Micrograph&)' at /build/relion-3.1.3/src/motioncorr_runner.cpp:749:28: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataSet; _Alloc = std::allocator]', - inlined from 'void CPlot2D::AddDataSet(CDataSet)' at /build/relion-3.1.3/src/CPlot2D.h:1198:26, - inlined from 'void MotioncorrRunner::plotShifts(FileName, Micrograph&)' at /build/relion-3.1.3/src/motioncorr_runner.cpp:750:21: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator]', - inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /build/relion-3.1.3/src/CPlot2D.h:168:33, - inlined from 'void MotioncorrRunner::plotShifts(FileName, Micrograph&)' at /build/relion-3.1.3/src/motioncorr_runner.cpp:776:20: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator]', - inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /build/relion-3.1.3/src/CPlot2D.h:168:33, - inlined from 'void MotioncorrRunner::plotShifts(FileName, Micrograph&)' at /build/relion-3.1.3/src/motioncorr_runner.cpp:778:20: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator]', - inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /build/relion-3.1.3/src/CPlot2D.h:168:33, - inlined from 'void MotioncorrRunner::plotShifts(FileName, Micrograph&)' at /build/relion-3.1.3/src/motioncorr_runner.cpp:779:44: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataSet; _Alloc = std::allocator]', - inlined from 'void CPlot2D::AddDataSet(CDataSet)' at /build/relion-3.1.3/src/CPlot2D.h:1198:26, - inlined from 'void MotioncorrRunner::plotShifts(FileName, Micrograph&)' at /build/relion-3.1.3/src/motioncorr_runner.cpp:782:21: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataSet; _Alloc = std::allocator]', - inlined from 'void CPlot2D::AddDataSet(CDataSet)' at /build/relion-3.1.3/src/CPlot2D.h:1198:26, - inlined from 'void MotioncorrRunner::plotShifts(FileName, Micrograph&)' at /build/relion-3.1.3/src/motioncorr_runner.cpp:783:21: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataSet; _Alloc = std::allocator]', - inlined from 'void CPlot2D::AddDataSet(CDataSet)' at /build/relion-3.1.3/src/CPlot2D.h:1198:26, - inlined from 'void MotioncorrRunner::plotShifts(FileName, Micrograph&)' at /build/relion-3.1.3/src/motioncorr_runner.cpp:785:21: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -[ 14%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/motioncorr_runner_mpi.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/motioncorr_runner_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/motioncorr_runner_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/motioncorr_runner_mpi.cpp.o -c /build/relion-3.1.3/src/motioncorr_runner_mpi.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/motioncorr_runner.h:32, from /build/relion-3.1.3/src/motioncorr_runner_mpi.h:25, @@ -4948,6 +4863,21 @@ /build/relion-3.1.3/src/numerical_recipes.cpp:579:13: note: declared here 579 | RFLOAT *xt=NULL; | ^~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'void MlOptimiser::initialiseGeneral(int)' at /build/relion-3.1.3/src/ml_optimiser.cpp:1933:33: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'void MlOptimiser::initialiseGeneral(int)' at /build/relion-3.1.3/src/ml_optimiser.cpp:1934:34: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'void MlOptimiser::initialiseGeneral(int)' at /build/relion-3.1.3/src/ml_optimiser.cpp:1938:32: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In function 'void free_Tvector(T*&, int, int) [with T = double]', inlined from 'void powell(double*, double*, int, double, int&, double&, double (*)(double*, void*), void*, bool)' at /build/relion-3.1.3/src/numerical_recipes.cpp:767:25: /build/relion-3.1.3/src/memory.h:74:13: warning: 'void free(void*)' called on pointer 'xit' with nonzero offset 8 [-Wfree-nonheap-object] @@ -4977,23 +4907,26 @@ | ^~ [ 15%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/parallel.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/parallel.cpp.o -MF CMakeFiles/relion_lib.dir/__/parallel.cpp.o.d -o CMakeFiles/relion_lib.dir/__/parallel.cpp.o -c /build/relion-3.1.3/src/parallel.cpp +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'void MlOptimiser::convertAllSquaredDifferencesToWeights(long int, int, int, int, int, int, int, int, int, int, int, int, int, MultidimArray&, MultidimArray&, std::vector >&, std::vector >&, std::vector >&, std::vector >&, std::vector >&, std::vector&, std::vector&, std::vector >&, std::vector >&)' at /build/relion-3.1.3/src/ml_optimiser.cpp:6682:23: +/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 1032 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'void MlOptimiser::convertAllSquaredDifferencesToWeights(long int, int, int, int, int, int, int, int, int, int, int, int, int, MultidimArray&, MultidimArray&, std::vector >&, std::vector >&, std::vector >&, std::vector >&, std::vector >&, std::vector&, std::vector&, std::vector >&, std::vector >&)' at /build/relion-3.1.3/src/ml_optimiser.cpp:7049:31: +/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 1032 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 16%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/particle_subtractor.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/particle_subtractor.cpp.o -MF CMakeFiles/relion_lib.dir/__/particle_subtractor.cpp.o.d -o CMakeFiles/relion_lib.dir/__/particle_subtractor.cpp.o -c /build/relion-3.1.3/src/particle_subtractor.cpp -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'bool MotioncorrRunner::executeOwnMotionCorrection(Micrograph&)' at /build/relion-3.1.3/src/motioncorr_runner.cpp:1442:30: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'bool MotioncorrRunner::executeOwnMotionCorrection(Micrograph&)' at /build/relion-3.1.3/src/motioncorr_runner.cpp:1443:30: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'bool MotioncorrRunner::executeOwnMotionCorrection(Micrograph&)' at /build/relion-3.1.3/src/motioncorr_runner.cpp:1453:29: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:70, + from /build/relion-3.1.3/src/motioncorr_runner.h:25: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const CDataPoint&}; _Tp = CDataPoint; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const CDataSet&}; _Tp = CDataSet; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/projector.h:25, from /build/relion-3.1.3/src/ml_model.h:23, @@ -5057,12 +4990,122 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +In file included from /usr/include/c++/12/vector:64: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator]', + inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /build/relion-3.1.3/src/CPlot2D.h:168:33, + inlined from 'void MotioncorrRunner::plotShifts(FileName, Micrograph&)' at /build/relion-3.1.3/src/motioncorr_runner.cpp:737:24: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataSet; _Alloc = std::allocator]', + inlined from 'void CPlot2D::AddDataSet(CDataSet)' at /build/relion-3.1.3/src/CPlot2D.h:1198:26, + inlined from 'void MotioncorrRunner::plotShifts(FileName, Micrograph&)' at /build/relion-3.1.3/src/motioncorr_runner.cpp:740:20: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator]', + inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /build/relion-3.1.3/src/CPlot2D.h:168:33, + inlined from 'void MotioncorrRunner::plotShifts(FileName, Micrograph&)' at /build/relion-3.1.3/src/motioncorr_runner.cpp:749:28: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataSet; _Alloc = std::allocator]', + inlined from 'void CPlot2D::AddDataSet(CDataSet)' at /build/relion-3.1.3/src/CPlot2D.h:1198:26, + inlined from 'void MotioncorrRunner::plotShifts(FileName, Micrograph&)' at /build/relion-3.1.3/src/motioncorr_runner.cpp:750:21: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator]', + inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /build/relion-3.1.3/src/CPlot2D.h:168:33, + inlined from 'void MotioncorrRunner::plotShifts(FileName, Micrograph&)' at /build/relion-3.1.3/src/motioncorr_runner.cpp:776:20: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator]', + inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /build/relion-3.1.3/src/CPlot2D.h:168:33, + inlined from 'void MotioncorrRunner::plotShifts(FileName, Micrograph&)' at /build/relion-3.1.3/src/motioncorr_runner.cpp:778:20: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator]', + inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /build/relion-3.1.3/src/CPlot2D.h:168:33, + inlined from 'void MotioncorrRunner::plotShifts(FileName, Micrograph&)' at /build/relion-3.1.3/src/motioncorr_runner.cpp:779:44: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataSet; _Alloc = std::allocator]', + inlined from 'void CPlot2D::AddDataSet(CDataSet)' at /build/relion-3.1.3/src/CPlot2D.h:1198:26, + inlined from 'void MotioncorrRunner::plotShifts(FileName, Micrograph&)' at /build/relion-3.1.3/src/motioncorr_runner.cpp:782:21: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataSet; _Alloc = std::allocator]', + inlined from 'void CPlot2D::AddDataSet(CDataSet)' at /build/relion-3.1.3/src/CPlot2D.h:1198:26, + inlined from 'void MotioncorrRunner::plotShifts(FileName, Micrograph&)' at /build/relion-3.1.3/src/motioncorr_runner.cpp:783:21: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataSet; _Alloc = std::allocator]', + inlined from 'void CPlot2D::AddDataSet(CDataSet)' at /build/relion-3.1.3/src/CPlot2D.h:1198:26, + inlined from 'void MotioncorrRunner::plotShifts(FileName, Micrograph&)' at /build/relion-3.1.3/src/motioncorr_runner.cpp:785:21: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ [ 16%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/pipeline_control.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/pipeline_control.cpp.o -MF CMakeFiles/relion_lib.dir/__/pipeline_control.cpp.o.d -o CMakeFiles/relion_lib.dir/__/pipeline_control.cpp.o -c /build/relion-3.1.3/src/pipeline_control.cpp [ 17%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/pipeline_jobs.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/pipeline_jobs.cpp.o -MF CMakeFiles/relion_lib.dir/__/pipeline_jobs.cpp.o.d -o CMakeFiles/relion_lib.dir/__/pipeline_jobs.cpp.o -c /build/relion-3.1.3/src/pipeline_jobs.cpp +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'void MlOptimiser::expectationSomeParticles(long int, long int)' at /build/relion-3.1.3/src/ml_optimiser.cpp:3402:33: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'void MlOptimiser::getAllSquaredDifferences(long int, int, int, int, int, int, int, int, int, int, int, int, int, std::vector >&, std::vector >&, std::vector > >&, std::vector >&, MultidimArray&, MultidimArray&, std::vector&, std::vector&, std::vector >&, std::vector >&, std::vector > > >&, std::vector >&, std::vector >&, std::vector >&)' at /build/relion-3.1.3/src/ml_optimiser.cpp:6108:22: +/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 1032 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'void MlOptimiser::storeWeightedSums(long int, int, int, int, int, int, int, int, int, int, int, int, std::vector >&, std::vector >&, std::vector > >&, std::vector > >&, std::vector >&, std::vector >&, std::vector >&, std::vector >&, MultidimArray&, MultidimArray&, std::vector >&, std::vector >&, std::vector >&, std::vector&, std::vector&, std::vector >&, std::vector >&, std::vector > > >&, std::vector > > >&, std::vector >&, std::vector >&, std::vector >&)' at /build/relion-3.1.3/src/ml_optimiser.cpp:7233:23: +/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 1032 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'void MlOptimiser::storeWeightedSums(long int, int, int, int, int, int, int, int, int, int, int, int, std::vector >&, std::vector >&, std::vector > >&, std::vector > >&, std::vector >&, std::vector >&, std::vector >&, std::vector >&, MultidimArray&, MultidimArray&, std::vector >&, std::vector >&, std::vector >&, std::vector&, std::vector&, std::vector >&, std::vector >&, std::vector > > >&, std::vector > > >&, std::vector >&, std::vector >&, std::vector >&)' at /build/relion-3.1.3/src/ml_optimiser.cpp:7315:23: +/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 1032 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'void MlOptimiser::storeWeightedSums(long int, int, int, int, int, int, int, int, int, int, int, int, std::vector >&, std::vector >&, std::vector > >&, std::vector > >&, std::vector >&, std::vector >&, std::vector >&, std::vector >&, MultidimArray&, MultidimArray&, std::vector >&, std::vector >&, std::vector >&, std::vector&, std::vector&, std::vector >&, std::vector >&, std::vector > > >&, std::vector > > >&, std::vector >&, std::vector >&, std::vector >&)' at /build/relion-3.1.3/src/ml_optimiser.cpp:7317:27: +/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 1032 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'bool MotioncorrRunner::executeOwnMotionCorrection(Micrograph&)' at /build/relion-3.1.3/src/motioncorr_runner.cpp:1442:30: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'bool MotioncorrRunner::executeOwnMotionCorrection(Micrograph&)' at /build/relion-3.1.3/src/motioncorr_runner.cpp:1443:30: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'bool MotioncorrRunner::executeOwnMotionCorrection(Micrograph&)' at /build/relion-3.1.3/src/motioncorr_runner.cpp:1453:29: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ [ 17%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/pipeliner.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/pipeliner.cpp.o -MF CMakeFiles/relion_lib.dir/__/pipeliner.cpp.o.d -o CMakeFiles/relion_lib.dir/__/pipeliner.cpp.o -c /build/relion-3.1.3/src/pipeliner.cpp +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'void MlOptimiser::expectationOneParticle(long int, int)' at /build/relion-3.1.3/src/ml_optimiser.cpp:3741:32: +/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 1032 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 17%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/postprocessing.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/postprocessing.cpp.o -MF CMakeFiles/relion_lib.dir/__/postprocessing.cpp.o.d -o CMakeFiles/relion_lib.dir/__/postprocessing.cpp.o -c /build/relion-3.1.3/src/postprocessing.cpp In file included from /build/relion-3.1.3/src/image.h:455, @@ -5274,6 +5317,8 @@ | ^~~~~~ [ 18%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/projector.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/projector.cpp.o -MF CMakeFiles/relion_lib.dir/__/projector.cpp.o.d -o CMakeFiles/relion_lib.dir/__/projector.cpp.o -c /build/relion-3.1.3/src/projector.cpp +[ 19%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/reconstructor.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/reconstructor.cpp.o -MF CMakeFiles/relion_lib.dir/__/reconstructor.cpp.o.d -o CMakeFiles/relion_lib.dir/__/reconstructor.cpp.o -c /build/relion-3.1.3/src/reconstructor.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/projector.h:25, from /build/relion-3.1.3/src/projector.cpp:20: @@ -5334,10 +5379,6 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 19%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/reconstructor.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/reconstructor.cpp.o -MF CMakeFiles/relion_lib.dir/__/reconstructor.cpp.o.d -o CMakeFiles/relion_lib.dir/__/reconstructor.cpp.o -c /build/relion-3.1.3/src/reconstructor.cpp -[ 19%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/reconstructor_mpi.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/reconstructor_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/reconstructor_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/reconstructor_mpi.cpp.o -c /build/relion-3.1.3/src/reconstructor_mpi.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/projector.h:25, from /build/relion-3.1.3/src/backprojector.h:33, @@ -5400,6 +5441,8 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +[ 19%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/reconstructor_mpi.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/reconstructor_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/reconstructor_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/reconstructor_mpi.cpp.o -c /build/relion-3.1.3/src/reconstructor_mpi.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/projector.h:25, from /build/relion-3.1.3/src/backprojector.h:33, @@ -5649,6 +5692,10 @@ cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/strings.cpp.o -MF CMakeFiles/relion_lib.dir/__/strings.cpp.o.d -o CMakeFiles/relion_lib.dir/__/strings.cpp.o -c /build/relion-3.1.3/src/strings.cpp [ 21%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/symmetries.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/symmetries.cpp.o -MF CMakeFiles/relion_lib.dir/__/symmetries.cpp.o.d -o CMakeFiles/relion_lib.dir/__/symmetries.cpp.o -c /build/relion-3.1.3/src/symmetries.cpp +[ 21%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/tabfuncs.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/tabfuncs.cpp.o -MF CMakeFiles/relion_lib.dir/__/tabfuncs.cpp.o.d -o CMakeFiles/relion_lib.dir/__/tabfuncs.cpp.o -c /build/relion-3.1.3/src/tabfuncs.cpp +[ 21%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/tiff_converter.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/tiff_converter.cpp.o -MF CMakeFiles/relion_lib.dir/__/tiff_converter.cpp.o.d -o CMakeFiles/relion_lib.dir/__/tiff_converter.cpp.o -c /build/relion-3.1.3/src/tiff_converter.cpp In file included from /usr/include/c++/12/map:60, from /build/relion-3.1.3/src/metadata_table.h:32: /usr/include/c++/12/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::allocator >&>, std::tuple<>}; _Key = std::__cxx11::basic_string; _Val = std::pair, SchedulerFloatVariable>; _KeyOfValue = std::_Select1st, SchedulerFloatVariable> >; _Compare = std::less >; _Alloc = std::allocator, SchedulerFloatVariable> >]': @@ -5718,61 +5765,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:70, - from /build/relion-3.1.3/src/time.h:31, - from /build/relion-3.1.3/src/scheduler.h:24: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector, std::allocator > >::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = std::pair; _Alloc = std::allocator >]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'void MultidimArray::sorted_index(MultidimArray&) const [with T = double]' at /build/relion-3.1.3/src/multidim_array.h:3618:22: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector, allocator > > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', - inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator*, vector, allocator > > >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18, - inlined from 'void MultidimArray::sorted_index(MultidimArray&) const [with T = double]' at /build/relion-3.1.3/src/multidim_array.h:3621:18: -/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >' changed in GCC 7.1 - 1937 | std::__introsort_loop(__first, __last, - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ - 1938 | std::__lg(__last - __first) * 2, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1939 | __comp); - | ~~~~~~~ -In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector, allocator > > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', - inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector, allocator > > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:1940:31, - inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator*, vector, allocator > > >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18, - inlined from 'void MultidimArray::sorted_index(MultidimArray&) const [with T = double]' at /build/relion-3.1.3/src/multidim_array.h:3621:18: -/usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >' changed in GCC 7.1 - 1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >' changed in GCC 7.1 - 1854 | std::__insertion_sort(__first, __last, __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string; _Tp = SchedulerFloatVariable; _Compare = std::less >; _Alloc = std::allocator, SchedulerFloatVariable> >]', - inlined from 'void Schedule::read(bool, FileName)' at /build/relion-3.1.3/src/scheduler.cpp:684:33: -/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, SchedulerFloatVariable>, std::_Select1st, SchedulerFloatVariable> >, std::less >, std::allocator, SchedulerFloatVariable> > >::const_iterator' changed in GCC 7.1 - 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 512 | std::tuple(__k), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 513 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ -[ 21%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/tabfuncs.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/tabfuncs.cpp.o -MF CMakeFiles/relion_lib.dir/__/tabfuncs.cpp.o.d -o CMakeFiles/relion_lib.dir/__/tabfuncs.cpp.o -c /build/relion-3.1.3/src/tabfuncs.cpp -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string; _Tp = SchedulerFloatVariable; _Compare = std::less >; _Alloc = std::allocator, SchedulerFloatVariable> >]', - inlined from 'void Schedule::setVariablesInJob(RelionJob&, FileName, bool&)' at /build/relion-3.1.3/src/scheduler.cpp:1628:59: -/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, SchedulerFloatVariable>, std::_Select1st, SchedulerFloatVariable> >, std::less >, std::allocator, SchedulerFloatVariable> > >::const_iterator' changed in GCC 7.1 - 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 512 | std::tuple(__k), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 513 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ -[ 21%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/tiff_converter.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/tiff_converter.cpp.o -MF CMakeFiles/relion_lib.dir/__/tiff_converter.cpp.o.d -o CMakeFiles/relion_lib.dir/__/tiff_converter.cpp.o -c /build/relion-3.1.3/src/tiff_converter.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/tiff_converter.cpp:24: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': @@ -5853,14 +5845,65 @@ /build/relion-3.1.3/src/tiff_converter.cpp:367:23: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | system(("mkdir -p " + fn_out.beforeLastOf("/")).c_str()); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:70, + from /build/relion-3.1.3/src/time.h:31, + from /build/relion-3.1.3/src/scheduler.h:24: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector, std::allocator > >::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ /build/relion-3.1.3/src/tiff_converter.cpp: In member function 'void TIFFConverter::run()': /build/relion-3.1.3/src/tiff_converter.cpp:530:31: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | system(("mkdir -p " + fn_tiff.beforeLastOf("/")).c_str()); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = std::pair; _Alloc = std::allocator >]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'void MultidimArray::sorted_index(MultidimArray&) const [with T = double]' at /build/relion-3.1.3/src/multidim_array.h:3618:22: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector, allocator > > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', + inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator*, vector, allocator > > >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18, + inlined from 'void MultidimArray::sorted_index(MultidimArray&) const [with T = double]' at /build/relion-3.1.3/src/multidim_array.h:3621:18: +/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >' changed in GCC 7.1 + 1937 | std::__introsort_loop(__first, __last, + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ + 1938 | std::__lg(__last - __first) * 2, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1939 | __comp); + | ~~~~~~~ +In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector, allocator > > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', + inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector, allocator > > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:1940:31, + inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator*, vector, allocator > > >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18, + inlined from 'void MultidimArray::sorted_index(MultidimArray&) const [with T = double]' at /build/relion-3.1.3/src/multidim_array.h:3621:18: +/usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >' changed in GCC 7.1 + 1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >' changed in GCC 7.1 + 1854 | std::__insertion_sort(__first, __last, __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ [ 22%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/time.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/time.cpp.o -MF CMakeFiles/relion_lib.dir/__/time.cpp.o.d -o CMakeFiles/relion_lib.dir/__/time.cpp.o -c /build/relion-3.1.3/src/time.cpp +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string; _Tp = SchedulerFloatVariable; _Compare = std::less >; _Alloc = std::allocator, SchedulerFloatVariable> >]', + inlined from 'void Schedule::read(bool, FileName)' at /build/relion-3.1.3/src/scheduler.cpp:684:33: +/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, SchedulerFloatVariable>, std::_Select1st, SchedulerFloatVariable> >, std::less >, std::allocator, SchedulerFloatVariable> > >::const_iterator' changed in GCC 7.1 + 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 512 | std::tuple(__k), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 513 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ [ 22%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/transformations.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/transformations.cpp.o -MF CMakeFiles/relion_lib.dir/__/transformations.cpp.o.d -o CMakeFiles/relion_lib.dir/__/transformations.cpp.o -c /build/relion-3.1.3/src/transformations.cpp +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string; _Tp = SchedulerFloatVariable; _Compare = std::less >; _Alloc = std::allocator, SchedulerFloatVariable> >]', + inlined from 'void Schedule::setVariablesInJob(RelionJob&, FileName, bool&)' at /build/relion-3.1.3/src/scheduler.cpp:1628:59: +/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, SchedulerFloatVariable>, std::_Select1st, SchedulerFloatVariable> >, std::less >, std::allocator, SchedulerFloatVariable> > >::const_iterator' changed in GCC 7.1 + 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 512 | std::tuple(__k), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 513 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ [ 23%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/Healpix_2.15a/cxxutils.cc.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/Healpix_2.15a/cxxutils.cc.o -MF CMakeFiles/relion_lib.dir/__/Healpix_2.15a/cxxutils.cc.o.d -o CMakeFiles/relion_lib.dir/__/Healpix_2.15a/cxxutils.cc.o -c /build/relion-3.1.3/src/Healpix_2.15a/cxxutils.cc [ 23%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/Healpix_2.15a/healpix_base.cc.o @@ -5931,6 +5974,8 @@ cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/Gaussian_pyramid.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/Gaussian_pyramid.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/Gaussian_pyramid.cpp.o -c /build/relion-3.1.3/src/jaz/Gaussian_pyramid.cpp [ 24%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/aberration_fit.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/aberration_fit.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/aberration_fit.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/aberration_fit.cpp.o -c /build/relion-3.1.3/src/jaz/aberration_fit.cpp +[ 25%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/complex_io.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/complex_io.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/complex_io.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/complex_io.cpp.o -c /build/relion-3.1.3/src/jaz/complex_io.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/aberration_fit.h:24, from /build/relion-3.1.3/src/jaz/aberration_fit.cpp:21: @@ -5991,8 +6036,6 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 25%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/complex_io.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/complex_io.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/complex_io.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/complex_io.cpp.o -c /build/relion-3.1.3/src/jaz/complex_io.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/complex_io.h:24, from /build/relion-3.1.3/src/jaz/complex_io.cpp:21: @@ -6117,6 +6160,8 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +[ 26%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/damage_helper.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/damage_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/damage_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/damage_helper.cpp.o -c /build/relion-3.1.3/src/jaz/damage_helper.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-3.1.3/src/ctf.h:50, @@ -6179,10 +6224,6 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 26%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/damage_helper.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/damage_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/damage_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/damage_helper.cpp.o -c /build/relion-3.1.3/src/jaz/damage_helper.cpp -[ 26%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/distribution_helper.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/distribution_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/distribution_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/distribution_helper.cpp.o -c /build/relion-3.1.3/src/jaz/distribution_helper.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-3.1.3/src/ctf.h:50, @@ -6245,6 +6286,10 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +[ 26%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/distribution_helper.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/distribution_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/distribution_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/distribution_helper.cpp.o -c /build/relion-3.1.3/src/jaz/distribution_helper.cpp +[ 26%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/fftw_helper.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/fftw_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/fftw_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/fftw_helper.cpp.o -c /build/relion-3.1.3/src/jaz/fftw_helper.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/distribution_helper.h:25, from /build/relion-3.1.3/src/jaz/distribution_helper.cpp:21: @@ -6305,12 +6350,8 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 26%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/fftw_helper.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/fftw_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/fftw_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/fftw_helper.cpp.o -c /build/relion-3.1.3/src/jaz/fftw_helper.cpp [ 27%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/fsc_helper.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/fsc_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/fsc_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/fsc_helper.cpp.o -c /build/relion-3.1.3/src/jaz/fsc_helper.cpp -[ 27%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/image_log.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/image_log.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/image_log.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/image_log.cpp.o -c /build/relion-3.1.3/src/jaz/image_log.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-3.1.3/src/ctf.h:50, @@ -6373,6 +6414,10 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +[ 27%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/image_log.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/image_log.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/image_log.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/image_log.cpp.o -c /build/relion-3.1.3/src/jaz/image_log.cpp +[ 28%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/interpolation.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/interpolation.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/interpolation.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/interpolation.cpp.o -c /build/relion-3.1.3/src/jaz/interpolation.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/image_log.h:24, from /build/relion-3.1.3/src/jaz/image_log.cpp:21: @@ -6433,14 +6478,6 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 28%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/interpolation.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/interpolation.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/interpolation.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/interpolation.cpp.o -c /build/relion-3.1.3/src/jaz/interpolation.cpp -[ 28%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/jaz_config.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/jaz_config.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/jaz_config.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/jaz_config.cpp.o -c /build/relion-3.1.3/src/jaz/jaz_config.cpp -[ 28%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/legacy_obs_model.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/legacy_obs_model.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/legacy_obs_model.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/legacy_obs_model.cpp.o -c /build/relion-3.1.3/src/jaz/legacy_obs_model.cpp -[ 29%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/local_motion_fit.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/local_motion_fit.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/local_motion_fit.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/local_motion_fit.cpp.o -c /build/relion-3.1.3/src/jaz/local_motion_fit.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/interpolation.h:24, from /build/relion-3.1.3/src/jaz/interpolation.cpp:21: @@ -6501,6 +6538,14 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +[ 28%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/jaz_config.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/jaz_config.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/jaz_config.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/jaz_config.cpp.o -c /build/relion-3.1.3/src/jaz/jaz_config.cpp +[ 28%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/legacy_obs_model.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/legacy_obs_model.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/legacy_obs_model.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/legacy_obs_model.cpp.o -c /build/relion-3.1.3/src/jaz/legacy_obs_model.cpp +[ 29%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/local_motion_fit.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/local_motion_fit.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/local_motion_fit.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/local_motion_fit.cpp.o -c /build/relion-3.1.3/src/jaz/local_motion_fit.cpp +[ 29%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/micrograph_handler.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/micrograph_handler.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/micrograph_handler.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/micrograph_handler.cpp.o -c /build/relion-3.1.3/src/jaz/micrograph_handler.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/legacy_obs_model.h:4, from /build/relion-3.1.3/src/jaz/legacy_obs_model.cpp:1: @@ -6537,30 +6582,6 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -/build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] - 185 | uint32 cur_width, cur_length; - | ^~~~~~~~~ -/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here - 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] - 185 | uint32 cur_width, cur_length; - | ^~~~~~~~~~ -/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here - 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 186 | uint16 cur_sampleFormat, cur_bitsPerSample; - | ^~~~~~~~~~~~~~~~ -/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 186 | uint16 cur_sampleFormat, cur_bitsPerSample; - | ^~~~~~~~~~~~~~~~~ -/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/local_motion_fit.h:24, from /build/relion-3.1.3/src/jaz/local_motion_fit.cpp:21: @@ -6621,12 +6642,30 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 29%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/micrograph_handler.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/micrograph_handler.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/micrograph_handler.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/micrograph_handler.cpp.o -c /build/relion-3.1.3/src/jaz/micrograph_handler.cpp -[ 29%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/new_ft.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/new_ft.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/new_ft.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/new_ft.cpp.o -c /build/relion-3.1.3/src/jaz/new_ft.cpp -[ 30%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/noise_helper.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/noise_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/noise_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/noise_helper.cpp.o -c /build/relion-3.1.3/src/jaz/noise_helper.cpp +/build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 185 | uint32 cur_width, cur_length; + | ^~~~~~~~~ +/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here + 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 185 | uint32 cur_width, cur_length; + | ^~~~~~~~~~ +/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here + 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 186 | uint16 cur_sampleFormat, cur_bitsPerSample; + | ^~~~~~~~~~~~~~~~ +/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 186 | uint16 cur_sampleFormat, cur_bitsPerSample; + | ^~~~~~~~~~~~~~~~~ +/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/micrograph_handler.h:31, from /build/relion-3.1.3/src/jaz/micrograph_handler.cpp:21: @@ -6687,6 +6726,12 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +[ 29%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/new_ft.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/new_ft.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/new_ft.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/new_ft.cpp.o -c /build/relion-3.1.3/src/jaz/new_ft.cpp +[ 30%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/noise_helper.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/noise_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/noise_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/noise_helper.cpp.o -c /build/relion-3.1.3/src/jaz/noise_helper.cpp +[ 30%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/obs_model.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/obs_model.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/obs_model.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/obs_model.cpp.o -c /build/relion-3.1.3/src/jaz/obs_model.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/projector.h:25, from /build/relion-3.1.3/src/jaz/noise_helper.h:25, @@ -6748,14 +6793,6 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -In file included from /usr/include/c++/12/vector:70, - from /build/relion-3.1.3/src/jaz/noise_helper.h:24: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -[ 30%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/obs_model.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/obs_model.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/obs_model.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/obs_model.cpp.o -c /build/relion-3.1.3/src/jaz/obs_model.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-3.1.3/src/jaz/obs_model.cpp:21: @@ -6816,18 +6853,16 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -In file included from /usr/include/c++/12/vector:64: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'static Image NoiseHelper::predictCCNoise(Projector&, double, double, int, int, Image&, CTF, double, double, double, int)' at /build/relion-3.1.3/src/jaz/noise_helper.cpp:134:40: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ [ 31%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/parallel_ft.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/parallel_ft.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/parallel_ft.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/parallel_ft.cpp.o -c /build/relion-3.1.3/src/jaz/parallel_ft.cpp +In file included from /usr/include/c++/12/vector:70, + from /build/relion-3.1.3/src/jaz/noise_helper.h:24: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ [ 31%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/reference_map.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/reference_map.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/reference_map.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/reference_map.cpp.o -c /build/relion-3.1.3/src/jaz/reference_map.cpp -[ 31%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/refinement_helper.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/refinement_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/refinement_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/refinement_helper.cpp.o -c /build/relion-3.1.3/src/jaz/refinement_helper.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/reference_map.h:24, from /build/relion-3.1.3/src/jaz/reference_map.cpp:21: @@ -6888,6 +6923,8 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +[ 31%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/refinement_helper.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/refinement_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/refinement_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/refinement_helper.cpp.o -c /build/relion-3.1.3/src/jaz/refinement_helper.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-3.1.3/src/ctf.h:50, @@ -6950,12 +6987,16 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +In file included from /usr/include/c++/12/vector:64: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'static Image NoiseHelper::predictCCNoise(Projector&, double, double, int, int, Image&, CTF, double, double, double, int)' at /build/relion-3.1.3/src/jaz/noise_helper.cpp:134:40: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ [ 32%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/resampling_helper.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/resampling_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/resampling_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/resampling_helper.cpp.o -c /build/relion-3.1.3/src/jaz/resampling_helper.cpp [ 32%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/slice_helper.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/slice_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/slice_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/slice_helper.cpp.o -c /build/relion-3.1.3/src/jaz/slice_helper.cpp -[ 32%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/spectral_helper.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/spectral_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/spectral_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/spectral_helper.cpp.o -c /build/relion-3.1.3/src/jaz/spectral_helper.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/slice_helper.h:24, from /build/relion-3.1.3/src/jaz/slice_helper.cpp:21: @@ -7016,6 +7057,12 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +[ 32%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/spectral_helper.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/spectral_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/spectral_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/spectral_helper.cpp.o -c /build/relion-3.1.3/src/jaz/spectral_helper.cpp +[ 33%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/stack_helper.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/stack_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/stack_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/stack_helper.cpp.o -c /build/relion-3.1.3/src/jaz/stack_helper.cpp +[ 33%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/structure_tensor.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/structure_tensor.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/structure_tensor.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/structure_tensor.cpp.o -c /build/relion-3.1.3/src/jaz/structure_tensor.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/spectral_helper.h:24, from /build/relion-3.1.3/src/jaz/spectral_helper.cpp:21: @@ -7076,10 +7123,6 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 33%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/stack_helper.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/stack_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/stack_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/stack_helper.cpp.o -c /build/relion-3.1.3/src/jaz/stack_helper.cpp -[ 33%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/structure_tensor.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/structure_tensor.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/structure_tensor.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/structure_tensor.cpp.o -c /build/relion-3.1.3/src/jaz/structure_tensor.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-3.1.3/src/ctf.h:50, @@ -7270,8 +7313,6 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 35%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/vtk_helper.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/vtk_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/vtk_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/vtk_helper.cpp.o -c /build/relion-3.1.3/src/jaz/vtk_helper.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/volume_integration.h:26, from /build/relion-3.1.3/src/jaz/volume_integration.cpp:21: @@ -7332,8 +7373,14 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +[ 35%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/vtk_helper.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/vtk_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/vtk_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/vtk_helper.cpp.o -c /build/relion-3.1.3/src/jaz/vtk_helper.cpp [ 36%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/gradient_descent.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/gradient_descent.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/optimization/gradient_descent.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/optimization/gradient_descent.cpp.o -c /build/relion-3.1.3/src/jaz/optimization/gradient_descent.cpp +[ 36%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/lbfgs.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/lbfgs.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/optimization/lbfgs.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/optimization/lbfgs.cpp.o -c /build/relion-3.1.3/src/jaz/optimization/lbfgs.cpp +[ 36%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/nelder_mead.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/nelder_mead.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/optimization/nelder_mead.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/optimization/nelder_mead.cpp.o -c /build/relion-3.1.3/src/jaz/optimization/nelder_mead.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/vtk_helper.h:24, from /build/relion-3.1.3/src/jaz/vtk_helper.cpp:21: @@ -7394,10 +7441,6 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 36%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/lbfgs.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/lbfgs.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/optimization/lbfgs.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/optimization/lbfgs.cpp.o -c /build/relion-3.1.3/src/jaz/optimization/lbfgs.cpp -[ 36%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/nelder_mead.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/nelder_mead.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/optimization/nelder_mead.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/optimization/nelder_mead.cpp.o -c /build/relion-3.1.3/src/jaz/optimization/nelder_mead.cpp [ 37%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/optimization.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/optimization.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/optimization/optimization.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/optimization/optimization.cpp.o -c /build/relion-3.1.3/src/jaz/optimization/optimization.cpp [ 37%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/aberration_estimator.cpp.o @@ -7524,54 +7567,8 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -In file included from /usr/include/c++/12/vector:70, - from /build/relion-3.1.3/src/funcs.h:56, - from /build/relion-3.1.3/src/image.h:58: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const CDataPoint&}; _Tp = CDataPoint; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ [ 38%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/ctf_refiner.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/ctf_refiner.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/ctf_refiner.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/ctf_refiner.cpp.o -c /build/relion-3.1.3/src/jaz/ctf/ctf_refiner.cpp -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const CDataSet&}; _Tp = CDataSet; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 -In file included from /usr/include/c++/12/vector:64: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator]', - inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /build/relion-3.1.3/src/CPlot2D.h:168:33, - inlined from 'void BFactorRefiner::writePerParticleEPS(const MetaDataTable&)' at /build/relion-3.1.3/src/jaz/ctf/bfactor_refiner.cpp:474:23: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataSet; _Alloc = std::allocator]', - inlined from 'void CPlot2D::AddDataSet(CDataSet)' at /build/relion-3.1.3/src/CPlot2D.h:1198:26, - inlined from 'void BFactorRefiner::writePerParticleEPS(const MetaDataTable&)' at /build/relion-3.1.3/src/jaz/ctf/bfactor_refiner.cpp:476:20: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator]', - inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /build/relion-3.1.3/src/CPlot2D.h:168:33, - inlined from 'void BFactorRefiner::writePerParticleDiagEPS(const MetaDataTable&, gravis::d2Vector, const std::vector >&, const std::vector >&, int)' at /build/relion-3.1.3/src/jaz/ctf/bfactor_refiner.cpp:405:21: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator]', - inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /build/relion-3.1.3/src/CPlot2D.h:168:33, - inlined from 'void BFactorRefiner::writePerParticleDiagEPS(const MetaDataTable&, gravis::d2Vector, const std::vector >&, const std::vector >&, int)' at /build/relion-3.1.3/src/jaz/ctf/bfactor_refiner.cpp:419:24: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataSet; _Alloc = std::allocator]', - inlined from 'void CPlot2D::AddDataSet(CDataSet)' at /build/relion-3.1.3/src/CPlot2D.h:1198:26, - inlined from 'void BFactorRefiner::writePerParticleDiagEPS(const MetaDataTable&, gravis::d2Vector, const std::vector >&, const std::vector >&, int)' at /build/relion-3.1.3/src/jaz/ctf/bfactor_refiner.cpp:421:21: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataSet; _Alloc = std::allocator]', - inlined from 'void CPlot2D::AddDataSet(CDataSet)' at /build/relion-3.1.3/src/CPlot2D.h:1198:26, - inlined from 'void BFactorRefiner::writePerParticleDiagEPS(const MetaDataTable&, gravis::d2Vector, const std::vector >&, const std::vector >&, int)' at /build/relion-3.1.3/src/jaz/ctf/bfactor_refiner.cpp:425:19: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, @@ -7633,6 +7630,52 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +In file included from /usr/include/c++/12/vector:70, + from /build/relion-3.1.3/src/funcs.h:56, + from /build/relion-3.1.3/src/image.h:58: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const CDataPoint&}; _Tp = CDataPoint; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const CDataSet&}; _Tp = CDataSet; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 +In file included from /usr/include/c++/12/vector:64: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator]', + inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /build/relion-3.1.3/src/CPlot2D.h:168:33, + inlined from 'void BFactorRefiner::writePerParticleEPS(const MetaDataTable&)' at /build/relion-3.1.3/src/jaz/ctf/bfactor_refiner.cpp:474:23: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataSet; _Alloc = std::allocator]', + inlined from 'void CPlot2D::AddDataSet(CDataSet)' at /build/relion-3.1.3/src/CPlot2D.h:1198:26, + inlined from 'void BFactorRefiner::writePerParticleEPS(const MetaDataTable&)' at /build/relion-3.1.3/src/jaz/ctf/bfactor_refiner.cpp:476:20: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator]', + inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /build/relion-3.1.3/src/CPlot2D.h:168:33, + inlined from 'void BFactorRefiner::writePerParticleDiagEPS(const MetaDataTable&, gravis::d2Vector, const std::vector >&, const std::vector >&, int)' at /build/relion-3.1.3/src/jaz/ctf/bfactor_refiner.cpp:405:21: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator]', + inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /build/relion-3.1.3/src/CPlot2D.h:168:33, + inlined from 'void BFactorRefiner::writePerParticleDiagEPS(const MetaDataTable&, gravis::d2Vector, const std::vector >&, const std::vector >&, int)' at /build/relion-3.1.3/src/jaz/ctf/bfactor_refiner.cpp:419:24: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataSet; _Alloc = std::allocator]', + inlined from 'void CPlot2D::AddDataSet(CDataSet)' at /build/relion-3.1.3/src/CPlot2D.h:1198:26, + inlined from 'void BFactorRefiner::writePerParticleDiagEPS(const MetaDataTable&, gravis::d2Vector, const std::vector >&, const std::vector >&, int)' at /build/relion-3.1.3/src/jaz/ctf/bfactor_refiner.cpp:421:21: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataSet; _Alloc = std::allocator]', + inlined from 'void CPlot2D::AddDataSet(CDataSet)' at /build/relion-3.1.3/src/CPlot2D.h:1198:26, + inlined from 'void BFactorRefiner::writePerParticleDiagEPS(const MetaDataTable&, gravis::d2Vector, const std::vector >&, const std::vector >&, int)' at /build/relion-3.1.3/src/jaz/ctf/bfactor_refiner.cpp:425:19: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator]', inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /build/relion-3.1.3/src/CPlot2D.h:168:33, inlined from 'void BFactorRefiner::writePerMicrographEPS(const MetaDataTable&, const std::vector >&, const std::vector >&, int)' at /build/relion-3.1.3/src/jaz/ctf/bfactor_refiner.cpp:339:21: @@ -7676,30 +7719,6 @@ | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 38%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/ctf_refiner_mpi.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/ctf_refiner_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/ctf_refiner_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/ctf_refiner_mpi.cpp.o -c /build/relion-3.1.3/src/jaz/ctf/ctf_refiner_mpi.cpp -In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from '_ZN19AberrationEstimator13parametricFitERKSt6vectorI13MetaDataTableSaIS1_EERS1_RS0_I8FileNameSaIS7_EE._omp_fn.0' at /build/relion-3.1.3/src/jaz/ctf/aberration_estimator.cpp:303:19: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from '_ZN19AberrationEstimator13parametricFitERKSt6vectorI13MetaDataTableSaIS1_EERS1_RS0_I8FileNameSaIS7_EE._omp_fn.0' at /build/relion-3.1.3/src/jaz/ctf/aberration_estimator.cpp:306:19: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from '_ZN19AberrationEstimator13parametricFitERKSt6vectorI13MetaDataTableSaIS1_EERS1_RS0_I8FileNameSaIS7_EE._omp_fn.0' at /build/relion-3.1.3/src/jaz/ctf/aberration_estimator.cpp:341:20: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from '_ZN19AberrationEstimator13parametricFitERKSt6vectorI13MetaDataTableSaIS1_EERS1_RS0_I8FileNameSaIS7_EE._omp_fn.0' at /build/relion-3.1.3/src/jaz/ctf/aberration_estimator.cpp:344:20: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, @@ -7766,11 +7785,11 @@ cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/defocus_estimator.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/defocus_estimator.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/defocus_estimator.cpp.o -c /build/relion-3.1.3/src/jaz/ctf/defocus_estimator.cpp [ 39%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/defocus_helper.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/defocus_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/defocus_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/defocus_helper.cpp.o -c /build/relion-3.1.3/src/jaz/ctf/defocus_helper.cpp +[ 39%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/delocalisation_helper.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/delocalisation_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/delocalisation_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/delocalisation_helper.cpp.o -c /build/relion-3.1.3/src/jaz/ctf/delocalisation_helper.cpp In file included from /build/relion-3.1.3/src/image.h:455, - from /build/relion-3.1.3/src/jaz/obs_model.h:24, - from /build/relion-3.1.3/src/ctf.h:50, - from /build/relion-3.1.3/src/jaz/ctf/defocus_helper.h:24, - from /build/relion-3.1.3/src/jaz/ctf/defocus_helper.cpp:21: + from /build/relion-3.1.3/src/jaz/ctf/defocus_estimator.h:24, + from /build/relion-3.1.3/src/jaz/ctf/defocus_estimator.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -7829,8 +7848,10 @@ 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-3.1.3/src/image.h:455, - from /build/relion-3.1.3/src/jaz/ctf/defocus_estimator.h:24, - from /build/relion-3.1.3/src/jaz/ctf/defocus_estimator.cpp:21: + from /build/relion-3.1.3/src/jaz/obs_model.h:24, + from /build/relion-3.1.3/src/ctf.h:50, + from /build/relion-3.1.3/src/jaz/ctf/delocalisation_helper.h:4, + from /build/relion-3.1.3/src/jaz/ctf/delocalisation_helper.cpp:1: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -7888,13 +7909,11 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 39%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/delocalisation_helper.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/delocalisation_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/delocalisation_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/delocalisation_helper.cpp.o -c /build/relion-3.1.3/src/jaz/ctf/delocalisation_helper.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-3.1.3/src/ctf.h:50, - from /build/relion-3.1.3/src/jaz/ctf/delocalisation_helper.h:4, - from /build/relion-3.1.3/src/jaz/ctf/delocalisation_helper.cpp:1: + from /build/relion-3.1.3/src/jaz/ctf/defocus_helper.h:24, + from /build/relion-3.1.3/src/jaz/ctf/defocus_helper.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -7952,6 +7971,34 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from '_ZN19AberrationEstimator13parametricFitERKSt6vectorI13MetaDataTableSaIS1_EERS1_RS0_I8FileNameSaIS7_EE._omp_fn.0' at /build/relion-3.1.3/src/jaz/ctf/aberration_estimator.cpp:303:19: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from '_ZN19AberrationEstimator13parametricFitERKSt6vectorI13MetaDataTableSaIS1_EERS1_RS0_I8FileNameSaIS7_EE._omp_fn.0' at /build/relion-3.1.3/src/jaz/ctf/aberration_estimator.cpp:306:19: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from '_ZN19AberrationEstimator13parametricFitERKSt6vectorI13MetaDataTableSaIS1_EERS1_RS0_I8FileNameSaIS7_EE._omp_fn.0' at /build/relion-3.1.3/src/jaz/ctf/aberration_estimator.cpp:341:20: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from '_ZN19AberrationEstimator13parametricFitERKSt6vectorI13MetaDataTableSaIS1_EERS1_RS0_I8FileNameSaIS7_EE._omp_fn.0' at /build/relion-3.1.3/src/jaz/ctf/aberration_estimator.cpp:344:20: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 40%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/equation2x2.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/equation2x2.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/equation2x2.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/equation2x2.cpp.o -c /build/relion-3.1.3/src/jaz/ctf/equation2x2.cpp +[ 40%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_estimator.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_estimator.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_estimator.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_estimator.cpp.o -c /build/relion-3.1.3/src/jaz/ctf/magnification_estimator.cpp In file included from /usr/include/c++/12/vector:70, from /build/relion-3.1.3/src/funcs.h:56, from /build/relion-3.1.3/src/image.h:58: @@ -7974,12 +8021,6 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 40%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/equation2x2.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/equation2x2.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/equation2x2.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/equation2x2.cpp.o -c /build/relion-3.1.3/src/jaz/ctf/equation2x2.cpp -[ 40%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_estimator.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_estimator.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_estimator.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_estimator.cpp.o -c /build/relion-3.1.3/src/jaz/ctf/magnification_estimator.cpp -[ 40%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_helper.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_helper.cpp.o -c /build/relion-3.1.3/src/jaz/ctf/magnification_helper.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/ctf/magnification_estimator.h:28, from /build/relion-3.1.3/src/jaz/ctf/magnification_estimator.cpp:21: @@ -8040,6 +8081,16 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +[ 40%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_helper.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_helper.cpp.o -c /build/relion-3.1.3/src/jaz/ctf/magnification_helper.cpp +[ 41%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/modular_ctf_optimisation.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/modular_ctf_optimisation.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/modular_ctf_optimisation.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/modular_ctf_optimisation.cpp.o -c /build/relion-3.1.3/src/jaz/ctf/modular_ctf_optimisation.cpp +In file included from /usr/include/c++/12/vector:70, + from /build/relion-3.1.3/src/jaz/ctf/magnification_estimator.h:24: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-3.1.3/src/ctf.h:50, @@ -8102,8 +8153,8 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 41%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/modular_ctf_optimisation.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/modular_ctf_optimisation.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/modular_ctf_optimisation.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/modular_ctf_optimisation.cpp.o -c /build/relion-3.1.3/src/jaz/ctf/modular_ctf_optimisation.cpp +[ 41%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_estimator.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_estimator.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_estimator.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_estimator.cpp.o -c /build/relion-3.1.3/src/jaz/ctf/tilt_estimator.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/ctf/modular_ctf_optimisation.h:5, from /build/relion-3.1.3/src/jaz/ctf/modular_ctf_optimisation.cpp:1: @@ -8164,14 +8215,6 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -In file included from /usr/include/c++/12/vector:70, - from /build/relion-3.1.3/src/jaz/ctf/magnification_estimator.h:24: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -[ 41%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_estimator.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_estimator.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_estimator.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_estimator.cpp.o -c /build/relion-3.1.3/src/jaz/ctf/tilt_estimator.cpp In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from '_ZN22MagnificationEstimator13parametricFitERSt6vectorI13MetaDataTableSaIS1_EERS1_RS0_I8FileNameSaIS6_EE._omp_fn.0' at /build/relion-3.1.3/src/jaz/ctf/magnification_estimator.cpp:219:19: @@ -8395,6 +8438,8 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 43%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/gp_motion_fit.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/gp_motion_fit.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/gp_motion_fit.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/gp_motion_fit.cpp.o -c /build/relion-3.1.3/src/jaz/motion/gp_motion_fit.cpp In file included from /usr/include/c++/12/vector:70, from /build/relion-3.1.3/src/funcs.h:56, from /build/relion-3.1.3/src/multidim_array.h:52, @@ -8414,8 +8459,68 @@ /usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1032 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 43%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/gp_motion_fit.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/gp_motion_fit.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/gp_motion_fit.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/gp_motion_fit.cpp.o -c /build/relion-3.1.3/src/jaz/motion/gp_motion_fit.cpp +[ 43%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_estimator.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_estimator.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/motion_estimator.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/motion_estimator.cpp.o -c /build/relion-3.1.3/src/jaz/motion/motion_estimator.cpp +In file included from /build/relion-3.1.3/src/image.h:455, + from /build/relion-3.1.3/src/jaz/motion/gp_motion_fit.h:24, + from /build/relion-3.1.3/src/jaz/motion/gp_motion_fit.cpp:21: +/build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': +/build/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 43 | uint32 width, length; // apparent dimensions in the file + | ^~~~~ +In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31, + from /build/relion-3.1.3/src/image.h:57: +/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here + 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 43 | uint32 width, length; // apparent dimensions in the file + | ^~~~~~ +/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here + 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; + | ^~~~~~~~~~~~ +/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; + | ^~~~~~~~~~~~~ +/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; + | ^~~~~~~~~~~~~~ +/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 185 | uint32 cur_width, cur_length; + | ^~~~~~~~~ +/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here + 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 185 | uint32 cur_width, cur_length; + | ^~~~~~~~~~ +/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here + 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 186 | uint16 cur_sampleFormat, cur_bitsPerSample; + | ^~~~~~~~~~~~~~~~ +/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 186 | uint16 cur_sampleFormat, cur_bitsPerSample; + | ^~~~~~~~~~~~~~~~~ +/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from '_ZN13TiltEstimator13parametricFitERKSt6vectorI13MetaDataTableSaIS1_EERS1_RS0_I8FileNameSaIS7_EE._omp_fn.0' at /build/relion-3.1.3/src/jaz/ctf/tilt_estimator.cpp:276:19: @@ -8441,8 +8546,8 @@ 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/relion-3.1.3/src/image.h:455, - from /build/relion-3.1.3/src/jaz/motion/gp_motion_fit.h:24, - from /build/relion-3.1.3/src/jaz/motion/gp_motion_fit.cpp:21: + from /build/relion-3.1.3/src/jaz/motion/motion_estimator.h:24, + from /build/relion-3.1.3/src/jaz/motion/motion_estimator.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -8500,13 +8605,13 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 43%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_estimator.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_estimator.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/motion_estimator.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/motion_estimator.cpp.o -c /build/relion-3.1.3/src/jaz/motion/motion_estimator.cpp [ 43%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_helper.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/motion_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/motion_helper.cpp.o -c /build/relion-3.1.3/src/jaz/motion/motion_helper.cpp In file included from /build/relion-3.1.3/src/image.h:455, - from /build/relion-3.1.3/src/jaz/motion/motion_estimator.h:24, - from /build/relion-3.1.3/src/jaz/motion/motion_estimator.cpp:21: + from /build/relion-3.1.3/src/jaz/obs_model.h:24, + from /build/relion-3.1.3/src/ctf.h:50, + from /build/relion-3.1.3/src/jaz/motion/motion_helper.h:24, + from /build/relion-3.1.3/src/jaz/motion/motion_helper.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -8564,11 +8669,12 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +[ 44%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_param_estimator.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_param_estimator.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/motion_param_estimator.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/motion_param_estimator.cpp.o -c /build/relion-3.1.3/src/jaz/motion/motion_param_estimator.cpp In file included from /build/relion-3.1.3/src/image.h:455, - from /build/relion-3.1.3/src/jaz/obs_model.h:24, - from /build/relion-3.1.3/src/ctf.h:50, - from /build/relion-3.1.3/src/jaz/motion/motion_helper.h:24, - from /build/relion-3.1.3/src/jaz/motion/motion_helper.cpp:21: + from /build/relion-3.1.3/src/jaz/motion/alignment_set.h:24, + from /build/relion-3.1.3/src/jaz/motion/motion_param_estimator.h:24, + from /build/relion-3.1.3/src/jaz/motion/motion_param_estimator.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -8635,12 +8741,13 @@ | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const CDataSet&}; _Tp = CDataSet; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 -[ 44%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_param_estimator.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_param_estimator.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/motion_param_estimator.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/motion_param_estimator.cpp.o -c /build/relion-3.1.3/src/jaz/motion/motion_param_estimator.cpp +[ 44%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner.cpp.o -c /build/relion-3.1.3/src/jaz/motion/motion_refiner.cpp In file included from /build/relion-3.1.3/src/image.h:455, - from /build/relion-3.1.3/src/jaz/motion/alignment_set.h:24, - from /build/relion-3.1.3/src/jaz/motion/motion_param_estimator.h:24, - from /build/relion-3.1.3/src/jaz/motion/motion_param_estimator.cpp:21: + from /build/relion-3.1.3/src/jaz/obs_model.h:24, + from /build/relion-3.1.3/src/ctf.h:50, + from /build/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, + from /build/relion-3.1.3/src/jaz/motion/motion_refiner.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -8698,13 +8805,14 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 44%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner.cpp.o -c /build/relion-3.1.3/src/jaz/motion/motion_refiner.cpp +[ 45%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner_mpi.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner_mpi.cpp.o -c /build/relion-3.1.3/src/jaz/motion/motion_refiner_mpi.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-3.1.3/src/ctf.h:50, from /build/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, - from /build/relion-3.1.3/src/jaz/motion/motion_refiner.cpp:21: + from /build/relion-3.1.3/src/jaz/motion/motion_refiner_mpi.h:27, + from /build/relion-3.1.3/src/jaz/motion/motion_refiner_mpi.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -8811,8 +8919,6 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 45%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner_mpi.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner_mpi.cpp.o -c /build/relion-3.1.3/src/jaz/motion/motion_refiner_mpi.cpp [ 45%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/three_hyperparameter_fit.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/three_hyperparameter_fit.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/three_hyperparameter_fit.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/three_hyperparameter_fit.cpp.o -c /build/relion-3.1.3/src/jaz/motion/three_hyperparameter_fit.cpp In file included from /build/relion-3.1.3/src/image.h:455, @@ -8876,75 +8982,10 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -In file included from /build/relion-3.1.3/src/image.h:455, - from /build/relion-3.1.3/src/jaz/obs_model.h:24, - from /build/relion-3.1.3/src/ctf.h:50, - from /build/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, - from /build/relion-3.1.3/src/jaz/motion/motion_refiner_mpi.h:27, - from /build/relion-3.1.3/src/jaz/motion/motion_refiner_mpi.cpp:21: -/build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': -/build/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] - 43 | uint32 width, length; // apparent dimensions in the file - | ^~~~~ -In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31, - from /build/relion-3.1.3/src/image.h:57: -/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here - 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/relion-3.1.3/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations] - 43 | uint32 width, length; // apparent dimensions in the file - | ^~~~~~ -/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here - 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; - | ^~~~~~~~~~~~ -/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; - | ^~~~~~~~~~~~~ -/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; - | ^~~~~~~~~~~~~~ -/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] - 185 | uint32 cur_width, cur_length; - | ^~~~~~~~~ -/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here - 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] - 185 | uint32 cur_width, cur_length; - | ^~~~~~~~~~ -/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here - 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 186 | uint16 cur_sampleFormat, cur_bitsPerSample; - | ^~~~~~~~~~~~~~~~ -/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 186 | uint16 cur_sampleFormat, cur_bitsPerSample; - | ^~~~~~~~~~~~~~~~~ -/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ [ 45%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/two_hyperparameter_fit.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/two_hyperparameter_fit.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/two_hyperparameter_fit.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/two_hyperparameter_fit.cpp.o -c /build/relion-3.1.3/src/jaz/motion/two_hyperparameter_fit.cpp [ 46%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/math/Zernike.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/math/Zernike.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/math/Zernike.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/math/Zernike.cpp.o -c /build/relion-3.1.3/src/jaz/math/Zernike.cpp -[ 46%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/img_proc/color_helper.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/img_proc/color_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/img_proc/color_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/img_proc/color_helper.cpp.o -c /build/relion-3.1.3/src/jaz/img_proc/color_helper.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/motion/alignment_set.h:24, from /build/relion-3.1.3/src/jaz/motion/motion_param_estimator.h:24, @@ -9006,6 +9047,14 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +[ 46%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/img_proc/color_helper.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/img_proc/color_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/img_proc/color_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/img_proc/color_helper.cpp.o -c /build/relion-3.1.3/src/jaz/img_proc/color_helper.cpp +[ 46%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/img_proc/filter_helper.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/img_proc/filter_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/img_proc/filter_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/img_proc/filter_helper.cpp.o -c /build/relion-3.1.3/src/jaz/img_proc/filter_helper.cpp +[ 47%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/img_proc/image_op.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/img_proc/image_op.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/img_proc/image_op.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/img_proc/image_op.cpp.o -c /build/relion-3.1.3/src/jaz/img_proc/image_op.cpp +[ 47%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/backprojection_helper.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/backprojection_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/tomo/backprojection_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/tomo/backprojection_helper.cpp.o -c /build/relion-3.1.3/src/jaz/tomo/backprojection_helper.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/img_proc/color_helper.h:5, from /build/relion-3.1.3/src/jaz/img_proc/color_helper.cpp:1: @@ -9066,14 +9115,6 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 46%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/img_proc/filter_helper.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/img_proc/filter_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/img_proc/filter_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/img_proc/filter_helper.cpp.o -c /build/relion-3.1.3/src/jaz/img_proc/filter_helper.cpp -[ 47%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/img_proc/image_op.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/img_proc/image_op.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/img_proc/image_op.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/img_proc/image_op.cpp.o -c /build/relion-3.1.3/src/jaz/img_proc/image_op.cpp -[ 47%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/backprojection_helper.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/backprojection_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/tomo/backprojection_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/tomo/backprojection_helper.cpp.o -c /build/relion-3.1.3/src/jaz/tomo/backprojection_helper.cpp -[ 48%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/imod_helper.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/imod_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/tomo/imod_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/tomo/imod_helper.cpp.o -c /build/relion-3.1.3/src/jaz/tomo/imod_helper.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/img_proc/filter_helper.h:24, from /build/relion-3.1.3/src/jaz/img_proc/filter_helper.cpp:21: @@ -9134,6 +9175,8 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +[ 48%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/imod_helper.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/imod_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/tomo/imod_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/tomo/imod_helper.cpp.o -c /build/relion-3.1.3/src/jaz/tomo/imod_helper.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/tomo/backprojection_helper.h:24, from /build/relion-3.1.3/src/jaz/tomo/backprojection_helper.cpp:23: @@ -9194,6 +9237,8 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +[ 48%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/projection_helper.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/projection_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/tomo/projection_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/tomo/projection_helper.cpp.o -c /build/relion-3.1.3/src/jaz/tomo/projection_helper.cpp In file included from /usr/include/c++/12/vector:70, from /build/relion-3.1.3/src/jaz/tomo/imod_helper.h:24, from /build/relion-3.1.3/src/jaz/tomo/imod_helper.cpp:21: @@ -9207,8 +9252,8 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 48%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/projection_helper.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/projection_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/tomo/projection_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/tomo/projection_helper.cpp.o -c /build/relion-3.1.3/src/jaz/tomo/projection_helper.cpp +[ 48%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/tomo_stack.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/tomo_stack.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/tomo/tomo_stack.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/tomo/tomo_stack.cpp.o -c /build/relion-3.1.3/src/jaz/tomo/tomo_stack.cpp In file included from /usr/include/c++/12/vector:70, from /build/relion-3.1.3/src/jaz/tomo/projection_helper.h:24, from /build/relion-3.1.3/src/jaz/tomo/projection_helper.cpp:21: @@ -9224,6 +9269,13 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:70, + from /build/relion-3.1.3/src/funcs.h:56, + from /build/relion-3.1.3/src/image.h:58: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'static std::vector > ProjectionHelper::loadTiltProjectionsVol(std::string, double, double, double, double, double, double)' at /build/relion-3.1.3/src/jaz/tomo/projection_helper.cpp:105:25: @@ -9236,13 +9288,8 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:70, - from /build/relion-3.1.3/src/funcs.h:56, - from /build/relion-3.1.3/src/image.h:58: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gravis::t4Matrix}; _Tp = gravis::t4Matrix; _Alloc = std::allocator >]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'static std::vector > ProjectionHelper::loadTiltProjections(std::string, double, double)' at /build/relion-3.1.3/src/jaz/tomo/projection_helper.cpp:54:25: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 @@ -9254,8 +9301,6 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gravis::t4Matrix}; _Tp = gravis::t4Matrix; _Alloc = std::allocator >]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'static void BackprojectionHelper::backprojectRaw(const Image&, std::string, Volume&, Volume&, gravis::d3Vector, double, int)' at /build/relion-3.1.3/src/jaz/tomo/backprojection_helper.cpp:75:25: @@ -9268,8 +9313,8 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 48%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/tomo_stack.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/tomo_stack.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/tomo/tomo_stack.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/tomo/tomo_stack.cpp.o -c /build/relion-3.1.3/src/jaz/tomo/tomo_stack.cpp +[ 49%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/io/star_converter.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/io/star_converter.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/io/star_converter.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/io/star_converter.cpp.o -c /build/relion-3.1.3/src/jaz/io/star_converter.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/tomo/tomo_stack.h:25, from /build/relion-3.1.3/src/jaz/tomo/tomo_stack.cpp:21: @@ -9330,8 +9375,6 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 49%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/io/star_converter.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/io/star_converter.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/io/star_converter.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/io/star_converter.cpp.o -c /build/relion-3.1.3/src/jaz/io/star_converter.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/io/star_converter.h:5, from /build/relion-3.1.3/src/jaz/io/star_converter.cpp:1: @@ -9392,6 +9435,12 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +[ 49%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyev2.c.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyev2.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyev2.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyev2.c.o -c /build/relion-3.1.3/src/jaz/d3x3/dsyev2.c +[ 50%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevc3.c.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevc3.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevc3.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevc3.c.o -c /build/relion-3.1.3/src/jaz/d3x3/dsyevc3.c +[ 50%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevd3.c.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevd3.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevd3.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevd3.c.o -c /build/relion-3.1.3/src/jaz/d3x3/dsyevd3.c In file included from /usr/include/c++/12/vector:70, from /build/relion-3.1.3/src/funcs.h:56, from /build/relion-3.1.3/src/image.h:58: @@ -9399,6 +9448,8 @@ /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +[ 50%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevh3.c.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevh3.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevh3.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevh3.c.o -c /build/relion-3.1.3/src/jaz/d3x3/dsyevh3.c In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gravis::t2Vector}; _Tp = gravis::t2Vector; _Alloc = std::allocator >]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gravis::t2Vector; _Alloc = std::allocator >]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'std::vector > > TomoStack::loadFiducials(std::string, double)' at /build/relion-3.1.3/src/jaz/tomo/tomo_stack.cpp:340:28: @@ -9411,6 +9462,18 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 51%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevj3.c.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevj3.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevj3.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevj3.c.o -c /build/relion-3.1.3/src/jaz/d3x3/dsyevj3.c +[ 51%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevq3.c.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevq3.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevq3.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevq3.c.o -c /build/relion-3.1.3/src/jaz/d3x3/dsyevq3.c +[ 51%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevv3.c.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevv3.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevv3.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevv3.c.o -c /build/relion-3.1.3/src/jaz/d3x3/dsyevv3.c +[ 52%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsytrd3.c.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsytrd3.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsytrd3.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsytrd3.c.o -c /build/relion-3.1.3/src/jaz/d3x3/dsytrd3.c +[ 52%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/slvsec3.c.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/slvsec3.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/slvsec3.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/slvsec3.c.o -c /build/relion-3.1.3/src/jaz/d3x3/slvsec3.c +[ 53%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/lbfgs/lbfgs.c.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/lbfgs/lbfgs.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/lbfgs/lbfgs.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/lbfgs/lbfgs.c.o -c /build/relion-3.1.3/src/jaz/lbfgs/lbfgs.c In file included from /usr/include/c++/12/vector:70, from /build/relion-3.1.3/src/funcs.h:56, from /build/relion-3.1.3/src/image.h:58: @@ -9457,26 +9520,6 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 49%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyev2.c.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyev2.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyev2.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyev2.c.o -c /build/relion-3.1.3/src/jaz/d3x3/dsyev2.c -[ 50%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevc3.c.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevc3.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevc3.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevc3.c.o -c /build/relion-3.1.3/src/jaz/d3x3/dsyevc3.c -[ 50%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevd3.c.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevd3.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevd3.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevd3.c.o -c /build/relion-3.1.3/src/jaz/d3x3/dsyevd3.c -[ 50%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevh3.c.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevh3.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevh3.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevh3.c.o -c /build/relion-3.1.3/src/jaz/d3x3/dsyevh3.c -[ 51%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevj3.c.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevj3.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevj3.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevj3.c.o -c /build/relion-3.1.3/src/jaz/d3x3/dsyevj3.c -[ 51%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevq3.c.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevq3.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevq3.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevq3.c.o -c /build/relion-3.1.3/src/jaz/d3x3/dsyevq3.c -[ 51%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevv3.c.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevv3.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevv3.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevv3.c.o -c /build/relion-3.1.3/src/jaz/d3x3/dsyevv3.c -[ 52%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsytrd3.c.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsytrd3.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsytrd3.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsytrd3.c.o -c /build/relion-3.1.3/src/jaz/d3x3/dsytrd3.c -[ 52%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/slvsec3.c.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/slvsec3.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/slvsec3.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/slvsec3.c.o -c /build/relion-3.1.3/src/jaz/d3x3/slvsec3.c -[ 53%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/lbfgs/lbfgs.c.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/lbfgs/lbfgs.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/lbfgs/lbfgs.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/lbfgs/lbfgs.c.o -c /build/relion-3.1.3/src/jaz/lbfgs/lbfgs.c [ 53%] Linking CXX static library ../../lib/librelion_lib.a cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -P CMakeFiles/relion_lib.dir/cmake_clean_target.cmake cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/relion_lib.dir/link.txt --verbose=1 @@ -9487,27 +9530,35 @@ /usr/bin/make -f src/apps/CMakeFiles/relion_gui_lib.dir/build.make src/apps/CMakeFiles/relion_gui_lib.dir/depend /usr/bin/make -f src/apps/CMakeFiles/align_symmetry.dir/build.make src/apps/CMakeFiles/align_symmetry.dir/depend /usr/bin/make -f src/apps/CMakeFiles/autopick.dir/build.make src/apps/CMakeFiles/autopick.dir/depend +/usr/bin/make -f src/apps/CMakeFiles/autopick_mpi.dir/build.make src/apps/CMakeFiles/autopick_mpi.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/relion_gui_lib.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/relion-3.1.3/build' +cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/autopick.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/align_symmetry.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/relion-3.1.3/build' -cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/autopick.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/relion-3.1.3/build' +cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/autopick_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.3/build' /usr/bin/make -f src/apps/CMakeFiles/relion_gui_lib.dir/build.make src/apps/CMakeFiles/relion_gui_lib.dir/build -/usr/bin/make -f src/apps/CMakeFiles/align_symmetry.dir/build.make src/apps/CMakeFiles/align_symmetry.dir/build +make[4]: Entering directory '/build/relion-3.1.3/build' make[4]: Leaving directory '/build/relion-3.1.3/build' /usr/bin/make -f src/apps/CMakeFiles/autopick.dir/build.make src/apps/CMakeFiles/autopick.dir/build +make[4]: Leaving directory '/build/relion-3.1.3/build' make[4]: Entering directory '/build/relion-3.1.3/build' +/usr/bin/make -f src/apps/CMakeFiles/align_symmetry.dir/build.make src/apps/CMakeFiles/align_symmetry.dir/build +make[4]: Leaving directory '/build/relion-3.1.3/build' make[4]: Entering directory '/build/relion-3.1.3/build' +/usr/bin/make -f src/apps/CMakeFiles/autopick_mpi.dir/build.make src/apps/CMakeFiles/autopick_mpi.dir/build make[4]: Entering directory '/build/relion-3.1.3/build' [ 53%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/displayer.cpp.o -[ 53%] Building CXX object src/apps/CMakeFiles/align_symmetry.dir/align_symmetry.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/align_symmetry.dir/align_symmetry.cpp.o -MF CMakeFiles/align_symmetry.dir/align_symmetry.cpp.o.d -o CMakeFiles/align_symmetry.dir/align_symmetry.cpp.o -c /build/relion-3.1.3/src/apps/align_symmetry.cpp cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_gui_lib.dir/__/displayer.cpp.o -MF CMakeFiles/relion_gui_lib.dir/__/displayer.cpp.o.d -o CMakeFiles/relion_gui_lib.dir/__/displayer.cpp.o -c /build/relion-3.1.3/src/displayer.cpp [ 54%] Building CXX object src/apps/CMakeFiles/autopick.dir/autopick.cpp.o +[ 54%] Building CXX object src/apps/CMakeFiles/autopick_mpi.dir/autopick_mpi.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/autopick_mpi.dir/autopick_mpi.cpp.o -MF CMakeFiles/autopick_mpi.dir/autopick_mpi.cpp.o.d -o CMakeFiles/autopick_mpi.dir/autopick_mpi.cpp.o -c /build/relion-3.1.3/src/apps/autopick_mpi.cpp cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/autopick.dir/autopick.cpp.o -MF CMakeFiles/autopick.dir/autopick.cpp.o.d -o CMakeFiles/autopick.dir/autopick.cpp.o -c /build/relion-3.1.3/src/apps/autopick.cpp +[ 54%] Building CXX object src/apps/CMakeFiles/align_symmetry.dir/align_symmetry.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/align_symmetry.dir/align_symmetry.cpp.o -MF CMakeFiles/align_symmetry.dir/align_symmetry.cpp.o.d -o CMakeFiles/align_symmetry.dir/align_symmetry.cpp.o -c /build/relion-3.1.3/src/apps/align_symmetry.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/projector.h:25, from /build/relion-3.1.3/src/apps/align_symmetry.cpp:21: @@ -9688,19 +9739,6 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 54%] Linking CXX executable ../../bin/relion_autopick -cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/autopick.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/autopick.dir/autopick.cpp.o -o ../../bin/relion_autopick ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 54%] Built target autopick -/usr/bin/make -f src/apps/CMakeFiles/autopick_mpi.dir/build.make src/apps/CMakeFiles/autopick_mpi.dir/depend -make[4]: Entering directory '/build/relion-3.1.3/build' -cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/autopick_mpi.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/autopick_mpi.dir/build.make src/apps/CMakeFiles/autopick_mpi.dir/build -make[4]: Entering directory '/build/relion-3.1.3/build' -[ 54%] Building CXX object src/apps/CMakeFiles/autopick_mpi.dir/autopick_mpi.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/autopick_mpi.dir/autopick_mpi.cpp.o -MF CMakeFiles/autopick_mpi.dir/autopick_mpi.cpp.o.d -o CMakeFiles/autopick_mpi.dir/autopick_mpi.cpp.o -c /build/relion-3.1.3/src/apps/autopick_mpi.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/autopicker.h:10, from /build/relion-3.1.3/src/autopicker_mpi.h:12, @@ -9762,11 +9800,14 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +[ 54%] Linking CXX executable ../../bin/relion_autopick +cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/autopick.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/autopick.dir/autopick.cpp.o -o ../../bin/relion_autopick ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 55%] Linking CXX executable ../../bin/relion_autopick_mpi cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/autopick_mpi.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/autopick_mpi.dir/autopick_mpi.cpp.o -o ../../bin/relion_autopick_mpi ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 55%] Built target autopick_mpi +[ 55%] Built target autopick /usr/bin/make -f src/apps/CMakeFiles/convert_star.dir/build.make src/apps/CMakeFiles/convert_star.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/convert_star.dir/DependInfo.cmake --color= @@ -9775,6 +9816,16 @@ make[4]: Entering directory '/build/relion-3.1.3/build' [ 55%] Building CXX object src/apps/CMakeFiles/convert_star.dir/convert_star.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/convert_star.dir/convert_star.cpp.o -MF CMakeFiles/convert_star.dir/convert_star.cpp.o.d -o CMakeFiles/convert_star.dir/convert_star.cpp.o -c /build/relion-3.1.3/src/apps/convert_star.cpp +make[4]: Leaving directory '/build/relion-3.1.3/build' +[ 55%] Built target autopick_mpi +/usr/bin/make -f src/apps/CMakeFiles/convert_to_tiff.dir/build.make src/apps/CMakeFiles/convert_to_tiff.dir/depend +make[4]: Entering directory '/build/relion-3.1.3/build' +cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/convert_to_tiff.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/relion-3.1.3/build' +/usr/bin/make -f src/apps/CMakeFiles/convert_to_tiff.dir/build.make src/apps/CMakeFiles/convert_to_tiff.dir/build +make[4]: Entering directory '/build/relion-3.1.3/build' +[ 55%] Building CXX object src/apps/CMakeFiles/convert_to_tiff.dir/convert_to_tiff.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/convert_to_tiff.dir/convert_to_tiff.cpp.o -MF CMakeFiles/convert_to_tiff.dir/convert_to_tiff.cpp.o.d -o CMakeFiles/convert_to_tiff.dir/convert_to_tiff.cpp.o -c /build/relion-3.1.3/src/apps/convert_to_tiff.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/io/star_converter.h:5, from /build/relion-3.1.3/src/apps/convert_star.cpp:24: @@ -9835,32 +9886,6 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 56%] Linking CXX executable ../../bin/relion_convert_star -cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/convert_star.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/convert_star.dir/convert_star.cpp.o -o ../../bin/relion_convert_star ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 56%] Built target convert_star -/usr/bin/make -f src/apps/CMakeFiles/convert_to_tiff.dir/build.make src/apps/CMakeFiles/convert_to_tiff.dir/depend -make[4]: Entering directory '/build/relion-3.1.3/build' -cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/convert_to_tiff.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/convert_to_tiff.dir/build.make src/apps/CMakeFiles/convert_to_tiff.dir/build -make[4]: Entering directory '/build/relion-3.1.3/build' -[ 56%] Building CXX object src/apps/CMakeFiles/convert_to_tiff.dir/convert_to_tiff.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/convert_to_tiff.dir/convert_to_tiff.cpp.o -MF CMakeFiles/convert_to_tiff.dir/convert_to_tiff.cpp.o.d -o CMakeFiles/convert_to_tiff.dir/convert_to_tiff.cpp.o -c /build/relion-3.1.3/src/apps/convert_to_tiff.cpp -[ 56%] Linking CXX executable ../../bin/relion_align_symmetry -cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/align_symmetry.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/align_symmetry.dir/align_symmetry.cpp.o -o ../../bin/relion_align_symmetry ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 56%] Built target align_symmetry -/usr/bin/make -f src/apps/CMakeFiles/convert_to_tiff_mpi.dir/build.make src/apps/CMakeFiles/convert_to_tiff_mpi.dir/depend -make[4]: Entering directory '/build/relion-3.1.3/build' -cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/convert_to_tiff_mpi.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/convert_to_tiff_mpi.dir/build.make src/apps/CMakeFiles/convert_to_tiff_mpi.dir/build -make[4]: Entering directory '/build/relion-3.1.3/build' -[ 57%] Building CXX object src/apps/CMakeFiles/convert_to_tiff_mpi.dir/convert_to_tiff_mpi.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/convert_to_tiff_mpi.dir/convert_to_tiff_mpi.cpp.o -MF CMakeFiles/convert_to_tiff_mpi.dir/convert_to_tiff_mpi.cpp.o.d -o CMakeFiles/convert_to_tiff_mpi.dir/convert_to_tiff_mpi.cpp.o -c /build/relion-3.1.3/src/apps/convert_to_tiff_mpi.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/tiff_converter.h:24, from /build/relion-3.1.3/src/apps/convert_to_tiff.cpp:21: @@ -9921,11 +9946,24 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 57%] Linking CXX executable ../../bin/relion_convert_to_tiff +[ 55%] Linking CXX executable ../../bin/relion_convert_to_tiff cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/convert_to_tiff.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/convert_to_tiff.dir/convert_to_tiff.cpp.o -o ../../bin/relion_convert_to_tiff ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 57%] Built target convert_to_tiff +[ 55%] Built target convert_to_tiff +/usr/bin/make -f src/apps/CMakeFiles/convert_to_tiff_mpi.dir/build.make src/apps/CMakeFiles/convert_to_tiff_mpi.dir/depend +make[4]: Entering directory '/build/relion-3.1.3/build' +cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/convert_to_tiff_mpi.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/relion-3.1.3/build' +/usr/bin/make -f src/apps/CMakeFiles/convert_to_tiff_mpi.dir/build.make src/apps/CMakeFiles/convert_to_tiff_mpi.dir/build +make[4]: Entering directory '/build/relion-3.1.3/build' +[ 56%] Building CXX object src/apps/CMakeFiles/convert_to_tiff_mpi.dir/convert_to_tiff_mpi.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/convert_to_tiff_mpi.dir/convert_to_tiff_mpi.cpp.o -MF CMakeFiles/convert_to_tiff_mpi.dir/convert_to_tiff_mpi.cpp.o.d -o CMakeFiles/convert_to_tiff_mpi.dir/convert_to_tiff_mpi.cpp.o -c /build/relion-3.1.3/src/apps/convert_to_tiff_mpi.cpp +[ 57%] Linking CXX executable ../../bin/relion_convert_star +cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/convert_star.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/convert_star.dir/convert_star.cpp.o -o ../../bin/relion_convert_star ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +make[4]: Leaving directory '/build/relion-3.1.3/build' +[ 57%] Built target convert_star /usr/bin/make -f src/apps/CMakeFiles/ctf_mask_test.dir/build.make src/apps/CMakeFiles/ctf_mask_test.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/ctf_mask_test.dir/DependInfo.cmake --color= @@ -9994,19 +10032,6 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 57%] Linking CXX executable ../../bin/relion_convert_to_tiff_mpi -cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/convert_to_tiff_mpi.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/convert_to_tiff_mpi.dir/convert_to_tiff_mpi.cpp.o -o ../../bin/relion_convert_to_tiff_mpi ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 57%] Built target convert_to_tiff_mpi -/usr/bin/make -f src/apps/CMakeFiles/ctf_refine.dir/build.make src/apps/CMakeFiles/ctf_refine.dir/depend -make[4]: Entering directory '/build/relion-3.1.3/build' -cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/ctf_refine.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/ctf_refine.dir/build.make src/apps/CMakeFiles/ctf_refine.dir/build -make[4]: Entering directory '/build/relion-3.1.3/build' -[ 57%] Building CXX object src/apps/CMakeFiles/ctf_refine.dir/ctf_refine.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/ctf_refine.dir/ctf_refine.cpp.o -MF CMakeFiles/ctf_refine.dir/ctf_refine.cpp.o.d -o CMakeFiles/ctf_refine.dir/ctf_refine.cpp.o -c /build/relion-3.1.3/src/apps/ctf_refine.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/apps/ctf_mask_test.cpp:7: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': @@ -10066,6 +10091,19 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +[ 57%] Linking CXX executable ../../bin/relion_convert_to_tiff_mpi +cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/convert_to_tiff_mpi.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/convert_to_tiff_mpi.dir/convert_to_tiff_mpi.cpp.o -o ../../bin/relion_convert_to_tiff_mpi ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +make[4]: Leaving directory '/build/relion-3.1.3/build' +[ 57%] Built target convert_to_tiff_mpi +/usr/bin/make -f src/apps/CMakeFiles/ctf_refine.dir/build.make src/apps/CMakeFiles/ctf_refine.dir/depend +make[4]: Entering directory '/build/relion-3.1.3/build' +cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/ctf_refine.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/relion-3.1.3/build' +/usr/bin/make -f src/apps/CMakeFiles/ctf_refine.dir/build.make src/apps/CMakeFiles/ctf_refine.dir/build +make[4]: Entering directory '/build/relion-3.1.3/build' +[ 57%] Building CXX object src/apps/CMakeFiles/ctf_refine.dir/ctf_refine.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/ctf_refine.dir/ctf_refine.cpp.o -MF CMakeFiles/ctf_refine.dir/ctf_refine.cpp.o.d -o CMakeFiles/ctf_refine.dir/ctf_refine.cpp.o -c /build/relion-3.1.3/src/apps/ctf_refine.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, @@ -10127,109 +10165,37 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 58%] Linking CXX executable ../../bin/relion_ctf_refine -cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/ctf_refine.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ctf_refine.dir/ctf_refine.cpp.o -o ../../bin/relion_ctf_refine ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +[ 57%] Linking CXX executable ../../bin/relion_align_symmetry +cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/align_symmetry.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/align_symmetry.dir/align_symmetry.cpp.o -o ../../bin/relion_align_symmetry ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 58%] Built target ctf_refine +[ 57%] Built target align_symmetry /usr/bin/make -f src/apps/CMakeFiles/ctf_refine_mpi.dir/build.make src/apps/CMakeFiles/ctf_refine_mpi.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/ctf_refine_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.3/build' /usr/bin/make -f src/apps/CMakeFiles/ctf_refine_mpi.dir/build.make src/apps/CMakeFiles/ctf_refine_mpi.dir/build make[4]: Entering directory '/build/relion-3.1.3/build' -[ 58%] Building CXX object src/apps/CMakeFiles/ctf_refine_mpi.dir/ctf_refine_mpi.cpp.o +[ 57%] Building CXX object src/apps/CMakeFiles/ctf_refine_mpi.dir/ctf_refine_mpi.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/ctf_refine_mpi.dir/ctf_refine_mpi.cpp.o -MF CMakeFiles/ctf_refine_mpi.dir/ctf_refine_mpi.cpp.o.d -o CMakeFiles/ctf_refine_mpi.dir/ctf_refine_mpi.cpp.o -c /build/relion-3.1.3/src/apps/ctf_refine_mpi.cpp -In file included from /build/relion-3.1.3/src/image.h:455, - from /build/relion-3.1.3/src/jaz/obs_model.h:24, - from /build/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, - from /build/relion-3.1.3/src/jaz/ctf/ctf_refiner_mpi.h:26, - from /build/relion-3.1.3/src/apps/ctf_refine_mpi.cpp:21: -/build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': -/build/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] - 43 | uint32 width, length; // apparent dimensions in the file - | ^~~~~ -In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31, - from /build/relion-3.1.3/src/image.h:57: -/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here - 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/relion-3.1.3/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations] - 43 | uint32 width, length; // apparent dimensions in the file - | ^~~~~~ -/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here - 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; - | ^~~~~~~~~~~~ -/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; - | ^~~~~~~~~~~~~ -/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; - | ^~~~~~~~~~~~~~ -/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] - 185 | uint32 cur_width, cur_length; - | ^~~~~~~~~ -/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here - 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] - 185 | uint32 cur_width, cur_length; - | ^~~~~~~~~~ -/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here - 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 186 | uint16 cur_sampleFormat, cur_bitsPerSample; - | ^~~~~~~~~~~~~~~~ -/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 186 | uint16 cur_sampleFormat, cur_bitsPerSample; - | ^~~~~~~~~~~~~~~~~ -/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ -[ 59%] Linking CXX executable ../../bin/relion_ctf_mask_test -cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/ctf_mask_test.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ctf_mask_test.dir/ctf_mask_test.cpp.o -o ../../bin/relion_ctf_mask_test ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -[ 59%] Linking CXX executable ../../bin/relion_ctf_refine_mpi -cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/ctf_refine_mpi.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ctf_refine_mpi.dir/ctf_refine_mpi.cpp.o -o ../../bin/relion_ctf_refine_mpi ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +[ 58%] Linking CXX executable ../../bin/relion_ctf_refine +cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/ctf_refine.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ctf_refine.dir/ctf_refine.cpp.o -o ../../bin/relion_ctf_refine ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 59%] Built target ctf_mask_test +[ 58%] Built target ctf_refine /usr/bin/make -f src/apps/CMakeFiles/ctf_toolbox.dir/build.make src/apps/CMakeFiles/ctf_toolbox.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/ctf_toolbox.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.3/build' /usr/bin/make -f src/apps/CMakeFiles/ctf_toolbox.dir/build.make src/apps/CMakeFiles/ctf_toolbox.dir/build make[4]: Entering directory '/build/relion-3.1.3/build' -[ 60%] Building CXX object src/apps/CMakeFiles/ctf_toolbox.dir/ctf_toolbox.cpp.o +[ 59%] Building CXX object src/apps/CMakeFiles/ctf_toolbox.dir/ctf_toolbox.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/ctf_toolbox.dir/ctf_toolbox.cpp.o -MF CMakeFiles/ctf_toolbox.dir/ctf_toolbox.cpp.o.d -o CMakeFiles/ctf_toolbox.dir/ctf_toolbox.cpp.o -c /build/relion-3.1.3/src/apps/ctf_toolbox.cpp -make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 60%] Built target ctf_refine_mpi -/usr/bin/make -f src/apps/CMakeFiles/demodulate.dir/build.make src/apps/CMakeFiles/demodulate.dir/depend -make[4]: Entering directory '/build/relion-3.1.3/build' -cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/demodulate.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/demodulate.dir/build.make src/apps/CMakeFiles/demodulate.dir/build -make[4]: Entering directory '/build/relion-3.1.3/build' -[ 60%] Building CXX object src/apps/CMakeFiles/demodulate.dir/demodulate.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/demodulate.dir/demodulate.cpp.o -MF CMakeFiles/demodulate.dir/demodulate.cpp.o.d -o CMakeFiles/demodulate.dir/demodulate.cpp.o -c /build/relion-3.1.3/src/apps/demodulate.cpp In file included from /build/relion-3.1.3/src/image.h:455, - from /build/relion-3.1.3/src/apps/ctf_toolbox.cpp:21: + from /build/relion-3.1.3/src/jaz/obs_model.h:24, + from /build/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, + from /build/relion-3.1.3/src/jaz/ctf/ctf_refiner_mpi.h:26, + from /build/relion-3.1.3/src/apps/ctf_refine_mpi.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -10288,8 +10254,7 @@ 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-3.1.3/src/image.h:455, - from /build/relion-3.1.3/src/jaz/vtk_helper.h:24, - from /build/relion-3.1.3/src/apps/demodulate.cpp:1: + from /build/relion-3.1.3/src/apps/ctf_toolbox.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -10347,38 +10312,35 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 61%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/gui_entries.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_gui_lib.dir/__/gui_entries.cpp.o -MF CMakeFiles/relion_gui_lib.dir/__/gui_entries.cpp.o.d -o CMakeFiles/relion_gui_lib.dir/__/gui_entries.cpp.o -c /build/relion-3.1.3/src/gui_entries.cpp -[ 61%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/gui_jobwindow.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_gui_lib.dir/__/gui_jobwindow.cpp.o -MF CMakeFiles/relion_gui_lib.dir/__/gui_jobwindow.cpp.o.d -o CMakeFiles/relion_gui_lib.dir/__/gui_jobwindow.cpp.o -c /build/relion-3.1.3/src/gui_jobwindow.cpp -[ 61%] Linking CXX executable ../../bin/relion_ctf_toolbox -cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/ctf_toolbox.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ctf_toolbox.dir/ctf_toolbox.cpp.o -o ../../bin/relion_ctf_toolbox ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -[ 62%] Linking CXX executable ../../bin/relion_demodulate -cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/demodulate.dir/link.txt --verbose=1 +[ 59%] Linking CXX executable ../../bin/relion_ctf_refine_mpi +cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/ctf_refine_mpi.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ctf_refine_mpi.dir/ctf_refine_mpi.cpp.o -o ../../bin/relion_ctf_refine_mpi ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +[ 60%] Linking CXX executable ../../bin/relion_ctf_mask_test +cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/ctf_mask_test.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ctf_mask_test.dir/ctf_mask_test.cpp.o -o ../../bin/relion_ctf_mask_test ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/demodulate.dir/demodulate.cpp.o -o ../../bin/relion_demodulate ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -[ 62%] Built target ctf_toolbox +[ 60%] Built target ctf_mask_test +/usr/bin/make -f src/apps/CMakeFiles/demodulate.dir/build.make src/apps/CMakeFiles/demodulate.dir/depend +make[4]: Entering directory '/build/relion-3.1.3/build' +cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/demodulate.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/relion-3.1.3/build' +[ 60%] Built target ctf_refine_mpi /usr/bin/make -f src/apps/CMakeFiles/estimate_gain.dir/build.make src/apps/CMakeFiles/estimate_gain.dir/depend +make[4]: Leaving directory '/build/relion-3.1.3/build' +/usr/bin/make -f src/apps/CMakeFiles/demodulate.dir/build.make src/apps/CMakeFiles/demodulate.dir/build +make[4]: Entering directory '/build/relion-3.1.3/build' make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/estimate_gain.dir/DependInfo.cmake --color= +[ 60%] Building CXX object src/apps/CMakeFiles/demodulate.dir/demodulate.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/demodulate.dir/demodulate.cpp.o -MF CMakeFiles/demodulate.dir/demodulate.cpp.o.d -o CMakeFiles/demodulate.dir/demodulate.cpp.o -c /build/relion-3.1.3/src/apps/demodulate.cpp make[4]: Leaving directory '/build/relion-3.1.3/build' /usr/bin/make -f src/apps/CMakeFiles/estimate_gain.dir/build.make src/apps/CMakeFiles/estimate_gain.dir/build make[4]: Entering directory '/build/relion-3.1.3/build' -[ 62%] Building CXX object src/apps/CMakeFiles/estimate_gain.dir/estimate_gain.cpp.o +[ 60%] Building CXX object src/apps/CMakeFiles/estimate_gain.dir/estimate_gain.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/estimate_gain.dir/estimate_gain.cpp.o -MF CMakeFiles/estimate_gain.dir/estimate_gain.cpp.o.d -o CMakeFiles/estimate_gain.dir/estimate_gain.cpp.o -c /build/relion-3.1.3/src/apps/estimate_gain.cpp -make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 62%] Built target demodulate -/usr/bin/make -f src/apps/CMakeFiles/external_reconstruct.dir/build.make src/apps/CMakeFiles/external_reconstruct.dir/depend -make[4]: Entering directory '/build/relion-3.1.3/build' -cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/external_reconstruct.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/external_reconstruct.dir/build.make src/apps/CMakeFiles/external_reconstruct.dir/build -make[4]: Entering directory '/build/relion-3.1.3/build' -[ 63%] Building CXX object src/apps/CMakeFiles/external_reconstruct.dir/external_reconstruct.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/external_reconstruct.dir/external_reconstruct.cpp.o -MF CMakeFiles/external_reconstruct.dir/external_reconstruct.cpp.o.d -o CMakeFiles/external_reconstruct.dir/external_reconstruct.cpp.o -c /build/relion-3.1.3/src/apps/external_reconstruct.cpp In file included from /build/relion-3.1.3/src/image.h:455, - from /build/relion-3.1.3/src/apps/estimate_gain.cpp:27: + from /build/relion-3.1.3/src/jaz/vtk_helper.h:24, + from /build/relion-3.1.3/src/apps/demodulate.cpp:1: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -10437,7 +10399,7 @@ 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-3.1.3/src/image.h:455, - from /build/relion-3.1.3/src/apps/external_reconstruct.cpp:24: + from /build/relion-3.1.3/src/apps/estimate_gain.cpp:27: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -10495,13 +10457,21 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 63%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/gui_mainwindow.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_gui_lib.dir/__/gui_mainwindow.cpp.o -MF CMakeFiles/relion_gui_lib.dir/__/gui_mainwindow.cpp.o.d -o CMakeFiles/relion_gui_lib.dir/__/gui_mainwindow.cpp.o -c /build/relion-3.1.3/src/gui_mainwindow.cpp +[ 60%] Linking CXX executable ../../bin/relion_ctf_toolbox +cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/ctf_toolbox.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ctf_toolbox.dir/ctf_toolbox.cpp.o -o ../../bin/relion_ctf_toolbox ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +make[4]: Leaving directory '/build/relion-3.1.3/build' +[ 60%] Built target ctf_toolbox +/usr/bin/make -f src/apps/CMakeFiles/external_reconstruct.dir/build.make src/apps/CMakeFiles/external_reconstruct.dir/depend +make[4]: Entering directory '/build/relion-3.1.3/build' +cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/external_reconstruct.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/relion-3.1.3/build' +/usr/bin/make -f src/apps/CMakeFiles/external_reconstruct.dir/build.make src/apps/CMakeFiles/external_reconstruct.dir/build +make[4]: Entering directory '/build/relion-3.1.3/build' +[ 61%] Building CXX object src/apps/CMakeFiles/external_reconstruct.dir/external_reconstruct.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/external_reconstruct.dir/external_reconstruct.cpp.o -MF CMakeFiles/external_reconstruct.dir/external_reconstruct.cpp.o.d -o CMakeFiles/external_reconstruct.dir/external_reconstruct.cpp.o -c /build/relion-3.1.3/src/apps/external_reconstruct.cpp In file included from /build/relion-3.1.3/src/image.h:455, - from /build/relion-3.1.3/src/jaz/obs_model.h:24, - from /build/relion-3.1.3/src/scheduler.h:26, - from /build/relion-3.1.3/src/gui_mainwindow.h:28, - from /build/relion-3.1.3/src/gui_mainwindow.cpp:22: + from /build/relion-3.1.3/src/apps/external_reconstruct.cpp:24: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -10559,24 +10529,28 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 63%] Linking CXX executable ../../bin/relion_estimate_gain +[ 62%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/gui_entries.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_gui_lib.dir/__/gui_entries.cpp.o -MF CMakeFiles/relion_gui_lib.dir/__/gui_entries.cpp.o.d -o CMakeFiles/relion_gui_lib.dir/__/gui_entries.cpp.o -c /build/relion-3.1.3/src/gui_entries.cpp +[ 62%] Linking CXX executable ../../bin/relion_estimate_gain cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/estimate_gain.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/estimate_gain.dir/estimate_gain.cpp.o -o ../../bin/relion_estimate_gain ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 63%] Built target estimate_gain +[ 62%] Built target estimate_gain /usr/bin/make -f src/apps/CMakeFiles/find_tiltpairs.dir/build.make src/apps/CMakeFiles/find_tiltpairs.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/find_tiltpairs.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.3/build' /usr/bin/make -f src/apps/CMakeFiles/find_tiltpairs.dir/build.make src/apps/CMakeFiles/find_tiltpairs.dir/build make[4]: Entering directory '/build/relion-3.1.3/build' -[ 63%] Building CXX object src/apps/CMakeFiles/find_tiltpairs.dir/find_tiltpairs.cpp.o +[ 62%] Building CXX object src/apps/CMakeFiles/find_tiltpairs.dir/find_tiltpairs.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/find_tiltpairs.dir/find_tiltpairs.cpp.o -MF CMakeFiles/find_tiltpairs.dir/find_tiltpairs.cpp.o.d -o CMakeFiles/find_tiltpairs.dir/find_tiltpairs.cpp.o -c /build/relion-3.1.3/src/apps/find_tiltpairs.cpp -[ 63%] Linking CXX executable ../../bin/relion_external_reconstruct -cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/external_reconstruct.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/external_reconstruct.dir/external_reconstruct.cpp.o -o ../../bin/relion_external_reconstruct ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +[ 62%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/gui_jobwindow.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_gui_lib.dir/__/gui_jobwindow.cpp.o -MF CMakeFiles/relion_gui_lib.dir/__/gui_jobwindow.cpp.o.d -o CMakeFiles/relion_gui_lib.dir/__/gui_jobwindow.cpp.o -c /build/relion-3.1.3/src/gui_jobwindow.cpp +[ 63%] Linking CXX executable ../../bin/relion_demodulate +cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/demodulate.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/demodulate.dir/demodulate.cpp.o -o ../../bin/relion_demodulate ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 63%] Built target external_reconstruct +[ 63%] Built target demodulate /usr/bin/make -f src/apps/CMakeFiles/flex_analyse.dir/build.make src/apps/CMakeFiles/flex_analyse.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/flex_analyse.dir/DependInfo.cmake --color= @@ -10646,32 +10620,35 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 64%] Linking CXX executable ../../bin/relion_flex_analyse -cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/flex_analyse.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/flex_analyse.dir/flex_analyse.cpp.o -o ../../bin/relion_flex_analyse ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -[ 65%] Linking CXX executable ../../bin/relion_find_tiltpairs +[ 63%] Linking CXX executable ../../bin/relion_external_reconstruct +cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/external_reconstruct.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/external_reconstruct.dir/external_reconstruct.cpp.o -o ../../bin/relion_external_reconstruct ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +[ 64%] Linking CXX executable ../../bin/relion_find_tiltpairs cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/find_tiltpairs.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/find_tiltpairs.dir/find_tiltpairs.cpp.o -o ../../bin/relion_find_tiltpairs ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 65%] Built target flex_analyse +[ 64%] Built target find_tiltpairs /usr/bin/make -f src/apps/CMakeFiles/flex_analyse_mpi.dir/build.make src/apps/CMakeFiles/flex_analyse_mpi.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/flex_analyse_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.3/build' /usr/bin/make -f src/apps/CMakeFiles/flex_analyse_mpi.dir/build.make src/apps/CMakeFiles/flex_analyse_mpi.dir/build make[4]: Entering directory '/build/relion-3.1.3/build' -[ 65%] Building CXX object src/apps/CMakeFiles/flex_analyse_mpi.dir/flex_analyse_mpi.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/flex_analyse_mpi.dir/flex_analyse_mpi.cpp.o -MF CMakeFiles/flex_analyse_mpi.dir/flex_analyse_mpi.cpp.o.d -o CMakeFiles/flex_analyse_mpi.dir/flex_analyse_mpi.cpp.o -c /build/relion-3.1.3/src/apps/flex_analyse_mpi.cpp make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 65%] Built target find_tiltpairs +[ 64%] Building CXX object src/apps/CMakeFiles/flex_analyse_mpi.dir/flex_analyse_mpi.cpp.o +[ 64%] Built target external_reconstruct +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/flex_analyse_mpi.dir/flex_analyse_mpi.cpp.o -MF CMakeFiles/flex_analyse_mpi.dir/flex_analyse_mpi.cpp.o.d -o CMakeFiles/flex_analyse_mpi.dir/flex_analyse_mpi.cpp.o -c /build/relion-3.1.3/src/apps/flex_analyse_mpi.cpp /usr/bin/make -f src/apps/CMakeFiles/helix_inimodel2d.dir/build.make src/apps/CMakeFiles/helix_inimodel2d.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/helix_inimodel2d.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.3/build' /usr/bin/make -f src/apps/CMakeFiles/helix_inimodel2d.dir/build.make src/apps/CMakeFiles/helix_inimodel2d.dir/build make[4]: Entering directory '/build/relion-3.1.3/build' -[ 66%] Building CXX object src/apps/CMakeFiles/helix_inimodel2d.dir/helix_inimodel2d.cpp.o +[ 65%] Building CXX object src/apps/CMakeFiles/helix_inimodel2d.dir/helix_inimodel2d.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/helix_inimodel2d.dir/helix_inimodel2d.cpp.o -MF CMakeFiles/helix_inimodel2d.dir/helix_inimodel2d.cpp.o.d -o CMakeFiles/helix_inimodel2d.dir/helix_inimodel2d.cpp.o -c /build/relion-3.1.3/src/apps/helix_inimodel2d.cpp +[ 66%] Linking CXX executable ../../bin/relion_flex_analyse +cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/flex_analyse.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/flex_analyse.dir/flex_analyse.cpp.o -o ../../bin/relion_flex_analyse ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/exp_model.h:24, from /build/relion-3.1.3/src/apps/../flex_analyser.h:24, @@ -10793,11 +10770,8 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 66%] Linking CXX executable ../../bin/relion_helix_inimodel2d -cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/helix_inimodel2d.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/helix_inimodel2d.dir/helix_inimodel2d.cpp.o -o ../../bin/relion_helix_inimodel2d ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 66%] Built target helix_inimodel2d +[ 66%] Built target flex_analyse /usr/bin/make -f src/apps/CMakeFiles/helix_toolbox.dir/build.make src/apps/CMakeFiles/helix_toolbox.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/helix_toolbox.dir/DependInfo.cmake --color= @@ -10806,6 +10780,19 @@ make[4]: Entering directory '/build/relion-3.1.3/build' [ 67%] Building CXX object src/apps/CMakeFiles/helix_toolbox.dir/helix_toolbox.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/helix_toolbox.dir/helix_toolbox.cpp.o -MF CMakeFiles/helix_toolbox.dir/helix_toolbox.cpp.o.d -o CMakeFiles/helix_toolbox.dir/helix_toolbox.cpp.o -c /build/relion-3.1.3/src/apps/helix_toolbox.cpp +[ 67%] Linking CXX executable ../../bin/relion_helix_inimodel2d +cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/helix_inimodel2d.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/helix_inimodel2d.dir/helix_inimodel2d.cpp.o -o ../../bin/relion_helix_inimodel2d ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +make[4]: Leaving directory '/build/relion-3.1.3/build' +[ 67%] Built target helix_inimodel2d +/usr/bin/make -f src/apps/CMakeFiles/image_handler.dir/build.make src/apps/CMakeFiles/image_handler.dir/depend +make[4]: Entering directory '/build/relion-3.1.3/build' +cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/image_handler.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/relion-3.1.3/build' +/usr/bin/make -f src/apps/CMakeFiles/image_handler.dir/build.make src/apps/CMakeFiles/image_handler.dir/build +make[4]: Entering directory '/build/relion-3.1.3/build' +[ 67%] Building CXX object src/apps/CMakeFiles/image_handler.dir/image_handler.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/image_handler.dir/image_handler.cpp.o -MF CMakeFiles/image_handler.dir/image_handler.cpp.o.d -o CMakeFiles/image_handler.dir/image_handler.cpp.o -c /build/relion-3.1.3/src/apps/image_handler.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/helix.h:30, from /build/relion-3.1.3/src/apps/helix_toolbox.cpp:22: @@ -10866,19 +10853,6 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 67%] Linking CXX executable ../../bin/relion_flex_analyse_mpi -cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/flex_analyse_mpi.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/flex_analyse_mpi.dir/flex_analyse_mpi.cpp.o -o ../../bin/relion_flex_analyse_mpi ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 67%] Built target flex_analyse_mpi -/usr/bin/make -f src/apps/CMakeFiles/image_handler.dir/build.make src/apps/CMakeFiles/image_handler.dir/depend -make[4]: Entering directory '/build/relion-3.1.3/build' -cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/image_handler.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/image_handler.dir/build.make src/apps/CMakeFiles/image_handler.dir/build -make[4]: Entering directory '/build/relion-3.1.3/build' -[ 67%] Building CXX object src/apps/CMakeFiles/image_handler.dir/image_handler.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/image_handler.dir/image_handler.cpp.o -MF CMakeFiles/image_handler.dir/image_handler.cpp.o.d -o CMakeFiles/image_handler.dir/image_handler.cpp.o -c /build/relion-3.1.3/src/apps/image_handler.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/apps/image_handler.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': @@ -10938,12 +10912,26 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 68%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/manualpicker.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_gui_lib.dir/__/manualpicker.cpp.o -MF CMakeFiles/relion_gui_lib.dir/__/manualpicker.cpp.o.d -o CMakeFiles/relion_gui_lib.dir/__/manualpicker.cpp.o -c /build/relion-3.1.3/src/manualpicker.cpp +[ 67%] Linking CXX executable ../../bin/relion_flex_analyse_mpi +cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/flex_analyse_mpi.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/flex_analyse_mpi.dir/flex_analyse_mpi.cpp.o -o ../../bin/relion_flex_analyse_mpi ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +[ 67%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/gui_mainwindow.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_gui_lib.dir/__/gui_mainwindow.cpp.o -MF CMakeFiles/relion_gui_lib.dir/__/gui_mainwindow.cpp.o.d -o CMakeFiles/relion_gui_lib.dir/__/gui_mainwindow.cpp.o -c /build/relion-3.1.3/src/gui_mainwindow.cpp +make[4]: Leaving directory '/build/relion-3.1.3/build' +[ 67%] Built target flex_analyse_mpi +/usr/bin/make -f src/apps/CMakeFiles/import.dir/build.make src/apps/CMakeFiles/import.dir/depend +make[4]: Entering directory '/build/relion-3.1.3/build' +cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/import.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/relion-3.1.3/build' +/usr/bin/make -f src/apps/CMakeFiles/import.dir/build.make src/apps/CMakeFiles/import.dir/build +make[4]: Entering directory '/build/relion-3.1.3/build' +[ 67%] Building CXX object src/apps/CMakeFiles/import.dir/import.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/import.dir/import.cpp.o -MF CMakeFiles/import.dir/import.cpp.o.d -o CMakeFiles/import.dir/import.cpp.o -c /build/relion-3.1.3/src/apps/import.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/obs_model.h:24, - from /build/relion-3.1.3/src/manualpicker.h:43, - from /build/relion-3.1.3/src/manualpicker.cpp:21: + from /build/relion-3.1.3/src/scheduler.h:26, + from /build/relion-3.1.3/src/gui_mainwindow.h:28, + from /build/relion-3.1.3/src/gui_mainwindow.cpp:22: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -11001,21 +10989,6 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 68%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/cxxutils.cc.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/cxxutils.cc.o -MF CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/cxxutils.cc.o.d -o CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/cxxutils.cc.o -c /build/relion-3.1.3/src/Healpix_2.15a/cxxutils.cc -[ 68%] Linking CXX executable ../../bin/relion_helix_toolbox -cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/helix_toolbox.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/helix_toolbox.dir/helix_toolbox.cpp.o -o ../../bin/relion_helix_toolbox ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 68%] Built target helix_toolbox -/usr/bin/make -f src/apps/CMakeFiles/import.dir/build.make src/apps/CMakeFiles/import.dir/depend -make[4]: Entering directory '/build/relion-3.1.3/build' -cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/import.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/import.dir/build.make src/apps/CMakeFiles/import.dir/build -make[4]: Entering directory '/build/relion-3.1.3/build' -[ 68%] Building CXX object src/apps/CMakeFiles/import.dir/import.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/import.dir/import.cpp.o -MF CMakeFiles/import.dir/import.cpp.o.d -o CMakeFiles/import.dir/import.cpp.o -c /build/relion-3.1.3/src/apps/import.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-3.1.3/src/apps/import.cpp:22: @@ -11076,36 +11049,19 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 69%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/healpix_base.cc.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/healpix_base.cc.o -MF CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/healpix_base.cc.o.d -o CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/healpix_base.cc.o -c /build/relion-3.1.3/src/Healpix_2.15a/healpix_base.cc -[ 70%] Linking CXX executable ../../bin/relion_image_handler -cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/image_handler.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/image_handler.dir/image_handler.cpp.o -o ../../bin/relion_image_handler ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +[ 67%] Linking CXX executable ../../bin/relion_import +cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/import.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/import.dir/import.cpp.o -o ../../bin/relion_import ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 70%] Built target image_handler +[ 67%] Built target import /usr/bin/make -f src/apps/CMakeFiles/localsym.dir/build.make src/apps/CMakeFiles/localsym.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/localsym.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.3/build' /usr/bin/make -f src/apps/CMakeFiles/localsym.dir/build.make src/apps/CMakeFiles/localsym.dir/build make[4]: Entering directory '/build/relion-3.1.3/build' -[ 71%] Building CXX object src/apps/CMakeFiles/localsym.dir/localsym.cpp.o +[ 68%] Building CXX object src/apps/CMakeFiles/localsym.dir/localsym.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/localsym.dir/localsym.cpp.o -MF CMakeFiles/localsym.dir/localsym.cpp.o.d -o CMakeFiles/localsym.dir/localsym.cpp.o -c /build/relion-3.1.3/src/apps/localsym.cpp -[ 71%] Linking CXX static library ../../lib/librelion_gui_lib.a -cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -P CMakeFiles/relion_gui_lib.dir/cmake_clean_target.cmake -cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/relion_gui_lib.dir/link.txt --verbose=1 -/usr/bin/ar qc ../../lib/librelion_gui_lib.a CMakeFiles/relion_gui_lib.dir/__/displayer.cpp.o CMakeFiles/relion_gui_lib.dir/__/gui_entries.cpp.o CMakeFiles/relion_gui_lib.dir/__/gui_jobwindow.cpp.o CMakeFiles/relion_gui_lib.dir/__/gui_mainwindow.cpp.o CMakeFiles/relion_gui_lib.dir/__/manualpicker.cpp.o CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/cxxutils.cc.o CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/healpix_base.cc.o -/usr/bin/ranlib ../../lib/librelion_gui_lib.a -make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 71%] Built target relion_gui_lib -/usr/bin/make -f src/apps/CMakeFiles/localsym_mpi.dir/build.make src/apps/CMakeFiles/localsym_mpi.dir/depend -make[4]: Entering directory '/build/relion-3.1.3/build' -cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/localsym_mpi.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/localsym_mpi.dir/build.make src/apps/CMakeFiles/localsym_mpi.dir/build -make[4]: Entering directory '/build/relion-3.1.3/build' -[ 72%] Building CXX object src/apps/CMakeFiles/localsym_mpi.dir/localsym_mpi.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/localsym_mpi.dir/localsym_mpi.cpp.o -MF CMakeFiles/localsym_mpi.dir/localsym_mpi.cpp.o.d -o CMakeFiles/localsym_mpi.dir/localsym_mpi.cpp.o -c /build/relion-3.1.3/src/apps/localsym_mpi.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/local_symmetry.h:30, from /build/relion-3.1.3/src/apps/localsym.cpp:21: @@ -11166,12 +11122,19 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 72%] Linking CXX executable ../../bin/relion_import -cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/import.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/import.dir/import.cpp.o -o ../../bin/relion_import ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -[ 72%] Linking CXX executable ../../bin/relion_localsym +[ 68%] Linking CXX executable ../../bin/relion_localsym cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/localsym.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/localsym.dir/localsym.cpp.o -o ../../bin/relion_localsym ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +make[4]: Leaving directory '/build/relion-3.1.3/build' +[ 68%] Built target localsym +/usr/bin/make -f src/apps/CMakeFiles/localsym_mpi.dir/build.make src/apps/CMakeFiles/localsym_mpi.dir/depend +make[4]: Entering directory '/build/relion-3.1.3/build' +cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/localsym_mpi.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/relion-3.1.3/build' +/usr/bin/make -f src/apps/CMakeFiles/localsym_mpi.dir/build.make src/apps/CMakeFiles/localsym_mpi.dir/build +make[4]: Entering directory '/build/relion-3.1.3/build' +[ 69%] Building CXX object src/apps/CMakeFiles/localsym_mpi.dir/localsym_mpi.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/localsym_mpi.dir/localsym_mpi.cpp.o -MF CMakeFiles/localsym_mpi.dir/localsym_mpi.cpp.o.d -o CMakeFiles/localsym_mpi.dir/localsym_mpi.cpp.o -c /build/relion-3.1.3/src/apps/localsym_mpi.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/local_symmetry.h:30, from /build/relion-3.1.3/src/local_symmetry_mpi.h:5, @@ -11233,103 +11196,21 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 72%] Built target import -/usr/bin/make -f src/apps/CMakeFiles/relion.dir/build.make src/apps/CMakeFiles/relion.dir/depend -make[4]: Entering directory '/build/relion-3.1.3/build' -cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/relion.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/relion.dir/build.make src/apps/CMakeFiles/relion.dir/build -make[4]: Entering directory '/build/relion-3.1.3/build' -[ 72%] Building CXX object src/apps/CMakeFiles/relion.dir/maingui.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion.dir/maingui.cpp.o -MF CMakeFiles/relion.dir/maingui.cpp.o.d -o CMakeFiles/relion.dir/maingui.cpp.o -c /build/relion-3.1.3/src/apps/maingui.cpp -make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 72%] Built target localsym -/usr/bin/make -f src/apps/CMakeFiles/manualpick.dir/build.make src/apps/CMakeFiles/manualpick.dir/depend -make[4]: Entering directory '/build/relion-3.1.3/build' -cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/manualpick.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/manualpick.dir/build.make src/apps/CMakeFiles/manualpick.dir/build -make[4]: Entering directory '/build/relion-3.1.3/build' -[ 72%] Building CXX object src/apps/CMakeFiles/manualpick.dir/manualpick.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/manualpick.dir/manualpick.cpp.o -MF CMakeFiles/manualpick.dir/manualpick.cpp.o.d -o CMakeFiles/manualpick.dir/manualpick.cpp.o -c /build/relion-3.1.3/src/apps/manualpick.cpp -[ 72%] Linking CXX executable ../../bin/relion_localsym_mpi +[ 69%] Linking CXX executable ../../bin/relion_localsym_mpi cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/localsym_mpi.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/localsym_mpi.dir/localsym_mpi.cpp.o -o ../../bin/relion_localsym_mpi ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 72%] Built target localsym_mpi +[ 69%] Built target localsym_mpi /usr/bin/make -f src/apps/CMakeFiles/mask_create.dir/build.make src/apps/CMakeFiles/mask_create.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/mask_create.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.3/build' /usr/bin/make -f src/apps/CMakeFiles/mask_create.dir/build.make src/apps/CMakeFiles/mask_create.dir/build make[4]: Entering directory '/build/relion-3.1.3/build' -[ 72%] Building CXX object src/apps/CMakeFiles/mask_create.dir/mask_create.cpp.o +[ 69%] Building CXX object src/apps/CMakeFiles/mask_create.dir/mask_create.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/mask_create.dir/mask_create.cpp.o -MF CMakeFiles/mask_create.dir/mask_create.cpp.o.d -o CMakeFiles/mask_create.dir/mask_create.cpp.o -c /build/relion-3.1.3/src/apps/mask_create.cpp In file included from /build/relion-3.1.3/src/image.h:455, - from /build/relion-3.1.3/src/jaz/obs_model.h:24, - from /build/relion-3.1.3/src/scheduler.h:26, - from /build/relion-3.1.3/src/gui_mainwindow.h:28, - from /build/relion-3.1.3/src/apps/maingui.cpp:23: -/build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': -/build/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] - 43 | uint32 width, length; // apparent dimensions in the file - | ^~~~~ -In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31, - from /build/relion-3.1.3/src/image.h:57: -/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here - 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/relion-3.1.3/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations] - 43 | uint32 width, length; // apparent dimensions in the file - | ^~~~~~ -/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here - 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; - | ^~~~~~~~~~~~ -/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; - | ^~~~~~~~~~~~~ -/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; - | ^~~~~~~~~~~~~~ -/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] - 185 | uint32 cur_width, cur_length; - | ^~~~~~~~~ -/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here - 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] - 185 | uint32 cur_width, cur_length; - | ^~~~~~~~~~ -/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here - 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 186 | uint16 cur_sampleFormat, cur_bitsPerSample; - | ^~~~~~~~~~~~~~~~ -/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 186 | uint16 cur_sampleFormat, cur_bitsPerSample; - | ^~~~~~~~~~~~~~~~~ -/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ -In file included from /build/relion-3.1.3/src/image.h:455, - from /build/relion-3.1.3/src/apps/manualpick.cpp:25: + from /build/relion-3.1.3/src/apps/mask_create.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -11387,8 +11268,38 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +[ 69%] Linking CXX executable ../../bin/relion_helix_toolbox +cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/helix_toolbox.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/helix_toolbox.dir/helix_toolbox.cpp.o -o ../../bin/relion_helix_toolbox ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +[ 70%] Linking CXX executable ../../bin/relion_image_handler +cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/image_handler.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/image_handler.dir/image_handler.cpp.o -o ../../bin/relion_image_handler ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +[ 71%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/manualpicker.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_gui_lib.dir/__/manualpicker.cpp.o -MF CMakeFiles/relion_gui_lib.dir/__/manualpicker.cpp.o.d -o CMakeFiles/relion_gui_lib.dir/__/manualpicker.cpp.o -c /build/relion-3.1.3/src/manualpicker.cpp +make[4]: Leaving directory '/build/relion-3.1.3/build' +[ 71%] Built target helix_toolbox +/usr/bin/make -f src/apps/CMakeFiles/merge_particles.dir/build.make src/apps/CMakeFiles/merge_particles.dir/depend +make[4]: Entering directory '/build/relion-3.1.3/build' +cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/merge_particles.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/relion-3.1.3/build' +/usr/bin/make -f src/apps/CMakeFiles/merge_particles.dir/build.make src/apps/CMakeFiles/merge_particles.dir/build +make[4]: Entering directory '/build/relion-3.1.3/build' +[ 72%] Building CXX object src/apps/CMakeFiles/merge_particles.dir/merge_particles.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/merge_particles.dir/merge_particles.cpp.o -MF CMakeFiles/merge_particles.dir/merge_particles.cpp.o.d -o CMakeFiles/merge_particles.dir/merge_particles.cpp.o -c /build/relion-3.1.3/src/apps/merge_particles.cpp +make[4]: Leaving directory '/build/relion-3.1.3/build' +[ 72%] Built target image_handler +/usr/bin/make -f src/apps/CMakeFiles/motion_refine.dir/build.make src/apps/CMakeFiles/motion_refine.dir/depend +make[4]: Entering directory '/build/relion-3.1.3/build' +cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/motion_refine.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/relion-3.1.3/build' +/usr/bin/make -f src/apps/CMakeFiles/motion_refine.dir/build.make src/apps/CMakeFiles/motion_refine.dir/build +make[4]: Entering directory '/build/relion-3.1.3/build' +[ 73%] Building CXX object src/apps/CMakeFiles/motion_refine.dir/motion_refine.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/motion_refine.dir/motion_refine.cpp.o -MF CMakeFiles/motion_refine.dir/motion_refine.cpp.o.d -o CMakeFiles/motion_refine.dir/motion_refine.cpp.o -c /build/relion-3.1.3/src/apps/motion_refine.cpp In file included from /build/relion-3.1.3/src/image.h:455, - from /build/relion-3.1.3/src/apps/mask_create.cpp:21: + from /build/relion-3.1.3/src/jaz/obs_model.h:24, + from /build/relion-3.1.3/src/manualpicker.h:43, + from /build/relion-3.1.3/src/manualpicker.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -11446,32 +11357,6 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 73%] Linking CXX executable ../../bin/relion_manualpick -cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/manualpick.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/manualpick.dir/manualpick.cpp.o -o ../../bin/relion_manualpick ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gui_lib.a /usr/lib/arm-linux-gnueabihf/libfltk_images.so /usr/lib/arm-linux-gnueabihf/libfltk_forms.so /usr/lib/arm-linux-gnueabihf/libfltk.so -lX11 -lm -ltiff ../../lib/librelion_lib.a -lfftw3f -lfftw3 -ltiff -[ 74%] Linking CXX executable ../../bin/relion -cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/relion.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/relion.dir/maingui.cpp.o -o ../../bin/relion ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gui_lib.a /usr/lib/arm-linux-gnueabihf/libfltk_images.so /usr/lib/arm-linux-gnueabihf/libfltk_forms.so /usr/lib/arm-linux-gnueabihf/libfltk.so -lX11 -lm -ltiff ../../lib/librelion_lib.a -lfftw3f -lfftw3 -ltiff -make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 74%] Built target manualpick -/usr/bin/make -f src/apps/CMakeFiles/merge_particles.dir/build.make src/apps/CMakeFiles/merge_particles.dir/depend -make[4]: Entering directory '/build/relion-3.1.3/build' -cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/merge_particles.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/merge_particles.dir/build.make src/apps/CMakeFiles/merge_particles.dir/build -make[4]: Entering directory '/build/relion-3.1.3/build' -[ 75%] Building CXX object src/apps/CMakeFiles/merge_particles.dir/merge_particles.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/merge_particles.dir/merge_particles.cpp.o -MF CMakeFiles/merge_particles.dir/merge_particles.cpp.o.d -o CMakeFiles/merge_particles.dir/merge_particles.cpp.o -c /build/relion-3.1.3/src/apps/merge_particles.cpp -make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 75%] Built target relion -/usr/bin/make -f src/apps/CMakeFiles/motion_refine.dir/build.make src/apps/CMakeFiles/motion_refine.dir/depend -make[4]: Entering directory '/build/relion-3.1.3/build' -cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/motion_refine.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/motion_refine.dir/build.make src/apps/CMakeFiles/motion_refine.dir/build -make[4]: Entering directory '/build/relion-3.1.3/build' -[ 76%] Building CXX object src/apps/CMakeFiles/motion_refine.dir/motion_refine.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/motion_refine.dir/motion_refine.cpp.o -MF CMakeFiles/motion_refine.dir/motion_refine.cpp.o.d -o CMakeFiles/motion_refine.dir/motion_refine.cpp.o -c /build/relion-3.1.3/src/apps/motion_refine.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/io/star_converter.h:5, from /build/relion-3.1.3/src/apps/merge_particles.cpp:2: @@ -11594,20 +11479,20 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 76%] Linking CXX executable ../../bin/relion_merge_particles +[ 73%] Linking CXX executable ../../bin/relion_merge_particles cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/merge_particles.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/merge_particles.dir/merge_particles.cpp.o -o ../../bin/relion_merge_particles ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 76%] Built target merge_particles +[ 73%] Built target merge_particles /usr/bin/make -f src/apps/CMakeFiles/motion_refine_mpi.dir/build.make src/apps/CMakeFiles/motion_refine_mpi.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/motion_refine_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.3/build' /usr/bin/make -f src/apps/CMakeFiles/motion_refine_mpi.dir/build.make src/apps/CMakeFiles/motion_refine_mpi.dir/build make[4]: Entering directory '/build/relion-3.1.3/build' -[ 76%] Building CXX object src/apps/CMakeFiles/motion_refine_mpi.dir/motion_refine_mpi.cpp.o +[ 73%] Building CXX object src/apps/CMakeFiles/motion_refine_mpi.dir/motion_refine_mpi.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/motion_refine_mpi.dir/motion_refine_mpi.cpp.o -MF CMakeFiles/motion_refine_mpi.dir/motion_refine_mpi.cpp.o.d -o CMakeFiles/motion_refine_mpi.dir/motion_refine_mpi.cpp.o -c /build/relion-3.1.3/src/apps/motion_refine_mpi.cpp -[ 76%] Linking CXX executable ../../bin/relion_motion_refine +[ 73%] Linking CXX executable ../../bin/relion_motion_refine cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/motion_refine.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/motion_refine.dir/motion_refine.cpp.o -o ../../bin/relion_motion_refine ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In file included from /build/relion-3.1.3/src/image.h:455, @@ -11674,18 +11559,15 @@ 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 76%] Built target motion_refine +[ 73%] Built target motion_refine /usr/bin/make -f src/apps/CMakeFiles/mrc2vtk.dir/build.make src/apps/CMakeFiles/mrc2vtk.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/mrc2vtk.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.3/build' /usr/bin/make -f src/apps/CMakeFiles/mrc2vtk.dir/build.make src/apps/CMakeFiles/mrc2vtk.dir/build make[4]: Entering directory '/build/relion-3.1.3/build' -[ 76%] Building CXX object src/apps/CMakeFiles/mrc2vtk.dir/mrc2vtk.cpp.o +[ 73%] Building CXX object src/apps/CMakeFiles/mrc2vtk.dir/mrc2vtk.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/mrc2vtk.dir/mrc2vtk.cpp.o -MF CMakeFiles/mrc2vtk.dir/mrc2vtk.cpp.o.d -o CMakeFiles/mrc2vtk.dir/mrc2vtk.cpp.o -c /build/relion-3.1.3/src/apps/mrc2vtk.cpp -[ 76%] Linking CXX executable ../../bin/relion_mask_create -cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/mask_create.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/mask_create.dir/mask_create.cpp.o -o ../../bin/relion_mask_create ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/apps/mrc2vtk.cpp:1: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': @@ -11745,28 +11627,31 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 77%] Linking CXX executable ../../bin/relion_motion_refine_mpi +[ 73%] Linking CXX executable ../../bin/relion_mask_create +cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/mask_create.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/mask_create.dir/mask_create.cpp.o -o ../../bin/relion_mask_create ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +[ 74%] Linking CXX executable ../../bin/relion_motion_refine_mpi cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/motion_refine_mpi.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/motion_refine_mpi.dir/motion_refine_mpi.cpp.o -o ../../bin/relion_motion_refine_mpi ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 77%] Built target mask_create +[ 74%] Built target mask_create /usr/bin/make -f src/apps/CMakeFiles/particle_FCC.dir/build.make src/apps/CMakeFiles/particle_FCC.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/particle_FCC.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.3/build' /usr/bin/make -f src/apps/CMakeFiles/particle_FCC.dir/build.make src/apps/CMakeFiles/particle_FCC.dir/build make[4]: Entering directory '/build/relion-3.1.3/build' -[ 78%] Building CXX object src/apps/CMakeFiles/particle_FCC.dir/particle_FCC.cpp.o +[ 75%] Building CXX object src/apps/CMakeFiles/particle_FCC.dir/particle_FCC.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/particle_FCC.dir/particle_FCC.cpp.o -MF CMakeFiles/particle_FCC.dir/particle_FCC.cpp.o.d -o CMakeFiles/particle_FCC.dir/particle_FCC.cpp.o -c /build/relion-3.1.3/src/apps/particle_FCC.cpp make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 78%] Built target motion_refine_mpi +[ 75%] Built target motion_refine_mpi /usr/bin/make -f src/apps/CMakeFiles/particle_reposition.dir/build.make src/apps/CMakeFiles/particle_reposition.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/particle_reposition.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.3/build' /usr/bin/make -f src/apps/CMakeFiles/particle_reposition.dir/build.make src/apps/CMakeFiles/particle_reposition.dir/build make[4]: Entering directory '/build/relion-3.1.3/build' -[ 79%] Building CXX object src/apps/CMakeFiles/particle_reposition.dir/particle_reposition.cpp.o +[ 76%] Building CXX object src/apps/CMakeFiles/particle_reposition.dir/particle_reposition.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/particle_reposition.dir/particle_reposition.cpp.o -MF CMakeFiles/particle_reposition.dir/particle_reposition.cpp.o.d -o CMakeFiles/particle_reposition.dir/particle_reposition.cpp.o -c /build/relion-3.1.3/src/apps/particle_reposition.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/apps/particle_FCC.cpp:7: @@ -11889,32 +11774,34 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 79%] Linking CXX executable ../../bin/relion_mrc2vtk +[ 76%] Linking CXX executable ../../bin/relion_particle_FCC +cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/particle_FCC.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/particle_FCC.dir/particle_FCC.cpp.o -o ../../bin/relion_particle_FCC ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +[ 76%] Linking CXX executable ../../bin/relion_mrc2vtk cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/mrc2vtk.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/mrc2vtk.dir/mrc2vtk.cpp.o -o ../../bin/relion_mrc2vtk ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 79%] Built target mrc2vtk +[ 76%] Built target mrc2vtk /usr/bin/make -f src/apps/CMakeFiles/particle_select.dir/build.make src/apps/CMakeFiles/particle_select.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/particle_select.dir/DependInfo.cmake --color= -[ 79%] Linking CXX executable ../../bin/relion_particle_FCC -cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/particle_FCC.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/relion-3.1.3/build' /usr/bin/make -f src/apps/CMakeFiles/particle_select.dir/build.make src/apps/CMakeFiles/particle_select.dir/build make[4]: Entering directory '/build/relion-3.1.3/build' -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/particle_FCC.dir/particle_FCC.cpp.o -o ../../bin/relion_particle_FCC ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -[ 79%] Building CXX object src/apps/CMakeFiles/particle_select.dir/particle_select.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/particle_select.dir/particle_select.cpp.o -MF CMakeFiles/particle_select.dir/particle_select.cpp.o.d -o CMakeFiles/particle_select.dir/particle_select.cpp.o -c /build/relion-3.1.3/src/apps/particle_select.cpp make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 79%] Built target particle_FCC +[ 76%] Building CXX object src/apps/CMakeFiles/particle_select.dir/particle_select.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/particle_select.dir/particle_select.cpp.o -MF CMakeFiles/particle_select.dir/particle_select.cpp.o.d -o CMakeFiles/particle_select.dir/particle_select.cpp.o -c /build/relion-3.1.3/src/apps/particle_select.cpp +[ 76%] Built target particle_FCC /usr/bin/make -f src/apps/CMakeFiles/particle_subtract.dir/build.make src/apps/CMakeFiles/particle_subtract.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/particle_subtract.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.3/build' /usr/bin/make -f src/apps/CMakeFiles/particle_subtract.dir/build.make src/apps/CMakeFiles/particle_subtract.dir/build make[4]: Entering directory '/build/relion-3.1.3/build' -[ 79%] Building CXX object src/apps/CMakeFiles/particle_subtract.dir/particle_subtract.cpp.o +[ 76%] Building CXX object src/apps/CMakeFiles/particle_subtract.dir/particle_subtract.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/particle_subtract.dir/particle_subtract.cpp.o -MF CMakeFiles/particle_subtract.dir/particle_subtract.cpp.o.d -o CMakeFiles/particle_subtract.dir/particle_subtract.cpp.o -c /build/relion-3.1.3/src/apps/particle_subtract.cpp +[ 76%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/cxxutils.cc.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/cxxutils.cc.o -MF CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/cxxutils.cc.o.d -o CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/cxxutils.cc.o -c /build/relion-3.1.3/src/Healpix_2.15a/cxxutils.cc In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-3.1.3/src/ctf.h:50, @@ -12040,19 +11927,24 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 80%] Linking CXX executable ../../bin/relion_particle_select +[ 77%] Linking CXX executable ../../bin/relion_particle_select cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/particle_select.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/particle_select.dir/particle_select.cpp.o -o ../../bin/relion_particle_select ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 80%] Built target particle_select +[ 77%] Built target particle_select /usr/bin/make -f src/apps/CMakeFiles/particle_subtract_mpi.dir/build.make src/apps/CMakeFiles/particle_subtract_mpi.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/particle_subtract_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.3/build' /usr/bin/make -f src/apps/CMakeFiles/particle_subtract_mpi.dir/build.make src/apps/CMakeFiles/particle_subtract_mpi.dir/build make[4]: Entering directory '/build/relion-3.1.3/build' -[ 80%] Building CXX object src/apps/CMakeFiles/particle_subtract_mpi.dir/particle_subtract_mpi.cpp.o +[ 77%] Building CXX object src/apps/CMakeFiles/particle_subtract_mpi.dir/particle_subtract_mpi.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/particle_subtract_mpi.dir/particle_subtract_mpi.cpp.o -MF CMakeFiles/particle_subtract_mpi.dir/particle_subtract_mpi.cpp.o.d -o CMakeFiles/particle_subtract_mpi.dir/particle_subtract_mpi.cpp.o -c /build/relion-3.1.3/src/apps/particle_subtract_mpi.cpp +[ 78%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/healpix_base.cc.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/healpix_base.cc.o -MF CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/healpix_base.cc.o.d -o CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/healpix_base.cc.o -c /build/relion-3.1.3/src/Healpix_2.15a/healpix_base.cc +[ 79%] Linking CXX executable ../../bin/relion_particle_subtract +cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/particle_subtract.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/particle_subtract.dir/particle_subtract.cpp.o -o ../../bin/relion_particle_subtract ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/projector.h:25, from /build/relion-3.1.3/src/ml_model.h:23, @@ -12116,19 +12008,21 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 81%] Linking CXX executable ../../bin/relion_particle_subtract -cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/particle_subtract.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/particle_subtract.dir/particle_subtract.cpp.o -o ../../bin/relion_particle_subtract ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 81%] Built target particle_subtract +[ 79%] Built target particle_subtract /usr/bin/make -f src/apps/CMakeFiles/particle_symmetry_expand.dir/build.make src/apps/CMakeFiles/particle_symmetry_expand.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/particle_symmetry_expand.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.3/build' /usr/bin/make -f src/apps/CMakeFiles/particle_symmetry_expand.dir/build.make src/apps/CMakeFiles/particle_symmetry_expand.dir/build make[4]: Entering directory '/build/relion-3.1.3/build' -[ 82%] Building CXX object src/apps/CMakeFiles/particle_symmetry_expand.dir/particle_symmetry_expand.cpp.o +[ 80%] Building CXX object src/apps/CMakeFiles/particle_symmetry_expand.dir/particle_symmetry_expand.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/particle_symmetry_expand.dir/particle_symmetry_expand.cpp.o -MF CMakeFiles/particle_symmetry_expand.dir/particle_symmetry_expand.cpp.o.d -o CMakeFiles/particle_symmetry_expand.dir/particle_symmetry_expand.cpp.o -c /build/relion-3.1.3/src/apps/particle_symmetry_expand.cpp +[ 80%] Linking CXX static library ../../lib/librelion_gui_lib.a +cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -P CMakeFiles/relion_gui_lib.dir/cmake_clean_target.cmake +cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/relion_gui_lib.dir/link.txt --verbose=1 +/usr/bin/ar qc ../../lib/librelion_gui_lib.a CMakeFiles/relion_gui_lib.dir/__/displayer.cpp.o CMakeFiles/relion_gui_lib.dir/__/gui_entries.cpp.o CMakeFiles/relion_gui_lib.dir/__/gui_jobwindow.cpp.o CMakeFiles/relion_gui_lib.dir/__/gui_mainwindow.cpp.o CMakeFiles/relion_gui_lib.dir/__/manualpicker.cpp.o CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/cxxutils.cc.o CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/healpix_base.cc.o +/usr/bin/ranlib ../../lib/librelion_gui_lib.a In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-3.1.3/src/apps/particle_symmetry_expand.cpp:26: @@ -12189,47 +12083,143 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 82%] Linking CXX executable ../../bin/relion_particle_subtract_mpi -cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/particle_subtract_mpi.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/particle_subtract_mpi.dir/particle_subtract_mpi.cpp.o -o ../../bin/relion_particle_subtract_mpi ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 82%] Built target particle_subtract_mpi +[ 80%] Built target relion_gui_lib /usr/bin/make -f src/apps/CMakeFiles/pipeliner.dir/build.make src/apps/CMakeFiles/pipeliner.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/pipeliner.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.3/build' /usr/bin/make -f src/apps/CMakeFiles/pipeliner.dir/build.make src/apps/CMakeFiles/pipeliner.dir/build make[4]: Entering directory '/build/relion-3.1.3/build' -[ 82%] Building CXX object src/apps/CMakeFiles/pipeliner.dir/pipeliner.cpp.o +[ 80%] Building CXX object src/apps/CMakeFiles/pipeliner.dir/pipeliner.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/pipeliner.dir/pipeliner.cpp.o -MF CMakeFiles/pipeliner.dir/pipeliner.cpp.o.d -o CMakeFiles/pipeliner.dir/pipeliner.cpp.o -c /build/relion-3.1.3/src/apps/pipeliner.cpp -[ 82%] Linking CXX executable ../../bin/relion_particle_symmetry_expand +[ 80%] Linking CXX executable ../../bin/relion_particle_symmetry_expand cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/particle_symmetry_expand.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/particle_symmetry_expand.dir/particle_symmetry_expand.cpp.o -o ../../bin/relion_particle_symmetry_expand ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +[ 80%] Linking CXX executable ../../bin/relion_particle_subtract_mpi +cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/particle_subtract_mpi.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/particle_subtract_mpi.dir/particle_subtract_mpi.cpp.o -o ../../bin/relion_particle_subtract_mpi ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 82%] Built target particle_symmetry_expand +[ 80%] Built target particle_symmetry_expand /usr/bin/make -f src/apps/CMakeFiles/plot_delocalisation.dir/build.make src/apps/CMakeFiles/plot_delocalisation.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/plot_delocalisation.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.3/build' /usr/bin/make -f src/apps/CMakeFiles/plot_delocalisation.dir/build.make src/apps/CMakeFiles/plot_delocalisation.dir/build make[4]: Entering directory '/build/relion-3.1.3/build' -[ 82%] Building CXX object src/apps/CMakeFiles/plot_delocalisation.dir/plot_delocalisation.cpp.o +[ 80%] Building CXX object src/apps/CMakeFiles/plot_delocalisation.dir/plot_delocalisation.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/plot_delocalisation.dir/plot_delocalisation.cpp.o -MF CMakeFiles/plot_delocalisation.dir/plot_delocalisation.cpp.o.d -o CMakeFiles/plot_delocalisation.dir/plot_delocalisation.cpp.o -c /build/relion-3.1.3/src/apps/plot_delocalisation.cpp -[ 82%] Linking CXX executable ../../bin/relion_particle_reposition +[ 80%] Linking CXX executable ../../bin/relion_particle_reposition cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/particle_reposition.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/particle_reposition.dir/particle_reposition.cpp.o -o ../../bin/relion_particle_reposition ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +In file included from /build/relion-3.1.3/src/image.h:455, + from /build/relion-3.1.3/src/apps/plot_delocalisation.cpp:7: +/build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': +/build/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 43 | uint32 width, length; // apparent dimensions in the file + | ^~~~~ +In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31, + from /build/relion-3.1.3/src/image.h:57: +/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here + 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 43 | uint32 width, length; // apparent dimensions in the file + | ^~~~~~ +/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here + 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; + | ^~~~~~~~~~~~ +/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; + | ^~~~~~~~~~~~~ +/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; + | ^~~~~~~~~~~~~~ +/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 185 | uint32 cur_width, cur_length; + | ^~~~~~~~~ +/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here + 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 185 | uint32 cur_width, cur_length; + | ^~~~~~~~~~ +/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here + 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 186 | uint16 cur_sampleFormat, cur_bitsPerSample; + | ^~~~~~~~~~~~~~~~ +/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 186 | uint16 cur_sampleFormat, cur_bitsPerSample; + | ^~~~~~~~~~~~~~~~~ +/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 82%] Built target particle_reposition +[ 80%] Built target particle_subtract_mpi /usr/bin/make -f src/apps/CMakeFiles/postprocess.dir/build.make src/apps/CMakeFiles/postprocess.dir/depend +make[4]: Leaving directory '/build/relion-3.1.3/build' make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/postprocess.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.3/build' /usr/bin/make -f src/apps/CMakeFiles/postprocess.dir/build.make src/apps/CMakeFiles/postprocess.dir/build make[4]: Entering directory '/build/relion-3.1.3/build' -[ 82%] Building CXX object src/apps/CMakeFiles/postprocess.dir/postprocess.cpp.o +In file included from /usr/include/c++/12/vector:70, + from /build/relion-3.1.3/src/args.h:52, + from /build/relion-3.1.3/src/apps/plot_delocalisation.cpp:6: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const CDataPoint&}; _Tp = CDataPoint; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +[ 80%] Building CXX object src/apps/CMakeFiles/postprocess.dir/postprocess.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/postprocess.dir/postprocess.cpp.o -MF CMakeFiles/postprocess.dir/postprocess.cpp.o.d -o CMakeFiles/postprocess.dir/postprocess.cpp.o -c /build/relion-3.1.3/src/apps/postprocess.cpp +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const CDataSet&}; _Tp = CDataSet; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 +[ 80%] Built target particle_reposition +/usr/bin/make -f src/apps/CMakeFiles/postprocess_mpi.dir/build.make src/apps/CMakeFiles/postprocess_mpi.dir/depend +make[4]: Entering directory '/build/relion-3.1.3/build' +cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/postprocess_mpi.dir/DependInfo.cmake --color= +In file included from /usr/include/c++/12/vector:64: +/usr/include/c++/12/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataSet; _Alloc = std::allocator]': +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +make[4]: Leaving directory '/build/relion-3.1.3/build' +/usr/bin/make -f src/apps/CMakeFiles/postprocess_mpi.dir/build.make src/apps/CMakeFiles/postprocess_mpi.dir/build +make[4]: Entering directory '/build/relion-3.1.3/build' +[ 81%] Building CXX object src/apps/CMakeFiles/postprocess_mpi.dir/postprocess_mpi.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/postprocess_mpi.dir/postprocess_mpi.cpp.o -MF CMakeFiles/postprocess_mpi.dir/postprocess_mpi.cpp.o.d -o CMakeFiles/postprocess_mpi.dir/postprocess_mpi.cpp.o -c /build/relion-3.1.3/src/apps/postprocess_mpi.cpp +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator]', + inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /build/relion-3.1.3/src/CPlot2D.h:168:33, + inlined from 'int main(int, char**)' at /build/relion-3.1.3/src/apps/plot_delocalisation.cpp:207:23: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator]', + inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /build/relion-3.1.3/src/CPlot2D.h:168:33, + inlined from 'int main(int, char**)' at /build/relion-3.1.3/src/apps/plot_delocalisation.cpp:213:21: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /build/relion-3.1.3/src/image.h:455, - from /build/relion-3.1.3/src/apps/plot_delocalisation.cpp:7: + from /build/relion-3.1.3/src/postprocessing.h:24, + from /build/relion-3.1.3/src/apps/postprocess.cpp:20: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -12289,7 +12279,7 @@ | ^~~~~~ In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/postprocessing.h:24, - from /build/relion-3.1.3/src/apps/postprocess.cpp:20: + from /build/relion-3.1.3/src/apps/postprocess_mpi.cpp:20: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -12347,74 +12337,61 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -In file included from /usr/include/c++/12/vector:70, - from /build/relion-3.1.3/src/args.h:52, - from /build/relion-3.1.3/src/apps/plot_delocalisation.cpp:6: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const CDataPoint&}; _Tp = CDataPoint; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const CDataSet&}; _Tp = CDataSet; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 -In file included from /usr/include/c++/12/vector:64: -/usr/include/c++/12/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataSet; _Alloc = std::allocator]': -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator]', - inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /build/relion-3.1.3/src/CPlot2D.h:168:33, - inlined from 'int main(int, char**)' at /build/relion-3.1.3/src/apps/plot_delocalisation.cpp:207:23: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator]', - inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /build/relion-3.1.3/src/CPlot2D.h:168:33, - inlined from 'int main(int, char**)' at /build/relion-3.1.3/src/apps/plot_delocalisation.cpp:213:21: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 83%] Linking CXX executable ../../bin/relion_pipeliner +[ 82%] Linking CXX executable ../../bin/relion_pipeliner cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/pipeliner.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/pipeliner.dir/pipeliner.cpp.o -o ../../bin/relion_pipeliner ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -[ 83%] Linking CXX executable ../../bin/relion_postprocess +[ 82%] Linking CXX executable ../../bin/relion_postprocess cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/postprocess.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/postprocess.dir/postprocess.cpp.o -o ../../bin/relion_postprocess ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +[ 82%] Linking CXX executable ../../bin/relion_postprocess_mpi +cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/postprocess_mpi.dir/link.txt --verbose=1 +[ 83%] Linking CXX executable ../../bin/relion_plot_delocalisation +cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/plot_delocalisation.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/postprocess_mpi.dir/postprocess_mpi.cpp.o -o ../../bin/relion_postprocess_mpi ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/plot_delocalisation.dir/plot_delocalisation.cpp.o -o ../../bin/relion_plot_delocalisation ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' [ 83%] Built target pipeliner -/usr/bin/make -f src/apps/CMakeFiles/postprocess_mpi.dir/build.make src/apps/CMakeFiles/postprocess_mpi.dir/depend -make[4]: Entering directory '/build/relion-3.1.3/build' -cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 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src/apps/CMakeFiles/postprocess_mpi.dir/postprocess_mpi.cpp.o -MF CMakeFiles/postprocess_mpi.dir/postprocess_mpi.cpp.o.d -o CMakeFiles/postprocess_mpi.dir/postprocess_mpi.cpp.o -c /build/relion-3.1.3/src/apps/postprocess_mpi.cpp -make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 84%] Built target postprocess /usr/bin/make -f src/apps/CMakeFiles/prepare_subtomo.dir/build.make src/apps/CMakeFiles/prepare_subtomo.dir/depend +make[4]: Leaving directory '/build/relion-3.1.3/build' make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/prepare_subtomo.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.3/build' +make[4]: Leaving directory '/build/relion-3.1.3/build' +[ 83%] Built target plot_delocalisation /usr/bin/make -f src/apps/CMakeFiles/prepare_subtomo.dir/build.make src/apps/CMakeFiles/prepare_subtomo.dir/build make[4]: Entering directory '/build/relion-3.1.3/build' -[ 84%] Building CXX object src/apps/CMakeFiles/prepare_subtomo.dir/prepare_subtomo.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/prepare_subtomo.dir/prepare_subtomo.cpp.o -MF CMakeFiles/prepare_subtomo.dir/prepare_subtomo.cpp.o.d -o CMakeFiles/prepare_subtomo.dir/prepare_subtomo.cpp.o -c /build/relion-3.1.3/src/apps/prepare_subtomo.cpp -[ 85%] Linking CXX executable ../../bin/relion_plot_delocalisation -cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/plot_delocalisation.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/plot_delocalisation.dir/plot_delocalisation.cpp.o -o ../../bin/relion_plot_delocalisation ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 85%] Built target plot_delocalisation /usr/bin/make -f src/apps/CMakeFiles/preprocess.dir/build.make src/apps/CMakeFiles/preprocess.dir/depend +[ 83%] Built target postprocess_mpi +/usr/bin/make -f src/apps/CMakeFiles/preprocess_mpi.dir/build.make src/apps/CMakeFiles/preprocess_mpi.dir/depend +[ 83%] Building CXX object src/apps/CMakeFiles/prepare_subtomo.dir/prepare_subtomo.cpp.o make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/preprocess.dir/DependInfo.cmake --color= +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/prepare_subtomo.dir/prepare_subtomo.cpp.o -MF CMakeFiles/prepare_subtomo.dir/prepare_subtomo.cpp.o.d -o CMakeFiles/prepare_subtomo.dir/prepare_subtomo.cpp.o -c /build/relion-3.1.3/src/apps/prepare_subtomo.cpp +make[4]: Entering directory '/build/relion-3.1.3/build' +cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/preprocess_mpi.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/relion-3.1.3/build' make[4]: Leaving directory '/build/relion-3.1.3/build' /usr/bin/make -f src/apps/CMakeFiles/preprocess.dir/build.make src/apps/CMakeFiles/preprocess.dir/build make[4]: Entering directory '/build/relion-3.1.3/build' -[ 85%] Building CXX object src/apps/CMakeFiles/preprocess.dir/preprocess.cpp.o +[ 83%] Built target postprocess +/usr/bin/make -f src/apps/CMakeFiles/project.dir/build.make src/apps/CMakeFiles/project.dir/depend +make[4]: Leaving directory '/build/relion-3.1.3/build' +/usr/bin/make -f src/apps/CMakeFiles/preprocess_mpi.dir/build.make src/apps/CMakeFiles/preprocess_mpi.dir/build +[ 83%] Building CXX object src/apps/CMakeFiles/preprocess.dir/preprocess.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/preprocess.dir/preprocess.cpp.o -MF CMakeFiles/preprocess.dir/preprocess.cpp.o.d -o CMakeFiles/preprocess.dir/preprocess.cpp.o -c /build/relion-3.1.3/src/apps/preprocess.cpp +make[4]: Entering directory '/build/relion-3.1.3/build' +make[4]: Entering directory '/build/relion-3.1.3/build' +cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/project.dir/DependInfo.cmake --color= +[ 83%] Building CXX object src/apps/CMakeFiles/preprocess_mpi.dir/preprocess_mpi.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/preprocess_mpi.dir/preprocess_mpi.cpp.o -MF CMakeFiles/preprocess_mpi.dir/preprocess_mpi.cpp.o.d -o CMakeFiles/preprocess_mpi.dir/preprocess_mpi.cpp.o -c /build/relion-3.1.3/src/apps/preprocess_mpi.cpp +make[4]: Leaving directory '/build/relion-3.1.3/build' +/usr/bin/make -f src/apps/CMakeFiles/project.dir/build.make src/apps/CMakeFiles/project.dir/build +make[4]: Entering directory '/build/relion-3.1.3/build' +[ 84%] Building CXX object src/apps/CMakeFiles/project.dir/project.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/project.dir/project.cpp.o -MF CMakeFiles/project.dir/project.cpp.o.d -o CMakeFiles/project.dir/project.cpp.o -c /build/relion-3.1.3/src/apps/project.cpp In file included from /build/relion-3.1.3/src/image.h:455, - from /build/relion-3.1.3/src/postprocessing.h:24, - from /build/relion-3.1.3/src/apps/postprocess_mpi.cpp:20: + from /build/relion-3.1.3/src/preprocessing.h:29, + from /build/relion-3.1.3/src/apps/preprocess.cpp:20: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -12533,8 +12510,69 @@ 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-3.1.3/src/image.h:455, + from /build/relion-3.1.3/src/projector.h:25, + from /build/relion-3.1.3/src/apps/project.cpp:21: +/build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': +/build/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 43 | uint32 width, length; // apparent dimensions in the file + | ^~~~~ +In file included from /usr/include/arm-linux-gnueabihf/tiffio.h:31, + from /build/relion-3.1.3/src/image.h:57: +/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here + 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 43 | uint32 width, length; // apparent dimensions in the file + | ^~~~~~ +/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here + 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; + | ^~~~~~~~~~~~ +/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; + | ^~~~~~~~~~~~~ +/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; + | ^~~~~~~~~~~~~~ +/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 185 | uint32 cur_width, cur_length; + | ^~~~~~~~~ +/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here + 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 185 | uint32 cur_width, cur_length; + | ^~~~~~~~~~ +/usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here + 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 186 | uint16 cur_sampleFormat, cur_bitsPerSample; + | ^~~~~~~~~~~~~~~~ +/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 186 | uint16 cur_sampleFormat, cur_bitsPerSample; + | ^~~~~~~~~~~~~~~~~ +/usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ +In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/preprocessing.h:29, - from /build/relion-3.1.3/src/apps/preprocess.cpp:20: + from /build/relion-3.1.3/src/preprocessing_mpi.h:24, + from /build/relion-3.1.3/src/apps/preprocess_mpi.cpp:20: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -12592,36 +12630,37 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 85%] Linking CXX executable ../../bin/relion_postprocess_mpi -cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/postprocess_mpi.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/postprocess_mpi.dir/postprocess_mpi.cpp.o -o ../../bin/relion_postprocess_mpi ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +[ 85%] Linking CXX executable ../../bin/relion_preprocess +cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/preprocess.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/preprocess.dir/preprocess.cpp.o -o ../../bin/relion_preprocess ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +[ 85%] Linking CXX executable ../../bin/relion_preprocess_mpi +cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/preprocess_mpi.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/preprocess_mpi.dir/preprocess_mpi.cpp.o -o ../../bin/relion_preprocess_mpi ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 85%] Built target postprocess_mpi -/usr/bin/make -f src/apps/CMakeFiles/preprocess_mpi.dir/build.make src/apps/CMakeFiles/preprocess_mpi.dir/depend +[ 85%] Built target preprocess +/usr/bin/make -f src/apps/CMakeFiles/reconstruct.dir/build.make src/apps/CMakeFiles/reconstruct.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' -cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/preprocess_mpi.dir/DependInfo.cmake --color= +cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/reconstruct.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/preprocess_mpi.dir/build.make src/apps/CMakeFiles/preprocess_mpi.dir/build +/usr/bin/make -f src/apps/CMakeFiles/reconstruct.dir/build.make src/apps/CMakeFiles/reconstruct.dir/build make[4]: Entering directory '/build/relion-3.1.3/build' -[ 85%] Building CXX object src/apps/CMakeFiles/preprocess_mpi.dir/preprocess_mpi.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/preprocess_mpi.dir/preprocess_mpi.cpp.o -MF CMakeFiles/preprocess_mpi.dir/preprocess_mpi.cpp.o.d -o CMakeFiles/preprocess_mpi.dir/preprocess_mpi.cpp.o -c /build/relion-3.1.3/src/apps/preprocess_mpi.cpp -[ 86%] Linking CXX executable ../../bin/relion_preprocess -cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/preprocess.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/preprocess.dir/preprocess.cpp.o -o ../../bin/relion_preprocess ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +[ 85%] Building CXX object src/apps/CMakeFiles/reconstruct.dir/reconstruct.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/reconstruct.dir/reconstruct.cpp.o -MF CMakeFiles/reconstruct.dir/reconstruct.cpp.o.d -o CMakeFiles/reconstruct.dir/reconstruct.cpp.o -c /build/relion-3.1.3/src/apps/reconstruct.cpp make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 86%] Built target preprocess -/usr/bin/make -f src/apps/CMakeFiles/project.dir/build.make src/apps/CMakeFiles/project.dir/depend +[ 85%] Built target preprocess_mpi +/usr/bin/make -f src/apps/CMakeFiles/reconstruct_mpi.dir/build.make src/apps/CMakeFiles/reconstruct_mpi.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' -cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/project.dir/DependInfo.cmake --color= +cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/reconstruct_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/project.dir/build.make src/apps/CMakeFiles/project.dir/build +/usr/bin/make -f src/apps/CMakeFiles/reconstruct_mpi.dir/build.make src/apps/CMakeFiles/reconstruct_mpi.dir/build make[4]: Entering directory '/build/relion-3.1.3/build' -[ 87%] Building CXX object src/apps/CMakeFiles/project.dir/project.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/project.dir/project.cpp.o -MF CMakeFiles/project.dir/project.cpp.o.d -o CMakeFiles/project.dir/project.cpp.o -c /build/relion-3.1.3/src/apps/project.cpp +[ 85%] Building CXX object src/apps/CMakeFiles/reconstruct_mpi.dir/reconstruct_mpi.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/reconstruct_mpi.dir/reconstruct_mpi.cpp.o -MF CMakeFiles/reconstruct_mpi.dir/reconstruct_mpi.cpp.o.d -o CMakeFiles/reconstruct_mpi.dir/reconstruct_mpi.cpp.o -c /build/relion-3.1.3/src/apps/reconstruct_mpi.cpp In file included from /build/relion-3.1.3/src/image.h:455, - from /build/relion-3.1.3/src/preprocessing.h:29, - from /build/relion-3.1.3/src/preprocessing_mpi.h:24, - from /build/relion-3.1.3/src/apps/preprocess_mpi.cpp:20: + from /build/relion-3.1.3/src/projector.h:25, + from /build/relion-3.1.3/src/backprojector.h:33, + from /build/relion-3.1.3/src/reconstructor.h:23, + from /build/relion-3.1.3/src/apps/reconstruct.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -12681,7 +12720,10 @@ | ^~~~~~ In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/projector.h:25, - from /build/relion-3.1.3/src/apps/project.cpp:21: + from /build/relion-3.1.3/src/backprojector.h:33, + from /build/relion-3.1.3/src/reconstructor.h:23, + from /build/relion-3.1.3/src/reconstructor_mpi.h:25, + from /build/relion-3.1.3/src/apps/reconstruct_mpi.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -12739,9 +12781,6 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 87%] Linking CXX executable ../../bin/relion_preprocess_mpi -cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/preprocess_mpi.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/preprocess_mpi.dir/preprocess_mpi.cpp.o -o ../../bin/relion_preprocess_mpi ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In file included from /usr/include/c++/12/vector:70, from /build/relion-3.1.3/src/args.h:52, from /build/relion-3.1.3/src/apps/prepare_subtomo.cpp:21: @@ -12751,21 +12790,37 @@ | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 +[ 86%] Linking CXX executable ../../bin/relion_reconstruct +cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/reconstruct.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/reconstruct.dir/reconstruct.cpp.o -o ../../bin/relion_reconstruct ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +[ 87%] Linking CXX executable ../../bin/relion_reconstruct_mpi +cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/reconstruct_mpi.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/reconstruct_mpi.dir/reconstruct_mpi.cpp.o -o ../../bin/relion_reconstruct_mpi ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 87%] Built target preprocess_mpi -/usr/bin/make -f src/apps/CMakeFiles/reconstruct.dir/build.make src/apps/CMakeFiles/reconstruct.dir/depend +[ 87%] Built target reconstruct +/usr/bin/make -f src/apps/CMakeFiles/refine.dir/build.make src/apps/CMakeFiles/refine.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' -cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/reconstruct.dir/DependInfo.cmake --color= +cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/refine.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/reconstruct.dir/build.make src/apps/CMakeFiles/reconstruct.dir/build +/usr/bin/make -f src/apps/CMakeFiles/refine.dir/build.make src/apps/CMakeFiles/refine.dir/build make[4]: Entering directory '/build/relion-3.1.3/build' -[ 87%] Building CXX object src/apps/CMakeFiles/reconstruct.dir/reconstruct.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/reconstruct.dir/reconstruct.cpp.o -MF CMakeFiles/reconstruct.dir/reconstruct.cpp.o.d -o CMakeFiles/reconstruct.dir/reconstruct.cpp.o -c /build/relion-3.1.3/src/apps/reconstruct.cpp +[ 87%] Building CXX object src/apps/CMakeFiles/refine.dir/refine.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/refine.dir/refine.cpp.o -MF CMakeFiles/refine.dir/refine.cpp.o.d -o CMakeFiles/refine.dir/refine.cpp.o -c /build/relion-3.1.3/src/apps/refine.cpp +make[4]: Leaving directory '/build/relion-3.1.3/build' +[ 87%] Built target reconstruct_mpi +/usr/bin/make -f src/apps/CMakeFiles/refine_mpi.dir/build.make src/apps/CMakeFiles/refine_mpi.dir/depend +make[4]: Entering directory '/build/relion-3.1.3/build' +cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/refine_mpi.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/relion-3.1.3/build' +/usr/bin/make -f src/apps/CMakeFiles/refine_mpi.dir/build.make src/apps/CMakeFiles/refine_mpi.dir/build +make[4]: Entering directory '/build/relion-3.1.3/build' +[ 88%] Building CXX object src/apps/CMakeFiles/refine_mpi.dir/refine_mpi.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/refine_mpi.dir/refine_mpi.cpp.o -MF CMakeFiles/refine_mpi.dir/refine_mpi.cpp.o.d -o CMakeFiles/refine_mpi.dir/refine_mpi.cpp.o -c /build/relion-3.1.3/src/apps/refine_mpi.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/projector.h:25, - from /build/relion-3.1.3/src/backprojector.h:33, - from /build/relion-3.1.3/src/reconstructor.h:23, - from /build/relion-3.1.3/src/apps/reconstruct.cpp:21: + from /build/relion-3.1.3/src/ml_model.h:23, + from /build/relion-3.1.3/src/ml_optimiser.h:35, + from /build/relion-3.1.3/src/apps/refine.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -12823,10 +12878,6 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 88%] Linking CXX executable ../../bin/relion_reconstruct -cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/reconstruct.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/reconstruct.dir/reconstruct.cpp.o -o ../../bin/relion_reconstruct ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -make[4]: Leaving directory '/build/relion-3.1.3/build' In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void prepare_subtomo::run()' at /build/relion-3.1.3/src/apps/prepare_subtomo.cpp:634:20: @@ -12839,10 +12890,6 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 88%] Built target reconstruct -/usr/bin/make -f src/apps/CMakeFiles/reconstruct_mpi.dir/build.make src/apps/CMakeFiles/reconstruct_mpi.dir/depend -make[4]: Entering directory '/build/relion-3.1.3/build' -cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/reconstruct_mpi.dir/DependInfo.cmake --color= In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void prepare_subtomo::run()' at /build/relion-3.1.3/src/apps/prepare_subtomo.cpp:801:26: @@ -12867,17 +12914,12 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -make[4]: Leaving directory '/build/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/reconstruct_mpi.dir/build.make src/apps/CMakeFiles/reconstruct_mpi.dir/build -make[4]: Entering directory '/build/relion-3.1.3/build' -[ 88%] Building CXX object src/apps/CMakeFiles/reconstruct_mpi.dir/reconstruct_mpi.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/reconstruct_mpi.dir/reconstruct_mpi.cpp.o -MF CMakeFiles/reconstruct_mpi.dir/reconstruct_mpi.cpp.o.d -o CMakeFiles/reconstruct_mpi.dir/reconstruct_mpi.cpp.o -c /build/relion-3.1.3/src/apps/reconstruct_mpi.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/projector.h:25, - from /build/relion-3.1.3/src/backprojector.h:33, - from /build/relion-3.1.3/src/reconstructor.h:23, - from /build/relion-3.1.3/src/reconstructor_mpi.h:25, - from /build/relion-3.1.3/src/apps/reconstruct_mpi.cpp:21: + from /build/relion-3.1.3/src/ml_model.h:23, + from /build/relion-3.1.3/src/ml_optimiser.h:35, + from /build/relion-3.1.3/src/ml_optimiser_mpi.h:24, + from /build/relion-3.1.3/src/apps/refine_mpi.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -12935,24 +12977,48 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 89%] Linking CXX executable ../../bin/relion_reconstruct_mpi -cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/reconstruct_mpi.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/reconstruct_mpi.dir/reconstruct_mpi.cpp.o -o ../../bin/relion_reconstruct_mpi ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +[ 88%] Linking CXX executable ../../bin/relion_refine +cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/refine.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/refine.dir/refine.cpp.o -o ../../bin/relion_refine ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +[ 88%] Linking CXX executable ../../bin/relion_project +cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/project.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/project.dir/project.cpp.o -o ../../bin/relion_project ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 89%] Built target reconstruct_mpi -/usr/bin/make -f src/apps/CMakeFiles/refine.dir/build.make src/apps/CMakeFiles/refine.dir/depend +[ 88%] Built target refine +/usr/bin/make -f src/apps/CMakeFiles/reposition.dir/build.make src/apps/CMakeFiles/reposition.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' -cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/refine.dir/DependInfo.cmake --color= +cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/reposition.dir/DependInfo.cmake --color= +[ 88%] Linking CXX executable ../../bin/relion_refine_mpi +cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/refine_mpi.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/refine.dir/build.make src/apps/CMakeFiles/refine.dir/build +/usr/bin/make -f src/apps/CMakeFiles/reposition.dir/build.make src/apps/CMakeFiles/reposition.dir/build make[4]: Entering directory '/build/relion-3.1.3/build' -[ 89%] Building CXX object src/apps/CMakeFiles/refine.dir/refine.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/refine.dir/refine.cpp.o -MF CMakeFiles/refine.dir/refine.cpp.o.d -o CMakeFiles/refine.dir/refine.cpp.o -c /build/relion-3.1.3/src/apps/refine.cpp +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/refine_mpi.dir/refine_mpi.cpp.o -o ../../bin/relion_refine_mpi ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +[ 88%] Building CXX object src/apps/CMakeFiles/reposition.dir/reposition.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/reposition.dir/reposition.cpp.o -MF CMakeFiles/reposition.dir/reposition.cpp.o.d -o CMakeFiles/reposition.dir/reposition.cpp.o -c /build/relion-3.1.3/src/apps/reposition.cpp +make[4]: Leaving directory '/build/relion-3.1.3/build' +[ 88%] Built target project +/usr/bin/make -f src/apps/CMakeFiles/run_ctffind.dir/build.make src/apps/CMakeFiles/run_ctffind.dir/depend +make[4]: Entering directory '/build/relion-3.1.3/build' +cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/run_ctffind.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/relion-3.1.3/build' +/usr/bin/make -f src/apps/CMakeFiles/run_ctffind.dir/build.make src/apps/CMakeFiles/run_ctffind.dir/build +make[4]: Entering directory '/build/relion-3.1.3/build' +[ 88%] Building CXX object src/apps/CMakeFiles/run_ctffind.dir/run_ctffind.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/run_ctffind.dir/run_ctffind.cpp.o -MF CMakeFiles/run_ctffind.dir/run_ctffind.cpp.o.d -o CMakeFiles/run_ctffind.dir/run_ctffind.cpp.o -c /build/relion-3.1.3/src/apps/run_ctffind.cpp +make[4]: Leaving directory '/build/relion-3.1.3/build' +[ 88%] Built target refine_mpi +/usr/bin/make -f src/apps/CMakeFiles/run_ctffind_mpi.dir/build.make src/apps/CMakeFiles/run_ctffind_mpi.dir/depend +make[4]: Entering directory '/build/relion-3.1.3/build' +cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/run_ctffind_mpi.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/relion-3.1.3/build' +/usr/bin/make -f src/apps/CMakeFiles/run_ctffind_mpi.dir/build.make src/apps/CMakeFiles/run_ctffind_mpi.dir/build +make[4]: Entering directory '/build/relion-3.1.3/build' +[ 89%] Building CXX object src/apps/CMakeFiles/run_ctffind_mpi.dir/run_ctffind_mpi.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/run_ctffind_mpi.dir/run_ctffind_mpi.cpp.o -MF CMakeFiles/run_ctffind_mpi.dir/run_ctffind_mpi.cpp.o.d -o CMakeFiles/run_ctffind_mpi.dir/run_ctffind_mpi.cpp.o -c /build/relion-3.1.3/src/apps/run_ctffind_mpi.cpp In file included from /build/relion-3.1.3/src/image.h:455, - from /build/relion-3.1.3/src/projector.h:25, - from /build/relion-3.1.3/src/ml_model.h:23, - from /build/relion-3.1.3/src/ml_optimiser.h:35, - from /build/relion-3.1.3/src/apps/refine.cpp:21: + from /build/relion-3.1.3/src/jaz/obs_model.h:24, + from /build/relion-3.1.3/src/apps/reposition.cpp:1: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -13010,25 +13076,9 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 89%] Linking CXX executable ../../bin/relion_project -cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/project.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/project.dir/project.cpp.o -o ../../bin/relion_project ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 89%] Built target project -/usr/bin/make -f src/apps/CMakeFiles/refine_mpi.dir/build.make src/apps/CMakeFiles/refine_mpi.dir/depend -make[4]: Entering directory '/build/relion-3.1.3/build' -cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/refine_mpi.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/refine_mpi.dir/build.make src/apps/CMakeFiles/refine_mpi.dir/build -make[4]: Entering directory '/build/relion-3.1.3/build' -[ 90%] Building CXX object src/apps/CMakeFiles/refine_mpi.dir/refine_mpi.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/refine_mpi.dir/refine_mpi.cpp.o -MF CMakeFiles/refine_mpi.dir/refine_mpi.cpp.o.d -o CMakeFiles/refine_mpi.dir/refine_mpi.cpp.o -c /build/relion-3.1.3/src/apps/refine_mpi.cpp In file included from /build/relion-3.1.3/src/image.h:455, - from /build/relion-3.1.3/src/projector.h:25, - from /build/relion-3.1.3/src/ml_model.h:23, - from /build/relion-3.1.3/src/ml_optimiser.h:35, - from /build/relion-3.1.3/src/ml_optimiser_mpi.h:24, - from /build/relion-3.1.3/src/apps/refine_mpi.cpp:21: + from /build/relion-3.1.3/src/ctffind_runner.h:31, + from /build/relion-3.1.3/src/apps/run_ctffind.cpp:20: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -13086,22 +13136,10 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 90%] Linking CXX executable ../../bin/relion_refine -cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/refine.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/refine.dir/refine.cpp.o -o ../../bin/relion_refine ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 90%] Built target refine -/usr/bin/make -f src/apps/CMakeFiles/reposition.dir/build.make src/apps/CMakeFiles/reposition.dir/depend -make[4]: Entering directory '/build/relion-3.1.3/build' -cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/reposition.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/reposition.dir/build.make src/apps/CMakeFiles/reposition.dir/build -make[4]: Entering directory '/build/relion-3.1.3/build' -[ 90%] Building CXX object src/apps/CMakeFiles/reposition.dir/reposition.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/reposition.dir/reposition.cpp.o -MF CMakeFiles/reposition.dir/reposition.cpp.o.d -o CMakeFiles/reposition.dir/reposition.cpp.o -c /build/relion-3.1.3/src/apps/reposition.cpp In file included from /build/relion-3.1.3/src/image.h:455, - from /build/relion-3.1.3/src/jaz/obs_model.h:24, - from /build/relion-3.1.3/src/apps/reposition.cpp:1: + from /build/relion-3.1.3/src/ctffind_runner.h:31, + from /build/relion-3.1.3/src/ctffind_runner_mpi.h:25, + from /build/relion-3.1.3/src/apps/run_ctffind_mpi.cpp:20: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -13159,35 +13197,35 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 91%] Linking CXX executable ../../bin/relion_prepare_subtomo -cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/prepare_subtomo.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/prepare_subtomo.dir/prepare_subtomo.cpp.o -o ../../bin/relion_prepare_subtomo ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +[ 89%] Linking CXX executable ../../bin/relion_run_ctffind +cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/run_ctffind.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/run_ctffind.dir/run_ctffind.cpp.o -o ../../bin/relion_run_ctffind ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 91%] Built target prepare_subtomo -/usr/bin/make -f src/apps/CMakeFiles/run_ctffind.dir/build.make src/apps/CMakeFiles/run_ctffind.dir/depend +[ 89%] Linking CXX executable ../../bin/relion_run_ctffind_mpi +cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/run_ctffind_mpi.dir/link.txt --verbose=1 +[ 89%] Built target run_ctffind +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/run_ctffind_mpi.dir/run_ctffind_mpi.cpp.o -o ../../bin/relion_run_ctffind_mpi ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +/usr/bin/make -f src/apps/CMakeFiles/run_motioncorr.dir/build.make src/apps/CMakeFiles/run_motioncorr.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' -cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/run_ctffind.dir/DependInfo.cmake --color= +cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/run_motioncorr.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/run_ctffind.dir/build.make src/apps/CMakeFiles/run_ctffind.dir/build +/usr/bin/make -f src/apps/CMakeFiles/run_motioncorr.dir/build.make src/apps/CMakeFiles/run_motioncorr.dir/build make[4]: Entering directory '/build/relion-3.1.3/build' -[ 91%] Building CXX object src/apps/CMakeFiles/run_ctffind.dir/run_ctffind.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/run_ctffind.dir/run_ctffind.cpp.o -MF CMakeFiles/run_ctffind.dir/run_ctffind.cpp.o.d -o CMakeFiles/run_ctffind.dir/run_ctffind.cpp.o -c /build/relion-3.1.3/src/apps/run_ctffind.cpp -[ 91%] Linking CXX executable ../../bin/relion_refine_mpi -cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/refine_mpi.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/refine_mpi.dir/refine_mpi.cpp.o -o ../../bin/relion_refine_mpi ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +[ 90%] Building CXX object src/apps/CMakeFiles/run_motioncorr.dir/run_motioncorr.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/run_motioncorr.dir/run_motioncorr.cpp.o -MF CMakeFiles/run_motioncorr.dir/run_motioncorr.cpp.o.d -o CMakeFiles/run_motioncorr.dir/run_motioncorr.cpp.o -c /build/relion-3.1.3/src/apps/run_motioncorr.cpp make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 91%] Built target refine_mpi -/usr/bin/make -f src/apps/CMakeFiles/run_ctffind_mpi.dir/build.make src/apps/CMakeFiles/run_ctffind_mpi.dir/depend +[ 90%] Built target run_ctffind_mpi +/usr/bin/make -f src/apps/CMakeFiles/run_motioncorr_mpi.dir/build.make src/apps/CMakeFiles/run_motioncorr_mpi.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' -cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/run_ctffind_mpi.dir/DependInfo.cmake --color= +cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/run_motioncorr_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/run_ctffind_mpi.dir/build.make src/apps/CMakeFiles/run_ctffind_mpi.dir/build +/usr/bin/make -f src/apps/CMakeFiles/run_motioncorr_mpi.dir/build.make src/apps/CMakeFiles/run_motioncorr_mpi.dir/build make[4]: Entering directory '/build/relion-3.1.3/build' -[ 92%] Building CXX object src/apps/CMakeFiles/run_ctffind_mpi.dir/run_ctffind_mpi.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/run_ctffind_mpi.dir/run_ctffind_mpi.cpp.o -MF CMakeFiles/run_ctffind_mpi.dir/run_ctffind_mpi.cpp.o.d -o CMakeFiles/run_ctffind_mpi.dir/run_ctffind_mpi.cpp.o -c /build/relion-3.1.3/src/apps/run_ctffind_mpi.cpp +[ 90%] Building CXX object src/apps/CMakeFiles/run_motioncorr_mpi.dir/run_motioncorr_mpi.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/run_motioncorr_mpi.dir/run_motioncorr_mpi.cpp.o -MF CMakeFiles/run_motioncorr_mpi.dir/run_motioncorr_mpi.cpp.o.d -o CMakeFiles/run_motioncorr_mpi.dir/run_motioncorr_mpi.cpp.o -c /build/relion-3.1.3/src/apps/run_motioncorr_mpi.cpp In file included from /build/relion-3.1.3/src/image.h:455, - from /build/relion-3.1.3/src/ctffind_runner.h:31, - from /build/relion-3.1.3/src/apps/run_ctffind.cpp:20: + from /build/relion-3.1.3/src/motioncorr_runner.h:32, + from /build/relion-3.1.3/src/apps/run_motioncorr.cpp:20: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -13245,13 +13283,10 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 92%] Linking CXX executable ../../bin/relion_run_ctffind -cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/run_ctffind.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/run_ctffind.dir/run_ctffind.cpp.o -o ../../bin/relion_run_ctffind ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In file included from /build/relion-3.1.3/src/image.h:455, - from /build/relion-3.1.3/src/ctffind_runner.h:31, - from /build/relion-3.1.3/src/ctffind_runner_mpi.h:25, - from /build/relion-3.1.3/src/apps/run_ctffind_mpi.cpp:20: + from /build/relion-3.1.3/src/motioncorr_runner.h:32, + from /build/relion-3.1.3/src/motioncorr_runner_mpi.h:25, + from /build/relion-3.1.3/src/apps/run_motioncorr_mpi.cpp:20: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -13309,45 +13344,47 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +[ 91%] Linking CXX executable ../../bin/relion_reposition +cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/reposition.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/reposition.dir/reposition.cpp.o -o ../../bin/relion_reposition ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +[ 91%] Linking CXX executable ../../bin/relion_run_motioncorr +cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/run_motioncorr.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/run_motioncorr.dir/run_motioncorr.cpp.o -o ../../bin/relion_run_motioncorr ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 92%] Built target run_ctffind -/usr/bin/make -f src/apps/CMakeFiles/run_motioncorr.dir/build.make src/apps/CMakeFiles/run_motioncorr.dir/depend +[ 91%] Built target reposition +/usr/bin/make -f src/apps/CMakeFiles/scheduler.dir/build.make src/apps/CMakeFiles/scheduler.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' -cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/run_motioncorr.dir/DependInfo.cmake --color= +cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/scheduler.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/run_motioncorr.dir/build.make src/apps/CMakeFiles/run_motioncorr.dir/build +/usr/bin/make -f src/apps/CMakeFiles/scheduler.dir/build.make src/apps/CMakeFiles/scheduler.dir/build make[4]: Entering directory '/build/relion-3.1.3/build' -[ 93%] Building CXX object src/apps/CMakeFiles/run_motioncorr.dir/run_motioncorr.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/run_motioncorr.dir/run_motioncorr.cpp.o -MF CMakeFiles/run_motioncorr.dir/run_motioncorr.cpp.o.d -o CMakeFiles/run_motioncorr.dir/run_motioncorr.cpp.o -c /build/relion-3.1.3/src/apps/run_motioncorr.cpp -[ 94%] Linking CXX executable ../../bin/relion_reposition -cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/reposition.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/reposition.dir/reposition.cpp.o -o ../../bin/relion_reposition ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -[ 94%] Linking CXX executable ../../bin/relion_run_ctffind_mpi -cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/run_ctffind_mpi.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/run_ctffind_mpi.dir/run_ctffind_mpi.cpp.o -o ../../bin/relion_run_ctffind_mpi ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +[ 91%] Building CXX object src/apps/CMakeFiles/scheduler.dir/scheduler.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/scheduler.dir/scheduler.cpp.o -MF CMakeFiles/scheduler.dir/scheduler.cpp.o.d -o CMakeFiles/scheduler.dir/scheduler.cpp.o -c /build/relion-3.1.3/src/apps/scheduler.cpp make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 94%] Built target reposition -/usr/bin/make -f src/apps/CMakeFiles/run_motioncorr_mpi.dir/build.make src/apps/CMakeFiles/run_motioncorr_mpi.dir/depend +[ 91%] Built target run_motioncorr +/usr/bin/make -f src/apps/CMakeFiles/stack_create.dir/build.make src/apps/CMakeFiles/stack_create.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' -cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/run_motioncorr_mpi.dir/DependInfo.cmake --color= +cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/stack_create.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/run_motioncorr_mpi.dir/build.make src/apps/CMakeFiles/run_motioncorr_mpi.dir/build +/usr/bin/make -f src/apps/CMakeFiles/stack_create.dir/build.make src/apps/CMakeFiles/stack_create.dir/build make[4]: Entering directory '/build/relion-3.1.3/build' -[ 94%] Building CXX object src/apps/CMakeFiles/run_motioncorr_mpi.dir/run_motioncorr_mpi.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/run_motioncorr_mpi.dir/run_motioncorr_mpi.cpp.o -MF CMakeFiles/run_motioncorr_mpi.dir/run_motioncorr_mpi.cpp.o.d -o CMakeFiles/run_motioncorr_mpi.dir/run_motioncorr_mpi.cpp.o -c /build/relion-3.1.3/src/apps/run_motioncorr_mpi.cpp +[ 92%] Building CXX object src/apps/CMakeFiles/stack_create.dir/stack_create.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/stack_create.dir/stack_create.cpp.o -MF CMakeFiles/stack_create.dir/stack_create.cpp.o.d -o CMakeFiles/stack_create.dir/stack_create.cpp.o -c /build/relion-3.1.3/src/apps/stack_create.cpp +[ 93%] Linking CXX executable ../../bin/relion_run_motioncorr_mpi +cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/run_motioncorr_mpi.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/run_motioncorr_mpi.dir/run_motioncorr_mpi.cpp.o -o ../../bin/relion_run_motioncorr_mpi ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 94%] Built target run_ctffind_mpi -/usr/bin/make -f src/apps/CMakeFiles/scheduler.dir/build.make src/apps/CMakeFiles/scheduler.dir/depend +[ 93%] Built target run_motioncorr_mpi +/usr/bin/make -f src/apps/CMakeFiles/star_handler.dir/build.make src/apps/CMakeFiles/star_handler.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' -cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/scheduler.dir/DependInfo.cmake --color= +cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/star_handler.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/scheduler.dir/build.make src/apps/CMakeFiles/scheduler.dir/build +/usr/bin/make -f src/apps/CMakeFiles/star_handler.dir/build.make src/apps/CMakeFiles/star_handler.dir/build make[4]: Entering directory '/build/relion-3.1.3/build' -[ 94%] Building CXX object src/apps/CMakeFiles/scheduler.dir/scheduler.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/scheduler.dir/scheduler.cpp.o -MF CMakeFiles/scheduler.dir/scheduler.cpp.o.d -o CMakeFiles/scheduler.dir/scheduler.cpp.o -c /build/relion-3.1.3/src/apps/scheduler.cpp +[ 94%] Building CXX object src/apps/CMakeFiles/star_handler.dir/star_handler.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/star_handler.dir/star_handler.cpp.o -MF CMakeFiles/star_handler.dir/star_handler.cpp.o.d -o CMakeFiles/star_handler.dir/star_handler.cpp.o -c /build/relion-3.1.3/src/apps/star_handler.cpp In file included from /build/relion-3.1.3/src/image.h:455, - from /build/relion-3.1.3/src/motioncorr_runner.h:32, - from /build/relion-3.1.3/src/apps/run_motioncorr.cpp:20: + from /build/relion-3.1.3/src/apps/stack_create.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -13406,9 +13443,9 @@ 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-3.1.3/src/image.h:455, - from /build/relion-3.1.3/src/motioncorr_runner.h:32, - from /build/relion-3.1.3/src/motioncorr_runner_mpi.h:25, - from /build/relion-3.1.3/src/apps/run_motioncorr_mpi.cpp:20: + from /build/relion-3.1.3/src/jaz/obs_model.h:24, + from /build/relion-3.1.3/src/scheduler.h:26, + from /build/relion-3.1.3/src/apps/scheduler.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -13466,10 +13503,19 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +[ 95%] Linking CXX executable ../../bin/relion_prepare_subtomo +cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/prepare_subtomo.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/prepare_subtomo.dir/prepare_subtomo.cpp.o -o ../../bin/relion_prepare_subtomo ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +make[4]: Leaving directory '/build/relion-3.1.3/build' +[ 95%] Built target prepare_subtomo +/usr/bin/make -f src/apps/CMakeFiles/tiltpair_plot.dir/build.make src/apps/CMakeFiles/tiltpair_plot.dir/depend +make[4]: Entering directory '/build/relion-3.1.3/build' +cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/tiltpair_plot.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/relion-3.1.3/build' +/usr/bin/make -f src/apps/CMakeFiles/tiltpair_plot.dir/build.make src/apps/CMakeFiles/tiltpair_plot.dir/build +make[4]: Entering directory '/build/relion-3.1.3/build' In file included from /build/relion-3.1.3/src/image.h:455, - from /build/relion-3.1.3/src/jaz/obs_model.h:24, - from /build/relion-3.1.3/src/scheduler.h:26, - from /build/relion-3.1.3/src/apps/scheduler.cpp:21: + from /build/relion-3.1.3/src/apps/star_handler.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -13503,6 +13549,7 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +[ 95%] Building CXX object src/apps/CMakeFiles/tiltpair_plot.dir/tiltpair_plot.cpp.o /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ @@ -13527,34 +13574,9 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 94%] Linking CXX executable ../../bin/relion_run_motioncorr -cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/run_motioncorr.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/run_motioncorr.dir/run_motioncorr.cpp.o -o ../../bin/relion_run_motioncorr ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 94%] Built target run_motioncorr -/usr/bin/make -f src/apps/CMakeFiles/stack_create.dir/build.make src/apps/CMakeFiles/stack_create.dir/depend -make[4]: Entering directory '/build/relion-3.1.3/build' -cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/stack_create.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/stack_create.dir/build.make src/apps/CMakeFiles/stack_create.dir/build -make[4]: Entering directory '/build/relion-3.1.3/build' -[ 95%] Building CXX object src/apps/CMakeFiles/stack_create.dir/stack_create.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/stack_create.dir/stack_create.cpp.o -MF CMakeFiles/stack_create.dir/stack_create.cpp.o.d -o CMakeFiles/stack_create.dir/stack_create.cpp.o -c /build/relion-3.1.3/src/apps/stack_create.cpp -[ 96%] Linking CXX executable ../../bin/relion_run_motioncorr_mpi -cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/run_motioncorr_mpi.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/run_motioncorr_mpi.dir/run_motioncorr_mpi.cpp.o -o ../../bin/relion_run_motioncorr_mpi ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 96%] Built target run_motioncorr_mpi -/usr/bin/make -f src/apps/CMakeFiles/star_handler.dir/build.make src/apps/CMakeFiles/star_handler.dir/depend -make[4]: Entering directory '/build/relion-3.1.3/build' -cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/star_handler.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/star_handler.dir/build.make src/apps/CMakeFiles/star_handler.dir/build -make[4]: Entering directory '/build/relion-3.1.3/build' -[ 97%] Building CXX object src/apps/CMakeFiles/star_handler.dir/star_handler.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/star_handler.dir/star_handler.cpp.o -MF CMakeFiles/star_handler.dir/star_handler.cpp.o.d -o CMakeFiles/star_handler.dir/star_handler.cpp.o -c /build/relion-3.1.3/src/apps/star_handler.cpp +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/tiltpair_plot.dir/tiltpair_plot.cpp.o -MF CMakeFiles/tiltpair_plot.dir/tiltpair_plot.cpp.o.d -o CMakeFiles/tiltpair_plot.dir/tiltpair_plot.cpp.o -c /build/relion-3.1.3/src/apps/tiltpair_plot.cpp In file included from /build/relion-3.1.3/src/image.h:455, - from /build/relion-3.1.3/src/apps/stack_create.cpp:21: + from /build/relion-3.1.3/src/apps/tiltpair_plot.cpp:25: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -13612,8 +13634,25 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +[ 96%] Linking CXX executable ../../bin/relion_tiltpair_plot +cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiltpair_plot.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/tiltpair_plot.dir/tiltpair_plot.cpp.o -o ../../bin/relion_tiltpair_plot ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +make[4]: Leaving directory '/build/relion-3.1.3/build' +[ 96%] Built target tiltpair_plot +/usr/bin/make -f src/apps/CMakeFiles/tomo_test.dir/build.make src/apps/CMakeFiles/tomo_test.dir/depend +make[4]: Entering directory '/build/relion-3.1.3/build' +cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/tomo_test.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/relion-3.1.3/build' +/usr/bin/make -f src/apps/CMakeFiles/tomo_test.dir/build.make src/apps/CMakeFiles/tomo_test.dir/build +make[4]: Entering directory '/build/relion-3.1.3/build' +[ 96%] Building CXX object src/apps/CMakeFiles/tomo_test.dir/tomo_test.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/tomo_test.dir/tomo_test.cpp.o -MF CMakeFiles/tomo_test.dir/tomo_test.cpp.o.d -o CMakeFiles/tomo_test.dir/tomo_test.cpp.o -c /build/relion-3.1.3/src/apps/tomo_test.cpp +[ 96%] Linking CXX executable ../../bin/relion_scheduler +cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/scheduler.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/scheduler.dir/scheduler.cpp.o -o ../../bin/relion_scheduler ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In file included from /build/relion-3.1.3/src/image.h:455, - from /build/relion-3.1.3/src/apps/star_handler.cpp:21: + from /build/relion-3.1.3/src/jaz/tomo/tomo_stack.h:25, + from /build/relion-3.1.3/src/apps/tomo_test.cpp:2: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -13671,21 +13710,45 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 97%] Linking CXX executable ../../bin/relion_scheduler -cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/scheduler.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/scheduler.dir/scheduler.cpp.o -o ../../bin/relion_scheduler ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +In file included from /usr/include/c++/12/vector:70, + from /build/relion-3.1.3/src/funcs.h:56, + from /build/relion-3.1.3/src/image.h:58: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:70, + from /build/relion-3.1.3/src/funcs.h:56, + from /build/relion-3.1.3/src/image.h:58: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const gravis::t3Vector&}; _Tp = gravis::t3Vector; _Alloc = std::allocator >]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 97%] Built target scheduler -/usr/bin/make -f src/apps/CMakeFiles/tiltpair_plot.dir/build.make src/apps/CMakeFiles/tiltpair_plot.dir/depend +[ 96%] Built target scheduler +/usr/bin/make -f src/apps/CMakeFiles/display.dir/build.make src/apps/CMakeFiles/display.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' -cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/tiltpair_plot.dir/DependInfo.cmake --color= +cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/display.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/tiltpair_plot.dir/build.make src/apps/CMakeFiles/tiltpair_plot.dir/build +/usr/bin/make -f src/apps/CMakeFiles/display.dir/build.make src/apps/CMakeFiles/display.dir/build make[4]: Entering directory '/build/relion-3.1.3/build' -[ 97%] Building CXX object src/apps/CMakeFiles/tiltpair_plot.dir/tiltpair_plot.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/tiltpair_plot.dir/tiltpair_plot.cpp.o -MF CMakeFiles/tiltpair_plot.dir/tiltpair_plot.cpp.o.d -o CMakeFiles/tiltpair_plot.dir/tiltpair_plot.cpp.o -c /build/relion-3.1.3/src/apps/tiltpair_plot.cpp +[ 96%] Building CXX object src/apps/CMakeFiles/display.dir/display.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/display.dir/display.cpp.o -MF CMakeFiles/display.dir/display.cpp.o.d -o CMakeFiles/display.dir/display.cpp.o -c /build/relion-3.1.3/src/apps/display.cpp +[ 96%] Linking CXX executable ../../bin/relion_stack_create +cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/stack_create.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/stack_create.dir/stack_create.cpp.o -o ../../bin/relion_stack_create ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +make[4]: Leaving directory '/build/relion-3.1.3/build' +[ 96%] Built target stack_create +/usr/bin/make -f src/apps/CMakeFiles/relion.dir/build.make src/apps/CMakeFiles/relion.dir/depend +make[4]: Entering directory '/build/relion-3.1.3/build' +cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/relion.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/relion-3.1.3/build' +/usr/bin/make -f src/apps/CMakeFiles/relion.dir/build.make src/apps/CMakeFiles/relion.dir/build +make[4]: Entering directory '/build/relion-3.1.3/build' +[ 96%] Building CXX object src/apps/CMakeFiles/relion.dir/maingui.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion.dir/maingui.cpp.o -MF CMakeFiles/relion.dir/maingui.cpp.o.d -o CMakeFiles/relion.dir/maingui.cpp.o -c /build/relion-3.1.3/src/apps/maingui.cpp In file included from /build/relion-3.1.3/src/image.h:455, - from /build/relion-3.1.3/src/apps/tiltpair_plot.cpp:25: + from /build/relion-3.1.3/src/apps/display.cpp:25: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -13743,42 +13806,22 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 98%] Linking CXX executable ../../bin/relion_tiltpair_plot -cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiltpair_plot.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/tiltpair_plot.dir/tiltpair_plot.cpp.o -o ../../bin/relion_tiltpair_plot ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 98%] Built target tiltpair_plot -/usr/bin/make -f src/apps/CMakeFiles/tomo_test.dir/build.make src/apps/CMakeFiles/tomo_test.dir/depend -make[4]: Entering directory '/build/relion-3.1.3/build' -cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/tomo_test.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/tomo_test.dir/build.make src/apps/CMakeFiles/tomo_test.dir/build -make[4]: Entering directory '/build/relion-3.1.3/build' -[ 98%] Building CXX object src/apps/CMakeFiles/tomo_test.dir/tomo_test.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/tomo_test.dir/tomo_test.cpp.o -MF CMakeFiles/tomo_test.dir/tomo_test.cpp.o.d -o CMakeFiles/tomo_test.dir/tomo_test.cpp.o -c /build/relion-3.1.3/src/apps/tomo_test.cpp -In file included from /usr/include/c++/12/vector:70, - from /build/relion-3.1.3/src/funcs.h:56, - from /build/relion-3.1.3/src/image.h:58: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -[ 98%] Linking CXX executable ../../bin/relion_stack_create -cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/stack_create.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/stack_create.dir/stack_create.cpp.o -o ../../bin/relion_stack_create ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 98%] Built target stack_create -/usr/bin/make -f src/apps/CMakeFiles/display.dir/build.make src/apps/CMakeFiles/display.dir/depend -make[4]: Entering directory '/build/relion-3.1.3/build' -cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/display.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/display.dir/build.make src/apps/CMakeFiles/display.dir/build -make[4]: Entering directory '/build/relion-3.1.3/build' -[ 98%] Building CXX object src/apps/CMakeFiles/display.dir/display.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/display.dir/display.cpp.o -MF CMakeFiles/display.dir/display.cpp.o.d -o CMakeFiles/display.dir/display.cpp.o -c /build/relion-3.1.3/src/apps/display.cpp +In file included from /usr/include/c++/12/vector:64: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'void star_handler_parameters::discard_on_image_stats()' at /build/relion-3.1.3/src/apps/star_handler.cpp:292:18: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'void star_handler_parameters::discard_on_image_stats()' at /build/relion-3.1.3/src/apps/star_handler.cpp:293:21: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /build/relion-3.1.3/src/image.h:455, - from /build/relion-3.1.3/src/jaz/tomo/tomo_stack.h:25, - from /build/relion-3.1.3/src/apps/tomo_test.cpp:2: + from /build/relion-3.1.3/src/jaz/obs_model.h:24, + from /build/relion-3.1.3/src/scheduler.h:26, + from /build/relion-3.1.3/src/gui_mainwindow.h:28, + from /build/relion-3.1.3/src/apps/maingui.cpp:23: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -13836,8 +13879,35 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +In file included from /usr/include/c++/12/vector:64: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = gravis::t3Vector; _Alloc = std::allocator >]', + inlined from 'int main(int, char**)' at /build/relion-3.1.3/src/apps/tomo_test.cpp:107:17: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +[ 97%] Linking CXX executable ../../bin/relion_display +cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/display.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/display.dir/display.cpp.o -o ../../bin/relion_display ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gui_lib.a /usr/lib/arm-linux-gnueabihf/libfltk_images.so /usr/lib/arm-linux-gnueabihf/libfltk_forms.so /usr/lib/arm-linux-gnueabihf/libfltk.so -lX11 -lm -ltiff ../../lib/librelion_lib.a -lfftw3f -lfftw3 -ltiff +make[4]: Leaving directory '/build/relion-3.1.3/build' +[ 97%] Built target display +/usr/bin/make -f src/apps/CMakeFiles/manualpick.dir/build.make src/apps/CMakeFiles/manualpick.dir/depend +make[4]: Entering directory '/build/relion-3.1.3/build' +cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/manualpick.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/relion-3.1.3/build' +/usr/bin/make -f src/apps/CMakeFiles/manualpick.dir/build.make src/apps/CMakeFiles/manualpick.dir/build +make[4]: Entering directory '/build/relion-3.1.3/build' +[ 97%] Building CXX object src/apps/CMakeFiles/manualpick.dir/manualpick.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/manualpick.dir/manualpick.cpp.o -MF CMakeFiles/manualpick.dir/manualpick.cpp.o.d -o CMakeFiles/manualpick.dir/manualpick.cpp.o -c /build/relion-3.1.3/src/apps/manualpick.cpp +[ 98%] Linking CXX executable ../../bin/relion_tomo_test +cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/tomo_test.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/tomo_test.dir/tomo_test.cpp.o -o ../../bin/relion_tomo_test ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +[ 99%] Linking CXX executable ../../bin/relion +cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/relion.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/relion.dir/maingui.cpp.o -o ../../bin/relion ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gui_lib.a /usr/lib/arm-linux-gnueabihf/libfltk_images.so /usr/lib/arm-linux-gnueabihf/libfltk_forms.so /usr/lib/arm-linux-gnueabihf/libfltk.so -lX11 -lm -ltiff ../../lib/librelion_lib.a -lfftw3f -lfftw3 -ltiff +make[4]: Leaving directory '/build/relion-3.1.3/build' +[ 99%] Built target tomo_test In file included from /build/relion-3.1.3/src/image.h:455, - from /build/relion-3.1.3/src/apps/display.cpp:25: + from /build/relion-3.1.3/src/apps/manualpick.cpp:25: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -13895,40 +13965,13 @@ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 99%] Linking CXX executable ../../bin/relion_display -cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/display.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/display.dir/display.cpp.o -o ../../bin/relion_display ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gui_lib.a /usr/lib/arm-linux-gnueabihf/libfltk_images.so /usr/lib/arm-linux-gnueabihf/libfltk_forms.so /usr/lib/arm-linux-gnueabihf/libfltk.so -lX11 -lm -ltiff ../../lib/librelion_lib.a -lfftw3f -lfftw3 -ltiff -In file included from /usr/include/c++/12/vector:70, - from /build/relion-3.1.3/src/funcs.h:56, - from /build/relion-3.1.3/src/image.h:58: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const gravis::t3Vector&}; _Tp = gravis::t3Vector; _Alloc = std::allocator >]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 99%] Built target display -In file included from /usr/include/c++/12/vector:64: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void star_handler_parameters::discard_on_image_stats()' at /build/relion-3.1.3/src/apps/star_handler.cpp:292:18: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void star_handler_parameters::discard_on_image_stats()' at /build/relion-3.1.3/src/apps/star_handler.cpp:293:21: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:64: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = gravis::t3Vector; _Alloc = std::allocator >]', - inlined from 'int main(int, char**)' at /build/relion-3.1.3/src/apps/tomo_test.cpp:107:17: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[100%] Linking CXX executable ../../bin/relion_tomo_test -cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/tomo_test.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/tomo_test.dir/tomo_test.cpp.o -o ../../bin/relion_tomo_test ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +[ 99%] Built target relion +[100%] Linking CXX executable ../../bin/relion_manualpick +cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/manualpick.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/manualpick.dir/manualpick.cpp.o -o ../../bin/relion_manualpick ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gui_lib.a /usr/lib/arm-linux-gnueabihf/libfltk_images.so /usr/lib/arm-linux-gnueabihf/libfltk_forms.so /usr/lib/arm-linux-gnueabihf/libfltk.so -lX11 -lm -ltiff ../../lib/librelion_lib.a -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' -[100%] Built target tomo_test +[100%] Built target manualpick [100%] Linking CXX executable ../../bin/relion_star_handler cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/star_handler.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/star_handler.dir/star_handler.cpp.o -o ../../bin/relion_star_handler ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff @@ -14513,71 +14556,71 @@ /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin --- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_merge_particles -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_demodulate --- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_ctf_refine_mpi --- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_import --- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_motion_refine --- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_motion_refine_mpi --- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_reposition --- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_ctf_toolbox --- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_star_loopheader +-- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_tomo_test +-- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_tiltpair_plot -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_manualpick --- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_run_motioncorr --- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_prepare_subtomo +-- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_star_loopheader +-- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_convert_to_tiff_mpi -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_plot_delocalisation --- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_postprocess --- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_particle_FCC --- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_reconstruct_mpi --- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_star_datablock_ctfdat --- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_particle_symmetry_expand --- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_mrc2vtk -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_helix_inimodel2d --- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_particle_subtract_mpi --- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_autopick --- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_particle_reposition +-- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_mask_create +-- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_stack_create +-- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_image_handler +-- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_estimate_gain +-- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_align_symmetry +-- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_run_motioncorr_mpi +-- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_flex_analyse_mpi +-- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_particle_subtract +-- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_scheduler -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_display --- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_project --- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_star_handler +-- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_particle_symmetry_expand +-- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_run_ctffind +-- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_mrc2vtk +-- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_preprocess_mpi +-- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_postprocess_mpi +-- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_ctf_mask_test -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_reconstruct --- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_particle_subtract +-- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_helix_toolbox -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_star_plottable +-- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_autopick +-- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_particle_select +-- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_localsym +-- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_star_handler +-- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_star_datablock_ctfdat +-- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_localsym_mpi +-- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_reposition +-- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_particle_subtract_mpi -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_star_datablock_singlefiles --- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_star_datablock_stack --- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_convert_to_tiff_mpi --- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_tiltpair_plot --- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_scheduler --- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_mask_create --- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_estimate_gain --- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_refine_mpi +-- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_ctf_toolbox +-- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_motion_refine_mpi +-- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_autopick_mpi -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_run_ctffind_mpi +-- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_ctf_refine_mpi -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_external_reconstruct --- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_run_ctffind --- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_ctf_mask_test --- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_star_printtable --- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_convert_to_tiff --- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_align_symmetry --- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_tomo_test --- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_stack_create +-- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_particle_reposition -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_preprocess -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_qsub.csh -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_flex_analyse --- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_autopick_mpi --- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_ctf_refine --- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_postprocess_mpi --- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_flex_analyse_mpi +-- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_project +-- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_prepare_subtomo -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_refine --- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_localsym --- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_particle_select --- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_pipeliner --- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_image_handler --- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_localsym_mpi --- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion --- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_run_motioncorr_mpi --- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_convert_star --- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_preprocess_mpi --- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_helix_toolbox +-- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_run_motioncorr +-- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_ctf_refine +-- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_star_datablock_stack -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_find_tiltpairs +-- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_reconstruct_mpi +-- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_refine_mpi +-- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_convert_star +-- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_convert_to_tiff +-- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_motion_refine +-- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_particle_FCC +-- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_postprocess +-- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_import +-- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion +-- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_merge_particles +-- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_pipeliner +-- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_star_printtable -- Up-to-date: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_align_symmetry -- Up-to-date: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_autopick -- Up-to-date: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_autopick_mpi @@ -14657,71 +14700,71 @@ dh_strip -a dh_makeshlibs -a dh_shlibdeps -a -dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_flex_analyse_mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/relion-gui/usr/bin/relion_manualpick contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_merge_particles contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_reposition contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_prepare_subtomo contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/relion-gui/usr/bin/relion_display contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_plot_delocalisation contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_demodulate contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_run_ctffind contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/relion-gui/usr/bin/relion_manualpick contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/relion-gui/usr/bin/relion contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_helix_toolbox contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_flex_analyse_mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_postprocess_mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_autopick contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_find_tiltpairs contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_convert_to_tiff_mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_star_handler contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_refine contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_ctf_mask_test contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_helix_inimodel2d contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_ctf_refine_mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_preprocess_mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_reconstruct contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_run_motioncorr contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_project contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_particle_select contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_estimate_gain contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_tomo_test contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_localsym contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_particle_symmetry_expand contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_ctf_refine contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_particle_subtract_mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_ctf_toolbox contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_image_handler contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_refine_mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_run_ctffind contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_autopick contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_preprocess contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_helix_toolbox contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_merge_particles contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_flex_analyse contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_convert_star contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_particle_subtract contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_convert_to_tiff contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_mrc2vtk contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_autopick_mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_particle_FCC contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_tiltpair_plot contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_import contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_reconstruct_mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_align_symmetry contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_postprocess contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_stack_create contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_mask_create contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_prepare_subtomo contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_external_reconstruct contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_pipeliner contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_autopick_mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_postprocess_mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_convert_to_tiff_mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_align_symmetry contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_demodulate contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_reconstruct_mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_reconstruct contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_particle_reposition contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_ctf_refine contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_preprocess_mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_ctf_refine_mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_particle_symmetry_expand contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_localsym contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_external_reconstruct contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_scheduler contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_mask_create contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_motion_refine contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_run_ctffind_mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_reposition contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_refine contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_plot_delocalisation contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_motion_refine_mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_postprocess contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_particle_select contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_convert_star contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_estimate_gain contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_mrc2vtk contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_particle_subtract contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_run_motioncorr_mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_flex_analyse contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_motion_refine contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_preprocess contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_ctf_toolbox contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_convert_to_tiff contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_helix_inimodel2d contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_import contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_project contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_tiltpair_plot contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_run_motioncorr contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_refine_mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_localsym_mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_find_tiltpairs contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_particle_subtract_mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_ctf_mask_test contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_star_handler contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_scheduler contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dh_installdeb dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'relion-gui' in '../relion-gui_3.1.3-3_armhf.deb'. dpkg-deb: building package 'relion' in '../relion_3.1.3-3_armhf.deb'. dpkg-deb: building package 'relion-gui-dbgsym' in '../relion-gui-dbgsym_3.1.3-3_armhf.deb'. +dpkg-deb: building package 'relion-gui' in '../relion-gui_3.1.3-3_armhf.deb'. dpkg-deb: building package 'relion-dbgsym' in '../relion-dbgsym_3.1.3-3_armhf.deb'. dpkg-genbuildinfo --build=binary -O../relion_3.1.3-3_armhf.buildinfo dpkg-genchanges --build=binary -O../relion_3.1.3-3_armhf.changes @@ -14730,12 +14773,14 @@ 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/29454/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/29454/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/22283 and its subdirectories -I: Current time: Fri Jun 9 00:49:32 -12 2023 -I: pbuilder-time-stamp: 1686314972 +I: removing directory /srv/workspace/pbuilder/29454 and its subdirectories +I: Current time: Sat Jun 10 04:07:23 +14 2023 +I: pbuilder-time-stamp: 1686319643