Diff of the two buildlogs: -- --- b1/build.log 2023-04-27 00:25:34.450244656 +0000 +++ b2/build.log 2023-04-27 00:42:18.325695058 +0000 @@ -1,6 +1,9 @@ -I: pbuilder: network access will be disabled during build -I: Current time: Tue May 28 18:41:53 -12 2024 -I: pbuilder-time-stamp: 1716964913 +W: cgroups are not available on the host, not using them. +unshare: unshare failed: Cannot allocate memory +W: pbuilder: unshare CLONE_NEWNET not available +I: pbuilder: network access is available during build! +I: Current time: Thu Apr 27 14:29:39 +14 2023 +I: pbuilder-time-stamp: 1682555379 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -17,7 +20,7 @@ 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 @@ -30,137 +33,168 @@ dpkg-source: info: applying typos.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/104210/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/14116/tmp/hooks/D01_modify_environment starting +debug: Running on ionos12-i386. +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 Apr 27 14:29 /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/14116/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/14116/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='i386' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16' - DISTRIBUTION='bookworm' - HOME='/root' - HOST_ARCH='i386' + 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]="i686-pc-linux-gnu") + BASH_VERSION='5.2.15(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=i386 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=7' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - INVOCATION_ID='4372b71219d644c8b686506a575a9fc6' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - LD_LIBRARY_PATH='/usr/lib/libeatmydata' - LD_PRELOAD='libeatmydata.so' - 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='104210' - PS1='# ' - PS2='> ' + LANG=C + LANGUAGE=de_CH:de + LC_ALL=C + LD_LIBRARY_PATH=/usr/lib/libeatmydata + LD_PRELOAD=libeatmydata.so + MACHTYPE=i686-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=14116 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.V6JWve7b/pbuilderrc_wXHV --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.V6JWve7b/b1 --logfile b1/build.log relion_3.1.3-3.dsc' - SUDO_GID='112' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://85.184.249.68:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.V6JWve7b/pbuilderrc_xvaM --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.V6JWve7b/b2 --logfile b2/build.log --extrapackages usrmerge relion_3.1.3-3.dsc' + SUDO_GID=112 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://78.137.99.97:3128 I: uname -a - Linux ionos16-i386 5.10.0-21-amd64 #1 SMP Debian 5.10.162-1 (2023-01-21) x86_64 GNU/Linux + Linux i-capture-the-hostname 5.10.0-21-686-pae #1 SMP Debian 5.10.162-1 (2023-01-21) i686 GNU/Linux I: ls -l /bin total 6036 - -rwxr-xr-x 1 root root 1408088 Apr 23 2023 bash - -rwxr-xr-x 3 root root 38404 Sep 18 2022 bunzip2 - -rwxr-xr-x 3 root root 38404 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 38404 Sep 18 2022 bzip2 - -rwxr-xr-x 1 root root 17892 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 42920 Sep 20 2022 cat - -rwxr-xr-x 1 root root 79816 Sep 20 2022 chgrp - -rwxr-xr-x 1 root root 67496 Sep 20 2022 chmod - -rwxr-xr-x 1 root root 79816 Sep 20 2022 chown - -rwxr-xr-x 1 root root 162024 Sep 20 2022 cp - -rwxr-xr-x 1 root root 136916 Jan 5 2023 dash - -rwxr-xr-x 1 root root 137160 Sep 20 2022 date - -rwxr-xr-x 1 root root 100364 Sep 20 2022 dd - -rwxr-xr-x 1 root root 108940 Sep 20 2022 df - -rwxr-xr-x 1 root root 162152 Sep 20 2022 dir - -rwxr-xr-x 1 root root 87760 Mar 22 2023 dmesg - lrwxrwxrwx 1 root root 8 Dec 19 2022 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Dec 19 2022 domainname -> hostname - -rwxr-xr-x 1 root root 38760 Sep 20 2022 echo - -rwxr-xr-x 1 root root 41 Jan 24 2023 egrep - -rwxr-xr-x 1 root root 34664 Sep 20 2022 false - -rwxr-xr-x 1 root root 41 Jan 24 2023 fgrep - -rwxr-xr-x 1 root root 84272 Mar 22 2023 findmnt - -rwsr-xr-x 1 root root 30240 Mar 22 2023 fusermount - -rwxr-xr-x 1 root root 218680 Jan 24 2023 grep - -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip - -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe - -rwxr-xr-x 1 root root 100952 Apr 9 2022 gzip - -rwxr-xr-x 1 root root 21916 Dec 19 2022 hostname - -rwxr-xr-x 1 root root 75756 Sep 20 2022 ln - -rwxr-xr-x 1 root root 55600 Mar 22 2023 login - -rwxr-xr-x 1 root root 162152 Sep 20 2022 ls - -rwxr-xr-x 1 root root 214568 Mar 22 2023 lsblk - -rwxr-xr-x 1 root root 96328 Sep 20 2022 mkdir - -rwxr-xr-x 1 root root 84008 Sep 20 2022 mknod - -rwxr-xr-x 1 root root 38792 Sep 20 2022 mktemp - -rwxr-xr-x 1 root root 63016 Mar 22 2023 more - -rwsr-xr-x 1 root root 58912 Mar 22 2023 mount - -rwxr-xr-x 1 root root 13856 Mar 22 2023 mountpoint - -rwxr-xr-x 1 root root 157932 Sep 20 2022 mv - lrwxrwxrwx 1 root root 8 Dec 19 2022 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 2 2023 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 38792 Sep 20 2022 pwd - lrwxrwxrwx 1 root root 4 Apr 23 2023 rbash -> bash - -rwxr-xr-x 1 root root 51080 Sep 20 2022 readlink - -rwxr-xr-x 1 root root 75720 Sep 20 2022 rm - -rwxr-xr-x 1 root root 51080 Sep 20 2022 rmdir - -rwxr-xr-x 1 root root 22308 Nov 2 2022 run-parts - -rwxr-xr-x 1 root root 133224 Jan 5 2023 sed - lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash - -rwxr-xr-x 1 root root 38760 Sep 20 2022 sleep - -rwxr-xr-x 1 root root 87976 Sep 20 2022 stty - -rwsr-xr-x 1 root root 83492 Mar 22 2023 su - -rwxr-xr-x 1 root root 38792 Sep 20 2022 sync - -rwxr-xr-x 1 root root 598456 Apr 6 2023 tar - -rwxr-xr-x 1 root root 13860 Nov 2 2022 tempfile - -rwxr-xr-x 1 root root 120776 Sep 20 2022 touch - -rwxr-xr-x 1 root root 34664 Sep 20 2022 true - -rwxr-xr-x 1 root root 17892 Mar 22 2023 ulockmgr_server - -rwsr-xr-x 1 root root 30236 Mar 22 2023 umount - -rwxr-xr-x 1 root root 38760 Sep 20 2022 uname - -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress - -rwxr-xr-x 1 root root 162152 Sep 20 2022 vdir - -rwxr-xr-x 1 root root 71216 Mar 22 2023 wdctl - lrwxrwxrwx 1 root root 8 Dec 19 2022 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat - -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp - -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff - -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep - -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep - -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce - -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep - -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless - -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore - -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew -I: user script /srv/workspace/pbuilder/104210/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1408088 Apr 24 11:24 bash + -rwxr-xr-x 3 root root 38404 Sep 19 2022 bunzip2 + -rwxr-xr-x 3 root root 38404 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 38404 Sep 19 2022 bzip2 + -rwxr-xr-x 1 root root 17892 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 42920 Sep 21 2022 cat + -rwxr-xr-x 1 root root 79816 Sep 21 2022 chgrp + -rwxr-xr-x 1 root root 67496 Sep 21 2022 chmod + -rwxr-xr-x 1 root root 79816 Sep 21 2022 chown + -rwxr-xr-x 1 root root 162024 Sep 21 2022 cp + -rwxr-xr-x 1 root root 136916 Jan 6 03:20 dash + -rwxr-xr-x 1 root root 137160 Sep 21 2022 date + -rwxr-xr-x 1 root root 100364 Sep 21 2022 dd + -rwxr-xr-x 1 root root 108940 Sep 21 2022 df + -rwxr-xr-x 1 root root 162152 Sep 21 2022 dir + -rwxr-xr-x 1 root root 87760 Mar 24 00:20 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 38760 Sep 21 2022 echo + -rwxr-xr-x 1 root root 41 Jan 25 04:43 egrep + -rwxr-xr-x 1 root root 34664 Sep 21 2022 false + -rwxr-xr-x 1 root root 41 Jan 25 04:43 fgrep + -rwxr-xr-x 1 root root 84272 Mar 24 00:20 findmnt + -rwsr-xr-x 1 root root 30240 Mar 23 22:38 fusermount + -rwxr-xr-x 1 root root 218680 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 100952 Apr 10 2022 gzip + -rwxr-xr-x 1 root root 21916 Dec 20 03:33 hostname + -rwxr-xr-x 1 root root 75756 Sep 21 2022 ln + -rwxr-xr-x 1 root root 55600 Mar 24 01:43 login + -rwxr-xr-x 1 root root 162152 Sep 21 2022 ls + -rwxr-xr-x 1 root root 214568 Mar 24 00:20 lsblk + -rwxr-xr-x 1 root root 96328 Sep 21 2022 mkdir + -rwxr-xr-x 1 root root 84008 Sep 21 2022 mknod + -rwxr-xr-x 1 root root 38792 Sep 21 2022 mktemp + -rwxr-xr-x 1 root root 63016 Mar 24 00:20 more + -rwsr-xr-x 1 root root 58912 Mar 24 00:20 mount + -rwxr-xr-x 1 root root 13856 Mar 24 00:20 mountpoint + -rwxr-xr-x 1 root root 157932 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 38792 Sep 21 2022 pwd + lrwxrwxrwx 1 root root 4 Apr 24 11:24 rbash -> bash + -rwxr-xr-x 1 root root 51080 Sep 21 2022 readlink + -rwxr-xr-x 1 root root 75720 Sep 21 2022 rm + -rwxr-xr-x 1 root root 51080 Sep 21 2022 rmdir + -rwxr-xr-x 1 root root 22308 Nov 3 06:31 run-parts + -rwxr-xr-x 1 root root 133224 Jan 6 09:55 sed + lrwxrwxrwx 1 root root 9 Apr 27 14:29 sh -> /bin/bash + -rwxr-xr-x 1 root root 38760 Sep 21 2022 sleep + -rwxr-xr-x 1 root root 87976 Sep 21 2022 stty + -rwsr-xr-x 1 root root 83492 Mar 24 00:20 su + -rwxr-xr-x 1 root root 38792 Sep 21 2022 sync + -rwxr-xr-x 1 root root 598456 Apr 7 04:25 tar + -rwxr-xr-x 1 root root 13860 Nov 3 06:31 tempfile + -rwxr-xr-x 1 root root 120776 Sep 21 2022 touch + -rwxr-xr-x 1 root root 34664 Sep 21 2022 true + -rwxr-xr-x 1 root root 17892 Mar 23 22:38 ulockmgr_server + -rwsr-xr-x 1 root root 30236 Mar 24 00:20 umount + -rwxr-xr-x 1 root root 38760 Sep 21 2022 uname + -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress + -rwxr-xr-x 1 root root 162152 Sep 21 2022 vdir + -rwxr-xr-x 1 root root 71216 Mar 24 00:20 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/14116/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -385,7 +419,7 @@ Get: 175 http://deb.debian.org/debian bookworm/main i386 libtiff6 i386 4.5.0-5 [332 kB] Get: 176 http://deb.debian.org/debian bookworm/main i386 libtiffxx6 i386 4.5.0-5 [144 kB] Get: 177 http://deb.debian.org/debian bookworm/main i386 libtiff-dev i386 4.5.0-5 [479 kB] -Fetched 121 MB in 2s (48.7 MB/s) +Fetched 121 MB in 2s (60.8 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libproc2-0:i386. (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 ... 19604 files and directories currently installed.) @@ -1111,8 +1145,18 @@ 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/14116/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/14116/tmp/hooks/A99_set_merged_usr finished +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 @@ -1243,7 +1287,7 @@ 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 -j16 -C build +/usr/bin/make -j7 -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 @@ -1263,54 +1307,34 @@ /usr/bin/make -f src/apps/CMakeFiles/relion_lib.dir/build.make src/apps/CMakeFiles/relion_lib.dir/build 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 -[ 1%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/__/macros.cpp.o -[ 1%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/CPlot2D.cpp.o -[ 2%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/autopicker.cpp.o -[ 2%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/assembly.cpp.o -[ 2%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/autopicker_mpi.cpp.o -[ 3%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/backprojector.cpp.o -[ 3%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ctf.cpp.o +[ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 -[ 3%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/complex.cpp.o +[ 1%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/CPlot2D.cpp.o +[ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 -[ 3%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 /usr/bin/cmake -E copy /build/relion-3.1.3/scripts/star_loopheader /build/relion-3.1.3/build/bin/relion_star_loopheader -[ 4%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 -[ 4%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ctffind_runner_mpi.cpp.o -[ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 +[ 2%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/autopicker_mpi.cpp.o +[ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 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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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/i386-linux-gnu/openmpi/include 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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 -[ 5%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ctffind_runner.cpp.o -[ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 -cd 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-I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 /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' -[ 6%] Built target copy_scripts -[ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 -[ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 +[ 2%] Built target copy_scripts +[ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 +[ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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/exp_model.h:24, - from /build/relion-3.1.3/src/exp_model.cpp:20: + 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 @@ -1369,9 +1393,9 @@ 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/jaz/obs_model.h:24, - from /build/relion-3.1.3/src/ctf.h:50, - from /build/relion-3.1.3/src/ctf.cpp:45: + 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/backprojector.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 @@ -1430,8 +1454,9 @@ 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/ctffind_runner.h:31, - from /build/relion-3.1.3/src/ctffind_runner.cpp:20: + 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 @@ -1465,9 +1490,34 @@ /usr/include/i386-linux-gnu/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/i386-linux-gnu/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/i386-linux-gnu/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/i386-linux-gnu/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/i386-linux-gnu/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/autopicker.h:10, - from /build/relion-3.1.3/src/autopicker.cpp:20: + 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/ctf.cpp:45: /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 @@ -1525,34 +1575,58 @@ /usr/include/i386-linux-gnu/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/i386-linux-gnu/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/i386-linux-gnu/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/i386-linux-gnu/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/i386-linux-gnu/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ +[ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 +[ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 +/build/relion-3.1.3/src/CPlot2D.cpp: In member function 'void CPlot2D::ComputeLabelTickSpacing(double, double, double*, double*, double*, int, std::string)': +/build/relion-3.1.3/src/CPlot2D.cpp:743:41: warning: '%d' directive writing between 1 and 10 bytes into a region of size 8 [-Wformat-overflow=] + 743 | sprintf(m_cYAxisLabelFormat,"%%.%df",nfrac); + | ^~ +/build/relion-3.1.3/src/CPlot2D.cpp:743:37: note: directive argument in the range [0, 2147483647] + 743 | sprintf(m_cYAxisLabelFormat,"%%.%df",nfrac); + | ^~~~~~~~ +In file included from /usr/include/stdio.h:906, + from /usr/include/c++/12/cstdio:42, + from /usr/include/c++/12/ext/string_conversions.h:43, + from /usr/include/c++/12/bits/basic_string.h:3960, + from /usr/include/c++/12/string:53, + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/ostream:38, + from /usr/include/c++/12/iostream:39, + from /build/relion-3.1.3/src/CPlot2D.cpp:21: +In function 'int sprintf(char*, const char*, ...)', + inlined from 'void CPlot2D::ComputeLabelTickSpacing(double, double, double*, double*, double*, int, std::string)' at /build/relion-3.1.3/src/CPlot2D.cpp:743:16: +/usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 5 and 14 bytes into a destination of size 10 + 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 31 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 32 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ +/build/relion-3.1.3/src/CPlot2D.cpp: In member function 'void CPlot2D::ComputeLabelTickSpacing(double, double, double*, double*, double*, int, std::string)': +/build/relion-3.1.3/src/CPlot2D.cpp:733:41: warning: '%d' directive writing between 1 and 10 bytes into a region of size 8 [-Wformat-overflow=] + 733 | sprintf(m_cXAxisLabelFormat,"%%.%df",nfrac); + | ^~ +/build/relion-3.1.3/src/CPlot2D.cpp:733:37: note: directive argument in the range [0, 2147483647] + 733 | sprintf(m_cXAxisLabelFormat,"%%.%df",nfrac); + | ^~~~~~~~ +In function 'int sprintf(char*, const char*, ...)', + inlined from 'void CPlot2D::ComputeLabelTickSpacing(double, double, double*, double*, double*, int, std::string)' at /build/relion-3.1.3/src/CPlot2D.cpp:733:16: +/usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 5 and 14 bytes into a destination of size 10 + 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 31 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 32 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ +[ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 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: + from /build/relion-3.1.3/src/ctffind_runner.h:31, + from /build/relion-3.1.3/src/ctffind_runner.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 @@ -1611,9 +1685,9 @@ 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/projector.h:25, - from /build/relion-3.1.3/src/backprojector.h:33, - from /build/relion-3.1.3/src/backprojector.cpp:27: + 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/ctffind_runner_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 @@ -1671,10 +1745,17 @@ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +[ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 +[ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 /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/ctffind_runner_mpi.cpp:20: + from /build/relion-3.1.3/src/exp_model.h:24, + from /build/relion-3.1.3/src/exp_model.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 @@ -1732,6 +1813,8 @@ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +[ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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, @@ -1793,10 +1876,46 @@ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 -[ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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/stdio.h:906, + from /usr/include/c++/12/cstdio:42, + from /usr/include/c++/12/ext/string_conversions.h:43, + from /usr/include/c++/12/bits/basic_string.h:3960, + from /usr/include/c++/12/string:53, + from /build/relion-3.1.3/src/ctffind_runner.h:26: +In function 'size_t fread(void*, size_t, size_t, FILE*)', + inlined from 'int Image::readSPIDER(long int) [with T = double]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: +/usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] + 239 | return __fread_chk_warn (__ptr, sz, __size, __n, __stream); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 file included from /usr/include/stdio.h:906, + from /usr/include/fftw3.h:50, + from /build/relion-3.1.3/src/fftw.h:49, + from /build/relion-3.1.3/src/projector.h:23: +In function 'size_t fread(void*, size_t, size_t, FILE*)', + inlined from 'int Image::readSPIDER(long int) [with T = double]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: +/usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] + 239 | return __fread_chk_warn (__ptr, sz, __size, __n, __stream); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/stdio.h:906, + from /usr/include/c++/12/cstdio:42, + from /usr/include/c++/12/ext/string_conversions.h:43, + from /usr/include/c++/12/bits/basic_string.h:3960, + from /usr/include/c++/12/string:53, + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/istream:38, + from /usr/include/c++/12/fstream:38, + from /build/relion-3.1.3/src/exp_model.h:22: +In function 'size_t fread(void*, size_t, size_t, FILE*)', + inlined from 'int Image::readSPIDER(long int) [with T = double]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: +/usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] + 239 | return __fread_chk_warn (__ptr, sz, __size, __n, __stream); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 /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, @@ -1858,8 +1977,15 @@ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 +[ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 +[ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 function 'size_t fread(void*, size_t, size_t, FILE*)', + inlined from 'int Image::readSPIDER(long int) [with T = float]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: +/usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] + 239 | return __fread_chk_warn (__ptr, sz, __size, __n, __stream); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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: @@ -1920,8 +2046,6 @@ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 /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: @@ -1982,10 +2106,31 @@ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 -[ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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/stdio.h:906, + from /usr/include/i386-linux-gnu/tiffio.h:267: +In function 'size_t fread(void*, size_t, size_t, FILE*)', + inlined from 'int Image::readSPIDER(long int) [with T = double]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: +/usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] + 239 | return __fread_chk_warn (__ptr, sz, __size, __n, __stream); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 /usr/include/stdio.h:906, + from /usr/include/c++/12/cstdio:42, + from /usr/include/c++/12/ext/string_conversions.h:43, + from /usr/include/c++/12/bits/basic_string.h:3960, + from /usr/include/c++/12/string:53, + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/istream:38, + from /usr/include/c++/12/fstream:38, + from /build/relion-3.1.3/src/exp_model.h:22: +In function 'size_t fread(void*, size_t, size_t, FILE*)', + inlined from 'int Image::readSPIDER(long int) [with T = double]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: +/usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] + 239 | return __fread_chk_warn (__ptr, sz, __size, __n, __stream); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/image.cpp:20: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': @@ -2045,8 +2190,15 @@ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 function 'size_t fread(void*, size_t, size_t, FILE*)', + inlined from 'int Image::readSPIDER(long int) [with T = int]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: +/usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] + 239 | return __fread_chk_warn (__ptr, sz, __size, __n, __stream); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 +[ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 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: @@ -2107,51 +2259,13 @@ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -/build/relion-3.1.3/src/CPlot2D.cpp: In member function 'void CPlot2D::ComputeLabelTickSpacing(double, double, double*, double*, double*, int, std::string)': -/build/relion-3.1.3/src/CPlot2D.cpp:743:41: warning: '%d' directive writing between 1 and 10 bytes into a region of size 8 [-Wformat-overflow=] - 743 | sprintf(m_cYAxisLabelFormat,"%%.%df",nfrac); - | ^~ -/build/relion-3.1.3/src/CPlot2D.cpp:743:37: note: directive argument in the range [0, 2147483647] - 743 | sprintf(m_cYAxisLabelFormat,"%%.%df",nfrac); - | ^~~~~~~~ -In file included from /usr/include/stdio.h:906, - from /usr/include/c++/12/cstdio:42, - from /usr/include/c++/12/ext/string_conversions.h:43, - from /usr/include/c++/12/bits/basic_string.h:3960, - from /usr/include/c++/12/string:53, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/ostream:38, - from /usr/include/c++/12/iostream:39, - from /build/relion-3.1.3/src/CPlot2D.cpp:21: -In function 'int sprintf(char*, const char*, ...)', - inlined from 'void CPlot2D::ComputeLabelTickSpacing(double, double, double*, double*, double*, int, std::string)' at /build/relion-3.1.3/src/CPlot2D.cpp:743:16: -/usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 5 and 14 bytes into a destination of size 10 - 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 31 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 32 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ -/build/relion-3.1.3/src/CPlot2D.cpp: In member function 'void CPlot2D::ComputeLabelTickSpacing(double, double, double*, double*, double*, int, std::string)': -/build/relion-3.1.3/src/CPlot2D.cpp:733:41: warning: '%d' directive writing between 1 and 10 bytes into a region of size 8 [-Wformat-overflow=] - 733 | sprintf(m_cXAxisLabelFormat,"%%.%df",nfrac); - | ^~ -/build/relion-3.1.3/src/CPlot2D.cpp:733:37: note: directive argument in the range [0, 2147483647] - 733 | sprintf(m_cXAxisLabelFormat,"%%.%df",nfrac); - | ^~~~~~~~ -In function 'int sprintf(char*, const char*, ...)', - inlined from 'void CPlot2D::ComputeLabelTickSpacing(double, double, double*, double*, double*, int, std::string)' at /build/relion-3.1.3/src/CPlot2D.cpp:733:16: -/usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 5 and 14 bytes into a destination of size 10 - 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 31 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 32 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ -[ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 function 'size_t fread(void*, size_t, size_t, FILE*)', + inlined from 'int Image::readSPIDER(long int) [with T = float]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: +/usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] + 239 | return __fread_chk_warn (__ptr, sz, __size, __n, __stream); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 /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, @@ -2213,8 +2327,30 @@ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +In file included from /usr/include/stdio.h:906, + from /build/relion-3.1.3/src/parallel.h:48, + from /build/relion-3.1.3/src/helix_inimodel2d.h:25: +In function 'size_t fread(void*, size_t, size_t, FILE*)', + inlined from 'int Image::readSPIDER(long int) [with T = double]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: +/usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] + 239 | return __fread_chk_warn (__ptr, sz, __size, __n, __stream); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 +In file included from /usr/include/stdio.h:906, + from /usr/lib/i386-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx/mpicxx.h:54, + from /usr/lib/i386-linux-gnu/openmpi/include/mpi.h:2887, + from /build/relion-3.1.3/src/mpi.h:47, + from /build/relion-3.1.3/src/local_symmetry_mpi.h:4: +In function 'size_t fread(void*, size_t, size_t, FILE*)', + inlined from 'int Image::readSPIDER(long int) [with T = double]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: +/usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] + 239 | return __fread_chk_warn (__ptr, sz, __size, __n, __stream); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 @@ -2225,15 +2361,8 @@ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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/stdio.h:906, from /usr/include/c++/12/cstdio:42, - from /usr/include/c++/12/ext/string_conversions.h:43, - from /usr/include/c++/12/bits/basic_string.h:3960, - from /usr/include/c++/12/string:53, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/istream:38, - from /usr/include/c++/12/fstream:38, - from /build/relion-3.1.3/src/exp_model.h:22: + from /build/relion-3.1.3/src/args.h:48, + from /build/relion-3.1.3/src/local_symmetry.h:24: In function 'size_t fread(void*, size_t, size_t, FILE*)', inlined from 'int Image::readSPIDER(long int) [with T = double]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: /usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] @@ -2241,19 +2370,6 @@ | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 12%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ml_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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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_model.cpp.o -MF CMakeFiles/relion_lib.dir/__/ml_model.cpp.o.d -o CMakeFiles/relion_lib.dir/__/ml_model.cpp.o -c /build/relion-3.1.3/src/ml_model.cpp -In file included from /usr/include/stdio.h:906, - from /usr/include/c++/12/cstdio:42, - from /usr/include/c++/12/ext/string_conversions.h:43, - from /usr/include/c++/12/bits/basic_string.h:3960, - from /usr/include/c++/12/string:53, - from /build/relion-3.1.3/src/ctffind_runner.h:26: -In function 'size_t fread(void*, size_t, size_t, FILE*)', - inlined from 'int Image::readSPIDER(long int) [with T = double]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: -/usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] - 239 | return __fread_chk_warn (__ptr, sz, __size, __n, __stream); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 13%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ml_optimiser.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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.cpp.o -MF CMakeFiles/relion_lib.dir/__/ml_optimiser.cpp.o.d -o CMakeFiles/relion_lib.dir/__/ml_optimiser.cpp.o -c /build/relion-3.1.3/src/ml_optimiser.cpp 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&)': @@ -2374,8 +2490,52 @@ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +In file included from /usr/include/stdio.h:906, + from /usr/include/c++/12/cstdio:42, + from /usr/include/c++/12/ext/string_conversions.h:43, + from /usr/include/c++/12/bits/basic_string.h:3960, + from /usr/include/c++/12/string:53, + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/ostream:38, + from /usr/include/c++/12/iostream:39, + from /build/relion-3.1.3/src/filename.h:48, + from /build/relion-3.1.3/src/micrograph_model.h:24, + from /build/relion-3.1.3/src/micrograph_model.cpp:21: +In function 'size_t fread(void*, size_t, size_t, FILE*)', + inlined from 'int Image::readSPIDER(long int) [with T = double]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: +/usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] + 239 | return __fread_chk_warn (__ptr, sz, __size, __n, __stream); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/stdio.h:906, + from /usr/include/c++/12/cstdio:42, + from /usr/include/c++/12/ext/string_conversions.h:43, + from /usr/include/c++/12/bits/basic_string.h:3960, + from /usr/include/c++/12/string:53, + from /build/relion-3.1.3/src/pipeline_control.h:24, + from /build/relion-3.1.3/src/macros.h:53, + from /build/relion-3.1.3/src/helix.cpp:21: +In function 'size_t fread(void*, size_t, size_t, FILE*)', + inlined from 'int Image::readSPIDER(long int) [with T = double]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: +/usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] + 239 | return __fread_chk_warn (__ptr, sz, __size, __n, __stream); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 13%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ml_optimiser.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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.cpp.o -MF CMakeFiles/relion_lib.dir/__/ml_optimiser.cpp.o.d -o CMakeFiles/relion_lib.dir/__/ml_optimiser.cpp.o -c /build/relion-3.1.3/src/ml_optimiser.cpp [ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 +[ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 +In file included from /usr/include/stdio.h:906, + from /usr/include/fftw3.h:50, + from /build/relion-3.1.3/src/fftw.h:49, + from /build/relion-3.1.3/src/projector.h:23: +In function 'size_t fread(void*, size_t, size_t, FILE*)', + inlined from 'int Image::readSPIDER(long int) [with T = double]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: +/usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] + 239 | return __fread_chk_warn (__ptr, sz, __size, __n, __stream); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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, @@ -2438,30 +2598,6 @@ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -In file included from /usr/include/stdio.h:906, - from /usr/lib/i386-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx/mpicxx.h:54, - from /usr/lib/i386-linux-gnu/openmpi/include/mpi.h:2887, - from /build/relion-3.1.3/src/mpi.h:47, - from /build/relion-3.1.3/src/local_symmetry_mpi.h:4: -In function 'size_t fread(void*, size_t, size_t, FILE*)', - inlined from 'int Image::readSPIDER(long int) [with T = double]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: -/usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] - 239 | return __fread_chk_warn (__ptr, sz, __size, __n, __stream); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/stdio.h:906, - from /usr/include/fftw3.h:50, - from /build/relion-3.1.3/src/fftw.h:49, - from /build/relion-3.1.3/src/projector.h:23: -In function 'size_t fread(void*, size_t, size_t, FILE*)', - inlined from 'int Image::readSPIDER(long int) [with T = double]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: -/usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] - 239 | return __fread_chk_warn (__ptr, sz, __size, __n, __stream); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In function 'size_t fread(void*, size_t, size_t, FILE*)', - inlined from 'int Image::readSPIDER(long int) [with T = float]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: -/usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] - 239 | return __fread_chk_warn (__ptr, sz, __size, __n, __stream); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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, @@ -2525,54 +2661,6 @@ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -In file included from /usr/include/stdio.h:906, - from /build/relion-3.1.3/src/parallel.h:48, - from /build/relion-3.1.3/src/helix_inimodel2d.h:25: -In function 'size_t fread(void*, size_t, size_t, FILE*)', - inlined from 'int Image::readSPIDER(long int) [with T = double]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: -/usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] - 239 | return __fread_chk_warn (__ptr, sz, __size, __n, __stream); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/stdio.h:906, - from /usr/include/c++/12/cstdio:42, - from /usr/include/c++/12/ext/string_conversions.h:43, - from /usr/include/c++/12/bits/basic_string.h:3960, - from /usr/include/c++/12/string:53, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/istream:38, - from /usr/include/c++/12/fstream:38, - from /build/relion-3.1.3/src/exp_model.h:22: -In function 'size_t fread(void*, size_t, size_t, FILE*)', - inlined from 'int Image::readSPIDER(long int) [with T = double]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: -/usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] - 239 | return __fread_chk_warn (__ptr, sz, __size, __n, __stream); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/stdio.h:906, - from /usr/include/c++/12/cstdio:42, - from /usr/include/c++/12/ext/string_conversions.h:43, - from /usr/include/c++/12/bits/basic_string.h:3960, - from /usr/include/c++/12/string:53, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/ostream:38, - from /usr/include/c++/12/iostream:39, - from /build/relion-3.1.3/src/filename.h:48, - from /build/relion-3.1.3/src/micrograph_model.h:24, - from /build/relion-3.1.3/src/micrograph_model.cpp:21: -In function 'size_t fread(void*, size_t, size_t, FILE*)', - inlined from 'int Image::readSPIDER(long int) [with T = double]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: -/usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] - 239 | return __fread_chk_warn (__ptr, sz, __size, __n, __stream); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 -[ 14%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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/__/mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/mpi.cpp.o -c /build/relion-3.1.3/src/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: @@ -2633,31 +2721,8 @@ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -In file included from /usr/include/stdio.h:906, - from /usr/include/c++/12/cstdio:42, - from /build/relion-3.1.3/src/args.h:48, - from /build/relion-3.1.3/src/local_symmetry.h:24: -In function 'size_t fread(void*, size_t, size_t, FILE*)', - inlined from 'int Image::readSPIDER(long int) [with T = double]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: -/usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] - 239 | return __fread_chk_warn (__ptr, sz, __size, __n, __stream); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/stdio.h:906, - from /usr/include/i386-linux-gnu/tiffio.h:267: -In function 'size_t fread(void*, size_t, size_t, FILE*)', - inlined from 'int Image::readSPIDER(long int) [with T = double]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: -/usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] - 239 | return __fread_chk_warn (__ptr, sz, __size, __n, __stream); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/stdio.h:906, - from /usr/include/fftw3.h:50, - from /build/relion-3.1.3/src/fftw.h:49, - from /build/relion-3.1.3/src/projector.h:23: -In function 'size_t fread(void*, size_t, size_t, FILE*)', - inlined from 'int Image::readSPIDER(long int) [with T = double]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: -/usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] - 239 | return __fread_chk_warn (__ptr, sz, __size, __n, __stream); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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, @@ -2719,6 +2784,18 @@ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +In file included from /usr/include/stdio.h:906, + from /usr/lib/i386-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx/mpicxx.h:54, + from /usr/lib/i386-linux-gnu/openmpi/include/mpi.h:2887, + from /build/relion-3.1.3/src/mpi.h:47, + from /build/relion-3.1.3/src/ml_optimiser_mpi.h:23: +In function 'size_t fread(void*, size_t, size_t, FILE*)', + inlined from 'int Image::readSPIDER(long int) [with T = double]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: +/usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] + 239 | return __fread_chk_warn (__ptr, sz, __size, __n, __stream); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 14%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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/__/mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/mpi.cpp.o -c /build/relion-3.1.3/src/mpi.cpp [ 15%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/multidim_array.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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/__/multidim_array.cpp.o -MF CMakeFiles/relion_lib.dir/__/multidim_array.cpp.o.d -o CMakeFiles/relion_lib.dir/__/multidim_array.cpp.o -c /build/relion-3.1.3/src/multidim_array.cpp [ 15%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/numerical_recipes.cpp.o @@ -2727,17 +2804,6 @@ cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 [ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 -[ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 function 'size_t fread(void*, size_t, size_t, FILE*)', - inlined from 'int Image::readSPIDER(long int) [with T = int]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: -/usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] - 239 | return __fread_chk_warn (__ptr, sz, __size, __n, __stream); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 file included from /build/relion-3.1.3/src/numerical_recipes.h:48, from /build/relion-3.1.3/src/numerical_recipes.cpp:49: In function 'void free_Tvector(T*&, int, int) [with T = double]', @@ -2749,8 +2815,6 @@ /build/relion-3.1.3/src/numerical_recipes.cpp:579:13: note: declared here 579 | RFLOAT *xt=NULL; | ^~ -[ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 function 'void free_Tvector(T*&, int, int) [with T = double]', inlined from 'void linmin(double*, double*, int, double&, double (*)(double*, void*), void*)' at /build/relion-3.1.3/src/numerical_recipes.cpp:691:17: /build/relion-3.1.3/src/memory.h:74:13: warning: 'void free(void*)' called on pointer 'xicom' with nonzero offset 8 [-Wfree-nonheap-object] @@ -2796,6 +2860,10 @@ /build/relion-3.1.3/src/numerical_recipes.cpp:703:13: note: declared here 703 | RFLOAT *pt, *ptt, *xit; | ^~ +[ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 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, @@ -2859,22 +2927,21 @@ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 18%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/preprocessing.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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/__/preprocessing.cpp.o -MF CMakeFiles/relion_lib.dir/__/preprocessing.cpp.o.d -o CMakeFiles/relion_lib.dir/__/preprocessing.cpp.o -c /build/relion-3.1.3/src/preprocessing.cpp -[ 18%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/preprocessing_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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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/__/preprocessing_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/preprocessing_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/preprocessing_mpi.cpp.o -c /build/relion-3.1.3/src/preprocessing_mpi.cpp -[ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 +[ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 file included from /usr/include/stdio.h:906, - from /usr/lib/i386-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx/mpicxx.h:54, - from /usr/lib/i386-linux-gnu/openmpi/include/mpi.h:2887, - from /build/relion-3.1.3/src/mpi.h:47, - from /build/relion-3.1.3/src/ml_optimiser_mpi.h:23: + from /usr/include/c++/12/cstdio:42, + from /usr/include/c++/12/ext/string_conversions.h:43, + from /usr/include/c++/12/bits/basic_string.h:3960, + from /usr/include/c++/12/string:53, + from /build/relion-3.1.3/src/motioncorr_runner.h:26: In function 'size_t fread(void*, size_t, size_t, FILE*)', inlined from 'int Image::readSPIDER(long int) [with T = double]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: /usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] 239 | return __fread_chk_warn (__ptr, sz, __size, __n, __stream); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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, from /build/relion-3.1.3/src/postprocessing.h:24, from /build/relion-3.1.3/src/postprocessing.cpp:21: @@ -2935,6 +3002,31 @@ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +In function 'size_t fread(void*, size_t, size_t, FILE*)', + inlined from 'int Image::readSPIDER(long int) [with T = float]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: +/usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] + 239 | return __fread_chk_warn (__ptr, sz, __size, __n, __stream); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/stdio.h:906, + from /build/relion-3.1.3/src/ml_optimiser.cpp:35: +In function 'size_t fread(void*, size_t, size_t, FILE*)', + inlined from 'int Image::readSPIDER(long int) [with T = double]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: +/usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] + 239 | return __fread_chk_warn (__ptr, sz, __size, __n, __stream); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/stdio.h:906, + from /usr/include/c++/12/cstdio:42, + from /usr/include/c++/12/ext/string_conversions.h:43, + from /usr/include/c++/12/bits/basic_string.h:3960, + from /usr/include/c++/12/string:53, + from /build/relion-3.1.3/src/ml_optimiser.h:31: +In function 'size_t fread(void*, size_t, size_t, FILE*)', + inlined from 'int Image::readSPIDER(long int) [with T = double]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: +/usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] + 239 | return __fread_chk_warn (__ptr, sz, __size, __n, __stream); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 18%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/preprocessing.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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/__/preprocessing.cpp.o -MF CMakeFiles/relion_lib.dir/__/preprocessing.cpp.o.d -o CMakeFiles/relion_lib.dir/__/preprocessing.cpp.o -c /build/relion-3.1.3/src/preprocessing.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.cpp:20: @@ -2995,6 +3087,17 @@ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +In file included from /usr/include/stdio.h:906, + from /usr/include/i386-linux-gnu/tiffio.h:267: +In function 'size_t fread(void*, size_t, size_t, FILE*)', + inlined from 'int Image::readSPIDER(long int) [with T = double]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: +/usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] + 239 | return __fread_chk_warn (__ptr, sz, __size, __n, __stream); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 18%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/preprocessing_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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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/__/preprocessing_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/preprocessing_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/preprocessing_mpi.cpp.o -c /build/relion-3.1.3/src/preprocessing_mpi.cpp +[ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 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, @@ -3118,11 +3221,6 @@ | ^~~~~~ [ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 function 'size_t fread(void*, size_t, size_t, FILE*)', - inlined from 'int Image::readSPIDER(long int) [with T = float]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: -/usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] - 239 | return __fread_chk_warn (__ptr, sz, __size, __n, __stream); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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, @@ -3185,21 +3283,21 @@ /usr/include/i386-linux-gnu/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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 /usr/include/stdio.h:906, from /usr/include/c++/12/cstdio:42, from /usr/include/c++/12/ext/string_conversions.h:43, from /usr/include/c++/12/bits/basic_string.h:3960, from /usr/include/c++/12/string:53, - from /build/relion-3.1.3/src/pipeline_control.h:24, - from /build/relion-3.1.3/src/macros.h:53, - from /build/relion-3.1.3/src/helix.cpp:21: + from /build/relion-3.1.3/src/preprocessing.h:26: In function 'size_t fread(void*, size_t, size_t, FILE*)', inlined from 'int Image::readSPIDER(long int) [with T = double]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: /usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] 239 | return __fread_chk_warn (__ptr, sz, __size, __n, __stream); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 +[ 20%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/renderEER.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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/__/renderEER.cpp.o -MF CMakeFiles/relion_lib.dir/__/renderEER.cpp.o.d -o CMakeFiles/relion_lib.dir/__/renderEER.cpp.o -c /build/relion-3.1.3/src/renderEER.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, @@ -3263,8 +3361,8 @@ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 20%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/renderEER.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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/__/renderEER.cpp.o -MF CMakeFiles/relion_lib.dir/__/renderEER.cpp.o.d -o CMakeFiles/relion_lib.dir/__/renderEER.cpp.o -c /build/relion-3.1.3/src/renderEER.cpp +[ 20%] Building CXX object src/apps/CMakeFiles/relion_lib.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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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/__/scheduler.cpp.o -MF CMakeFiles/relion_lib.dir/__/scheduler.cpp.o.d -o CMakeFiles/relion_lib.dir/__/scheduler.cpp.o -c /build/relion-3.1.3/src/scheduler.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/renderEER.cpp:10: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': @@ -3328,34 +3426,6 @@ /build/relion-3.1.3/src/renderEER.cpp:191:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 191 | fread(buf, sizeof(char), file_size, fh); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/stdio.h:906, - from /usr/include/c++/12/cstdio:42, - from /usr/include/c++/12/ext/string_conversions.h:43, - from /usr/include/c++/12/bits/basic_string.h:3960, - from /usr/include/c++/12/string:53, - from /build/relion-3.1.3/src/ml_optimiser.h:31: -In function 'size_t fread(void*, size_t, size_t, FILE*)', - inlined from 'int Image::readSPIDER(long int) [with T = double]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: -/usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] - 239 | return __fread_chk_warn (__ptr, sz, __size, __n, __stream); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 20%] Building CXX object src/apps/CMakeFiles/relion_lib.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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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/__/scheduler.cpp.o -MF CMakeFiles/relion_lib.dir/__/scheduler.cpp.o.d -o CMakeFiles/relion_lib.dir/__/scheduler.cpp.o -c /build/relion-3.1.3/src/scheduler.cpp -[ 20%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/strings.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 -In file included from /usr/include/stdio.h:906, - from /usr/include/c++/12/cstdio:42, - from /usr/include/c++/12/ext/string_conversions.h:43, - from /usr/include/c++/12/bits/basic_string.h:3960, - from /usr/include/c++/12/string:53, - from /build/relion-3.1.3/src/preprocessing.h:26: -In function 'size_t fread(void*, size_t, size_t, FILE*)', - inlined from 'int Image::readSPIDER(long int) [with T = double]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: -/usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] - 239 | return __fread_chk_warn (__ptr, sz, __size, __n, __stream); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 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, @@ -3417,37 +3487,16 @@ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -In file included from /usr/include/stdio.h:906, - from /usr/include/i386-linux-gnu/tiffio.h:267: -In function 'size_t fread(void*, size_t, size_t, FILE*)', - inlined from 'int Image::readSPIDER(long int) [with T = double]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: -/usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] - 239 | return __fread_chk_warn (__ptr, sz, __size, __n, __stream); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/stdio.h:906, - from /usr/include/c++/12/cstdio:42, - from /usr/include/c++/12/ext/string_conversions.h:43, - from /usr/include/c++/12/bits/basic_string.h:3960, - from /usr/include/c++/12/string:53, - from /build/relion-3.1.3/src/motioncorr_runner.h:26: -In function 'size_t fread(void*, size_t, size_t, FILE*)', - inlined from 'int Image::readSPIDER(long int) [with T = double]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: -/usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] - 239 | return __fread_chk_warn (__ptr, sz, __size, __n, __stream); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 20%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/strings.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 file included from /usr/include/stdio.h:906, - from /usr/include/fftw3.h:50, - from /build/relion-3.1.3/src/fftw.h:49, - from /build/relion-3.1.3/src/projector.h:23: -In function 'size_t fread(void*, size_t, size_t, FILE*)', - inlined from 'int Image::readSPIDER(long int) [with T = double]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: -/usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] - 239 | return __fread_chk_warn (__ptr, sz, __size, __n, __stream); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 +[ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 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&)': @@ -3507,8 +3556,6 @@ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 /build/relion-3.1.3/src/tiff_converter.cpp: In member function 'void TIFFConverter::estimate(FileName)': /build/relion-3.1.3/src/tiff_converter.cpp:141:101: warning: format '%d' expects argument of type 'int', but argument 7 has type 'long int' [-Wformat=] 141 | printf(" %s Frame %03d #Changed %10d #Mismatch %10d, #Negative %10d, #Unreliable %10d / %10d\n", @@ -3535,7 +3582,9 @@ 530 | system(("mkdir -p " + fn_tiff.beforeLastOf("/")).c_str()); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:906, - from /build/relion-3.1.3/src/ml_optimiser.cpp:35: + from /usr/include/fftw3.h:50, + from /build/relion-3.1.3/src/fftw.h:49, + from /build/relion-3.1.3/src/projector.h:23: In function 'size_t fread(void*, size_t, size_t, FILE*)', inlined from 'int Image::readSPIDER(long int) [with T = double]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: /usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] @@ -3543,11 +3592,6 @@ | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 function 'size_t fread(void*, size_t, size_t, FILE*)', - inlined from 'int Image::readSPIDER(long int) [with T = float]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: -/usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] - 239 | return __fread_chk_warn (__ptr, sz, __size, __n, __stream); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 @@ -3558,8 +3602,14 @@ cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 /usr/include/stdio.h:906, + from /usr/include/c++/12/cstdio:42, + from /build/relion-3.1.3/src/tiff_converter.cpp:21: +In function 'size_t fread(void*, size_t, size_t, FILE*)', + inlined from 'int Image::readSPIDER(long int) [with T = float]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: +/usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] + 239 | return __fread_chk_warn (__ptr, sz, __size, __n, __stream); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/Fourier_helper.h:24, from /build/relion-3.1.3/src/jaz/Fourier_helper.cpp:21: @@ -3620,12 +3670,8 @@ /usr/include/i386-linux-gnu/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/convolution_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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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/convolution_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/convolution_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/convolution_helper.cpp.o -c /build/relion-3.1.3/src/jaz/convolution_helper.cpp -[ 25%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf_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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf_helper.cpp.o -c /build/relion-3.1.3/src/jaz/ctf_helper.cpp -[ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 +[ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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: @@ -3686,11 +3732,11 @@ /usr/include/i386-linux-gnu/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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 +[ 25%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/convolution_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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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/convolution_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/convolution_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/convolution_helper.cpp.o -c /build/relion-3.1.3/src/jaz/convolution_helper.cpp In file included from /build/relion-3.1.3/src/image.h:455, - from /build/relion-3.1.3/src/jaz/convolution_helper.h:24, - from /build/relion-3.1.3/src/jaz/convolution_helper.cpp:21: + from /build/relion-3.1.3/src/jaz/complex_io.h:24, + from /build/relion-3.1.3/src/jaz/complex_io.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 @@ -3748,9 +3794,11 @@ /usr/include/i386-linux-gnu/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/ctf_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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf_helper.cpp.o -c /build/relion-3.1.3/src/jaz/ctf_helper.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: + from /build/relion-3.1.3/src/jaz/convolution_helper.h:24, + from /build/relion-3.1.3/src/jaz/convolution_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 @@ -3808,10 +3856,6 @@ /usr/include/i386-linux-gnu/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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 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, @@ -3874,8 +3918,15 @@ /usr/include/i386-linux-gnu/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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 +[ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 function 'size_t fread(void*, size_t, size_t, FILE*)', + inlined from 'int Image::readSPIDER(long int) [with T = double]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: +/usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] + 239 | return __fread_chk_warn (__ptr, sz, __size, __n, __stream); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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, @@ -3938,6 +3989,13 @@ /usr/include/i386-linux-gnu/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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 function 'size_t fread(void*, size_t, size_t, FILE*)', + inlined from 'int Image::readSPIDER(long int) [with T = short int]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: +/usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] + 239 | return __fread_chk_warn (__ptr, sz, __size, __n, __stream); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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: @@ -3998,8 +4056,8 @@ /usr/include/i386-linux-gnu/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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 +[ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 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, @@ -4062,22 +4120,15 @@ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -In file included from /usr/include/stdio.h:906, - from /usr/include/c++/12/cstdio:42, - from /build/relion-3.1.3/src/tiff_converter.cpp:21: In function 'size_t fread(void*, size_t, size_t, FILE*)', - inlined from 'int Image::readSPIDER(long int) [with T = float]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: + inlined from 'int Image::readSPIDER(long int) [with T = short unsigned int]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: /usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] 239 | return __fread_chk_warn (__ptr, sz, __size, __n, __stream); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 +[ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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: @@ -4138,8 +4189,10 @@ /usr/include/i386-linux-gnu/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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 +[ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 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: @@ -4200,11 +4253,14 @@ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 +In function 'size_t fread(void*, size_t, size_t, FILE*)', + inlined from 'int Image::readSPIDER(long int) [with T = unsigned char]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: +/usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] + 239 | return __fread_chk_warn (__ptr, sz, __size, __n, __stream); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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: + 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: /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 @@ -4262,9 +4318,22 @@ /usr/include/i386-linux-gnu/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/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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 +In function 'size_t fread(void*, size_t, size_t, FILE*)', + inlined from 'int Image::readSPIDER(long int) [with T = signed char]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: +/usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] + 239 | return __fread_chk_warn (__ptr, sz, __size, __n, __stream); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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: + 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: /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 @@ -4323,8 +4392,9 @@ 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/jaz/micrograph_handler.h:31, - from /build/relion-3.1.3/src/jaz/micrograph_handler.cpp:21: + from /build/relion-3.1.3/src/projector.h:25, + from /build/relion-3.1.3/src/jaz/noise_helper.h:25, + from /build/relion-3.1.3/src/jaz/noise_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 @@ -4383,9 +4453,8 @@ 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/jaz/noise_helper.h:25, - from /build/relion-3.1.3/src/jaz/noise_helper.cpp:21: + from /build/relion-3.1.3/src/jaz/micrograph_handler.h:31, + from /build/relion-3.1.3/src/jaz/micrograph_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 @@ -4445,17 +4514,6 @@ | ^~~~~~ [ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 function 'size_t fread(void*, size_t, size_t, FILE*)', - inlined from 'int Image::readSPIDER(long int) [with T = double]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: -/usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] - 239 | return __fread_chk_warn (__ptr, sz, __size, __n, __stream); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 -[ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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/jaz/obs_model.cpp:21: @@ -4516,24 +4574,30 @@ /usr/include/i386-linux-gnu/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/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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 +[ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 +[ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 +In file included from /usr/include/stdio.h:906, + from /usr/include/c++/12/cstdio:42, + from /usr/include/c++/12/ext/string_conversions.h:43, + from /usr/include/c++/12/bits/basic_string.h:3960, + from /usr/include/c++/12/string:53, + from /build/relion-3.1.3/src/jaz/micrograph_handler.h:24: In function 'size_t fread(void*, size_t, size_t, FILE*)', - inlined from 'int Image::readSPIDER(long int) [with T = short int]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: + inlined from 'int Image::readSPIDER(long int) [with T = double]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: /usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] 239 | return __fread_chk_warn (__ptr, sz, __size, __n, __stream); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 +[ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 +[ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 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/refinement_helper.h:24, - from /build/relion-3.1.3/src/jaz/refinement_helper.cpp:21: + from /build/relion-3.1.3/src/jaz/reference_map.h:24, + from /build/relion-3.1.3/src/jaz/reference_map.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 @@ -4592,8 +4656,10 @@ 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/reference_map.h:24, - from /build/relion-3.1.3/src/jaz/reference_map.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/refinement_helper.h:24, + from /build/relion-3.1.3/src/jaz/refinement_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 @@ -4652,8 +4718,8 @@ 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/spectral_helper.h:24, - from /build/relion-3.1.3/src/jaz/spectral_helper.cpp:21: + from /build/relion-3.1.3/src/jaz/slice_helper.h:24, + from /build/relion-3.1.3/src/jaz/slice_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 @@ -4711,9 +4777,11 @@ /usr/include/i386-linux-gnu/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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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: + from /build/relion-3.1.3/src/jaz/spectral_helper.h:24, + from /build/relion-3.1.3/src/jaz/spectral_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 @@ -4771,25 +4839,10 @@ /usr/include/i386-linux-gnu/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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 /usr/include/stdio.h:906, - from /usr/include/c++/12/cstdio:42, - from /usr/include/c++/12/ext/string_conversions.h:43, - from /usr/include/c++/12/bits/basic_string.h:3960, - from /usr/include/c++/12/string:53, - from /build/relion-3.1.3/src/jaz/micrograph_handler.h:24: -In function 'size_t fread(void*, size_t, size_t, FILE*)', - inlined from 'int Image::readSPIDER(long int) [with T = double]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: -/usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] - 239 | return __fread_chk_warn (__ptr, sz, __size, __n, __stream); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 34%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/svd_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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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/svd_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/svd_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/svd_helper.cpp.o -c /build/relion-3.1.3/src/jaz/svd_helper.cpp -[ 34%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/t_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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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/t_complex.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/t_complex.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/t_complex.cpp.o -c /build/relion-3.1.3/src/jaz/t_complex.cpp -[ 34%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/volume_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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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/volume_converter.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/volume_converter.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/volume_converter.cpp.o -c /build/relion-3.1.3/src/jaz/volume_converter.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, @@ -4852,10 +4905,15 @@ /usr/include/i386-linux-gnu/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/volume_integration.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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/volume_integration.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/volume_integration.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/volume_integration.cpp.o -c /build/relion-3.1.3/src/jaz/volume_integration.cpp -[ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 /usr/include/stdio.h:906, + from /usr/include/i386-linux-gnu/tiffio.h:267: +In function 'size_t fread(void*, size_t, size_t, FILE*)', + inlined from 'int Image::readSPIDER(long int) [with T = double]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: +/usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] + 239 | return __fread_chk_warn (__ptr, sz, __size, __n, __stream); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 34%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/svd_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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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/svd_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/svd_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/svd_helper.cpp.o -c /build/relion-3.1.3/src/jaz/svd_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/structure_tensor.cpp:22: @@ -4916,6 +4974,18 @@ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +[ 34%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/t_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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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/t_complex.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/t_complex.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/t_complex.cpp.o -c /build/relion-3.1.3/src/jaz/t_complex.cpp +[ 34%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/volume_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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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/volume_converter.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/volume_converter.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/volume_converter.cpp.o -c /build/relion-3.1.3/src/jaz/volume_converter.cpp +[ 35%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/volume_integration.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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/volume_integration.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/volume_integration.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/volume_integration.cpp.o -c /build/relion-3.1.3/src/jaz/volume_integration.cpp +[ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/volume_converter.h:25, from /build/relion-3.1.3/src/jaz/volume_converter.cpp:21: @@ -5036,12 +5106,6 @@ /usr/include/i386-linux-gnu/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/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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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: @@ -5102,35 +5166,19 @@ /usr/include/i386-linux-gnu/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/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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 -In function 'size_t fread(void*, size_t, size_t, FILE*)', - inlined from 'int Image::readSPIDER(long int) [with T = short unsigned int]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: -/usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] - 239 | return __fread_chk_warn (__ptr, sz, __size, __n, __stream); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 37%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/aberration_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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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/aberration_estimator.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/aberration_estimator.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/aberration_estimator.cpp.o -c /build/relion-3.1.3/src/jaz/ctf/aberration_estimator.cpp [ 37%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/bfactor_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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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/bfactor_refiner.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/bfactor_refiner.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/bfactor_refiner.cpp.o -c /build/relion-3.1.3/src/jaz/ctf/bfactor_refiner.cpp [ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 -In file included from /usr/include/stdio.h:906, - from /usr/include/i386-linux-gnu/tiffio.h:267: -In function 'size_t fread(void*, size_t, size_t, FILE*)', - inlined from 'int Image::readSPIDER(long int) [with T = double]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: -/usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] - 239 | return __fread_chk_warn (__ptr, sz, __size, __n, __stream); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 -[ 39%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/defocus_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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 In file included from /build/relion-3.1.3/src/image.h:455, - from /build/relion-3.1.3/src/jaz/ctf/bfactor_refiner.h:4, - from /build/relion-3.1.3/src/jaz/ctf/bfactor_refiner.cpp:1: + from /build/relion-3.1.3/src/jaz/ctf/aberration_estimator.h:4, + from /build/relion-3.1.3/src/jaz/ctf/aberration_estimator.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 @@ -5188,11 +5236,12 @@ /usr/include/i386-linux-gnu/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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 +[ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 file included from /build/relion-3.1.3/src/image.h:455, - from /build/relion-3.1.3/src/jaz/ctf/aberration_estimator.h:4, - from /build/relion-3.1.3/src/jaz/ctf/aberration_estimator.cpp:1: + 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.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 @@ -5251,9 +5300,8 @@ 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/jaz/ctf/ctf_refiner.h:24, - from /build/relion-3.1.3/src/jaz/ctf/ctf_refiner.cpp:21: + from /build/relion-3.1.3/src/jaz/ctf/bfactor_refiner.h:4, + from /build/relion-3.1.3/src/jaz/ctf/bfactor_refiner.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 @@ -5311,9 +5359,31 @@ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +In file included from /usr/include/stdio.h:906, + from /usr/include/c++/12/cstdio:42, + from /usr/include/c++/12/ext/string_conversions.h:43, + from /usr/include/c++/12/bits/basic_string.h:3960, + from /usr/include/c++/12/string:53, + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/ostream:38, + from /usr/include/c++/12/iostream:39, + from /build/relion-3.1.3/src/funcs.h:48, + from /build/relion-3.1.3/src/multidim_array.h:52, + from /build/relion-3.1.3/src/ctf.h:48: +In function 'size_t fread(void*, size_t, size_t, FILE*)', + inlined from 'int Image::readSPIDER(long int) [with T = double]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: +/usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] + 239 | return __fread_chk_warn (__ptr, sz, __size, __n, __stream); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 39%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/defocus_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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 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/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/jaz/ctf/ctf_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 @@ -5372,10 +5442,8 @@ 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/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/jaz/ctf/ctf_refiner_mpi.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 @@ -5433,10 +5501,22 @@ /usr/include/i386-linux-gnu/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/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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 +[ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 +In function 'size_t fread(void*, size_t, size_t, FILE*)', + inlined from 'int Image::readSPIDER(long int) [with T = float]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: +/usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] + 239 | return __fread_chk_warn (__ptr, sz, __size, __n, __stream); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 /usr/include/stdio.h:906, + from /usr/include/i386-linux-gnu/tiffio.h:267: +In function 'size_t fread(void*, size_t, size_t, FILE*)', + inlined from 'int Image::readSPIDER(long int) [with T = double]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: +/usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] + 239 | return __fread_chk_warn (__ptr, sz, __size, __n, __stream); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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, @@ -5499,11 +5579,6 @@ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -In function 'size_t fread(void*, size_t, size_t, FILE*)', - inlined from 'int Image::readSPIDER(long int) [with T = unsigned char]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: -/usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] - 239 | return __fread_chk_warn (__ptr, sz, __size, __n, __stream); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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, @@ -5566,10 +5641,12 @@ /usr/include/i386-linux-gnu/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/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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 /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: @@ -5630,14 +5707,10 @@ /usr/include/i386-linux-gnu/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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 -[ 42%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_helper.cpp.o -c /build/relion-3.1.3/src/jaz/ctf/tilt_helper.cpp -[ 42%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/alignment_set.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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/alignment_set.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/alignment_set.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/alignment_set.cpp.o -c /build/relion-3.1.3/src/jaz/motion/alignment_set.cpp -[ 42%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/frame_recombiner.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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/frame_recombiner.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/frame_recombiner.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/frame_recombiner.cpp.o -c /build/relion-3.1.3/src/jaz/motion/frame_recombiner.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, @@ -5760,6 +5833,12 @@ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +[ 42%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_helper.cpp.o -c /build/relion-3.1.3/src/jaz/ctf/tilt_helper.cpp +[ 42%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/alignment_set.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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/alignment_set.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/alignment_set.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/alignment_set.cpp.o -c /build/relion-3.1.3/src/jaz/motion/alignment_set.cpp +[ 42%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/frame_recombiner.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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/frame_recombiner.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/frame_recombiner.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/frame_recombiner.cpp.o -c /build/relion-3.1.3/src/jaz/motion/frame_recombiner.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/ctf/tilt_estimator.h:24, from /build/relion-3.1.3/src/jaz/ctf/tilt_estimator.cpp:21: @@ -5944,38 +6023,8 @@ | ^~~~~~ [ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 function 'size_t fread(void*, size_t, size_t, FILE*)', - inlined from 'int Image::readSPIDER(long int) [with T = signed char]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: -/usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] - 239 | return __fread_chk_warn (__ptr, sz, __size, __n, __stream); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 /usr/include/stdio.h:906, - from /usr/include/c++/12/cstdio:42, - from /usr/include/c++/12/ext/string_conversions.h:43, - from /usr/include/c++/12/bits/basic_string.h:3960, - from /usr/include/c++/12/string:53, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/ostream:38, - from /usr/include/c++/12/iostream:39, - from /build/relion-3.1.3/src/funcs.h:48, - from /build/relion-3.1.3/src/multidim_array.h:52, - from /build/relion-3.1.3/src/ctf.h:48: -In function 'size_t fread(void*, size_t, size_t, FILE*)', - inlined from 'int Image::readSPIDER(long int) [with T = double]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: -/usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] - 239 | return __fread_chk_warn (__ptr, sz, __size, __n, __stream); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/stdio.h:906, - from /usr/include/i386-linux-gnu/tiffio.h:267: -In function 'size_t fread(void*, size_t, size_t, FILE*)', - inlined from 'int Image::readSPIDER(long int) [with T = double]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: -/usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] - 239 | return __fread_chk_warn (__ptr, sz, __size, __n, __stream); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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: @@ -6036,8 +6085,6 @@ /usr/include/i386-linux-gnu/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_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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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: @@ -6098,8 +6145,33 @@ /usr/include/i386-linux-gnu/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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 /usr/include/stdio.h:906, + from /usr/include/c++/12/cstdio:42, + from /usr/include/c++/12/ext/string_conversions.h:43, + from /usr/include/c++/12/bits/basic_string.h:3960, + from /usr/include/c++/12/string:53, + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/ostream:38, + from /usr/include/c++/12/iostream:39, + from /build/relion-3.1.3/src/funcs.h:48, + from /build/relion-3.1.3/src/multidim_array.h:52, + from /build/relion-3.1.3/src/ctf.h:48: +In function 'size_t fread(void*, size_t, size_t, FILE*)', + inlined from 'int Image::readSPIDER(long int) [with T = double]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: +/usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] + 239 | return __fread_chk_warn (__ptr, sz, __size, __n, __stream); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 /usr/include/stdio.h:906, + from /usr/include/i386-linux-gnu/tiffio.h:267: +In function 'size_t fread(void*, size_t, size_t, FILE*)', + inlined from 'int Image::readSPIDER(long int) [with T = double]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: +/usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] + 239 | return __fread_chk_warn (__ptr, sz, __size, __n, __stream); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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, @@ -6162,11 +6234,8 @@ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -In function 'size_t fread(void*, size_t, size_t, FILE*)', - inlined from 'int Image::readSPIDER(long int) [with T = float]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: -/usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] - 239 | return __fread_chk_warn (__ptr, sz, __size, __n, __stream); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 /usr/include/stdio.h:906, @@ -6237,28 +6306,6 @@ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -In file included from /usr/include/stdio.h:906, - from /usr/include/c++/12/cstdio:42, - from /usr/include/c++/12/ext/string_conversions.h:43, - from /usr/include/c++/12/bits/basic_string.h:3960, - from /usr/include/c++/12/string:53, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/ostream:38, - from /usr/include/c++/12/iostream:39, - from /build/relion-3.1.3/src/funcs.h:48, - from /build/relion-3.1.3/src/multidim_array.h:52, - from /build/relion-3.1.3/src/ctf.h:48: -In function 'size_t fread(void*, size_t, size_t, FILE*)', - inlined from 'int Image::readSPIDER(long int) [with T = double]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: -/usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] - 239 | return __fread_chk_warn (__ptr, sz, __size, __n, __stream); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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, from /build/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-3.1.3/src/ctf.h:50, @@ -6321,10 +6368,8 @@ /usr/include/i386-linux-gnu/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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 +[ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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, @@ -6388,6 +6433,19 @@ /usr/include/i386-linux-gnu/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/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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 +[ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 +In file included from /usr/include/stdio.h:906, + from /usr/include/i386-linux-gnu/tiffio.h:267: +In function 'size_t fread(void*, size_t, size_t, FILE*)', + inlined from 'int Image::readSPIDER(long int) [with T = double]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: +/usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] + 239 | return __fread_chk_warn (__ptr, sz, __size, __n, __stream); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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, @@ -6449,17 +6507,6 @@ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -In file included from /usr/include/stdio.h:906, - from /usr/include/i386-linux-gnu/tiffio.h:267: -In function 'size_t fread(void*, size_t, size_t, FILE*)', - inlined from 'int Image::readSPIDER(long int) [with T = double]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: -/usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] - 239 | return __fread_chk_warn (__ptr, sz, __size, __n, __stream); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 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, @@ -6521,14 +6568,14 @@ /usr/include/i386-linux-gnu/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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 -[ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 /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: @@ -6589,8 +6636,6 @@ /usr/include/i386-linux-gnu/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/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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 /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: @@ -6651,8 +6696,12 @@ /usr/include/i386-linux-gnu/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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 +[ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 +[ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 /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: @@ -6713,24 +6762,14 @@ /usr/include/i386-linux-gnu/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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 [ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -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 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: @@ -6791,15 +6830,14 @@ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -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/stdio.h:906, - from /usr/include/i386-linux-gnu/tiffio.h:267: -In function 'size_t fread(void*, size_t, size_t, FILE*)', - inlined from 'int Image::readSPIDER(long int) [with T = double]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: -/usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] - 239 | return __fread_chk_warn (__ptr, sz, __size, __n, __stream); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -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 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: @@ -6860,6 +6898,12 @@ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +[ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -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/stdio.h:906, from /usr/include/c++/12/cstdio:42, from /usr/include/c++/12/ext/string_conversions.h:43, @@ -6900,131 +6944,60 @@ /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 /usr/bin/make -f src/apps/CMakeFiles/convert_star.dir/build.make src/apps/CMakeFiles/convert_star.dir/depend -/usr/bin/make -f src/apps/CMakeFiles/convert_to_tiff.dir/build.make src/apps/CMakeFiles/convert_to_tiff.dir/depend -/usr/bin/make -f src/apps/CMakeFiles/convert_to_tiff_mpi.dir/build.make src/apps/CMakeFiles/convert_to_tiff_mpi.dir/depend -/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/relion_gui_lib.dir/DependInfo.cmake --color= -/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/align_symmetry.dir/DependInfo.cmake --color= +/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/autopick.dir/DependInfo.cmake --color= -/usr/bin/make -f src/apps/CMakeFiles/ctf_refine_mpi.dir/build.make src/apps/CMakeFiles/ctf_refine_mpi.dir/depend +/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/autopick_mpi.dir/DependInfo.cmake --color= -/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/convert_star.dir/DependInfo.cmake --color= -/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/convert_to_tiff.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/convert_to_tiff_mpi.dir/DependInfo.cmake --color= -/usr/bin/make -f src/apps/CMakeFiles/estimate_gain.dir/build.make src/apps/CMakeFiles/estimate_gain.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]: 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= -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]: 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= -/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/demodulate.dir/DependInfo.cmake --color= -/usr/bin/make -f src/apps/CMakeFiles/find_tiltpairs.dir/build.make src/apps/CMakeFiles/find_tiltpairs.dir/depend -/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/external_reconstruct.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/estimate_gain.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/find_tiltpairs.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/flex_analyse.dir/DependInfo.cmake --color= 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' -/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]: 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/autopick_mpi.dir/build.make src/apps/CMakeFiles/autopick_mpi.dir/build make[4]: Entering directory '/build/relion-3.1.3/build' -make[4]: Entering directory '/build/relion-3.1.3/build' -make[4]: Entering directory '/build/relion-3.1.3/build' -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/align_symmetry.dir/build.make src/apps/CMakeFiles/align_symmetry.dir/build -make[4]: Leaving directory '/build/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/convert_star.dir/build.make src/apps/CMakeFiles/convert_star.dir/build -make[4]: Leaving directory '/build/relion-3.1.3/build' -make[4]: Leaving directory '/build/relion-3.1.3/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/convert_to_tiff.dir/build.make src/apps/CMakeFiles/convert_to_tiff.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/convert_to_tiff_mpi.dir/build.make src/apps/CMakeFiles/convert_to_tiff_mpi.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/ctf_refine.dir/build.make src/apps/CMakeFiles/ctf_refine.dir/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' 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/ctf_mask_test.dir/build.make src/apps/CMakeFiles/ctf_mask_test.dir/build -make[4]: Entering 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' -/usr/bin/make -f src/apps/CMakeFiles/demodulate.dir/build.make src/apps/CMakeFiles/demodulate.dir/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 +/usr/bin/make -f src/apps/CMakeFiles/convert_star.dir/build.make src/apps/CMakeFiles/convert_star.dir/build make[4]: Entering directory '/build/relion-3.1.3/build' make[4]: Entering directory '/build/relion-3.1.3/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/estimate_gain.dir/build.make src/apps/CMakeFiles/estimate_gain.dir/build -make[4]: Entering directory '/build/relion-3.1.3/build' -make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 54%] Building CXX object src/apps/CMakeFiles/autopick.dir/autopick.cpp.o -/usr/bin/make -f src/apps/CMakeFiles/external_reconstruct.dir/build.make src/apps/CMakeFiles/external_reconstruct.dir/build -/usr/bin/make -f src/apps/CMakeFiles/find_tiltpairs.dir/build.make src/apps/CMakeFiles/find_tiltpairs.dir/build -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 -make[4]: Entering directory '/build/relion-3.1.3/build' -[ 54%] Building CXX object src/apps/CMakeFiles/autopick_mpi.dir/autopick_mpi.cpp.o -[ 54%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/displayer.cpp.o -make[4]: Entering directory '/build/relion-3.1.3/build' +[ 53%] Building CXX object src/apps/CMakeFiles/align_symmetry.dir/align_symmetry.cpp.o +[ 53%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 -make[4]: Leaving directory '/build/relion-3.1.3/build' -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 -/usr/bin/make -f src/apps/CMakeFiles/flex_analyse.dir/build.make src/apps/CMakeFiles/flex_analyse.dir/build -[ 54%] Building CXX object src/apps/CMakeFiles/align_symmetry.dir/align_symmetry.cpp.o -[ 54%] Building CXX object src/apps/CMakeFiles/convert_star.dir/convert_star.cpp.o +[ 54%] Building CXX object src/apps/CMakeFiles/convert_to_tiff_mpi.dir/convert_to_tiff_mpi.cpp.o +[ 54%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/displayer.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 [ 54%] Building CXX object src/apps/CMakeFiles/convert_to_tiff.dir/convert_to_tiff.cpp.o -[ 55%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 -make[4]: Entering directory '/build/relion-3.1.3/build' -[ 55%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 +[ 55%] Building CXX object src/apps/CMakeFiles/autopick.dir/autopick.cpp.o +[ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 -[ 55%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 -[ 55%] Building CXX object src/apps/CMakeFiles/ctf_mask_test.dir/ctf_mask_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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 -[ 56%] Building CXX object src/apps/CMakeFiles/ctf_toolbox.dir/ctf_toolbox.cpp.o -[ 56%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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_mask_test.dir/ctf_mask_test.cpp.o -MF CMakeFiles/ctf_mask_test.dir/ctf_mask_test.cpp.o.d -o CMakeFiles/ctf_mask_test.dir/ctf_mask_test.cpp.o -c /build/relion-3.1.3/src/apps/ctf_mask_test.cpp -[ 56%] Building CXX object src/apps/CMakeFiles/estimate_gain.dir/estimate_gain.cpp.o -[ 57%] Building CXX object src/apps/CMakeFiles/external_reconstruct.dir/external_reconstruct.cpp.o -[ 57%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 -[ 57%] Building CXX object src/apps/CMakeFiles/flex_analyse.dir/flex_analyse.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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.dir/flex_analyse.cpp.o -MF CMakeFiles/flex_analyse.dir/flex_analyse.cpp.o.d -o CMakeFiles/flex_analyse.dir/flex_analyse.cpp.o -c /build/relion-3.1.3/src/apps/flex_analyse.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: + from /build/relion-3.1.3/src/tiff_converter.h:24, + from /build/relion-3.1.3/src/apps/convert_to_tiff.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 @@ -7083,8 +7056,8 @@ 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/align_symmetry.cpp:21: + from /build/relion-3.1.3/src/autopicker.h:10, + from /build/relion-3.1.3/src/apps/autopick.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 @@ -7118,46 +7091,33 @@ /usr/include/i386-linux-gnu/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/jaz/ctf/ctf_refiner.h:24, - from /build/relion-3.1.3/src/apps/ctf_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 - | ^~~~~ -In file included from /usr/include/i386-linux-gnu/tiffio.h:31, - from /build/relion-3.1.3/src/image.h:57: +/build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 185 | uint32 cur_width, cur_length; + | ^~~~~~~~~ /usr/include/i386-linux-gnu/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 - | ^~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 185 | uint32 cur_width, cur_length; + | ^~~~~~~~~~ /usr/include/i386-linux-gnu/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/i386-linux-gnu/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; - | ^~~~~~~~~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 186 | uint16 cur_sampleFormat, cur_bitsPerSample; + | ^~~~~~~~~~~~~~~~ /usr/include/i386-linux-gnu/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; - | ^~~~~~~~~~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 186 | uint16 cur_sampleFormat, cur_bitsPerSample; + | ^~~~~~~~~~~~~~~~~ /usr/include/i386-linux-gnu/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/vtk_helper.h:24, - from /build/relion-3.1.3/src/apps/demodulate.cpp:1: + from /build/relion-3.1.3/src/projector.h:25, + from /build/relion-3.1.3/src/apps/align_symmetry.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 @@ -7215,27 +7175,39 @@ /usr/include/i386-linux-gnu/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; - | ^~~~~~~~~ +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: +/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/i386-linux-gnu/tiffio.h:31, + from /build/relion-3.1.3/src/image.h:57: /usr/include/i386-linux-gnu/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; - | ^~~~~~~~~~ +/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/i386-linux-gnu/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; - | ^~~~~~~~~~~~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; + | ^~~~~~~~~~~~ /usr/include/i386-linux-gnu/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; - | ^~~~~~~~~~~~~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; + | ^~~~~~~~~~~~~ +/usr/include/i386-linux-gnu/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/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ @@ -7264,7 +7236,8 @@ 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/ctf_toolbox.cpp:21: + from /build/relion-3.1.3/src/tiff_converter.h:24, + from /build/relion-3.1.3/src/apps/convert_to_tiff_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 @@ -7298,44 +7271,35 @@ /usr/include/i386-linux-gnu/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/autopicker.h:10, - from /build/relion-3.1.3/src/apps/autopick.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/i386-linux-gnu/tiffio.h:31, - from /build/relion-3.1.3/src/image.h:57: +/build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 185 | uint32 cur_width, cur_length; + | ^~~~~~~~~ /usr/include/i386-linux-gnu/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 - | ^~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 185 | uint32 cur_width, cur_length; + | ^~~~~~~~~~ /usr/include/i386-linux-gnu/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/i386-linux-gnu/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; - | ^~~~~~~~~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 186 | uint16 cur_sampleFormat, cur_bitsPerSample; + | ^~~~~~~~~~~~~~~~ /usr/include/i386-linux-gnu/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; - | ^~~~~~~~~~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 186 | uint16 cur_sampleFormat, cur_bitsPerSample; + | ^~~~~~~~~~~~~~~~~ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +[ 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 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/displayer.h:40, + from /build/relion-3.1.3/src/displayer.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 @@ -7370,8 +7334,9 @@ 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/tiff_converter.h:24, - from /build/relion-3.1.3/src/apps/convert_to_tiff_mpi.cpp:21: + 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/apps/autopick_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 @@ -7453,56 +7418,35 @@ /usr/include/i386-linux-gnu/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/i386-linux-gnu/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/i386-linux-gnu/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/i386-linux-gnu/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/i386-linux-gnu/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/i386-linux-gnu/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/i386-linux-gnu/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/i386-linux-gnu/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/i386-linux-gnu/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ +/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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +make[4]: Leaving directory '/build/relion-3.1.3/build' +[ 55%] Built target convert_to_tiff +/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= +make[4]: Leaving directory '/build/relion-3.1.3/build' +/usr/bin/make -f src/apps/CMakeFiles/ctf_mask_test.dir/build.make src/apps/CMakeFiles/ctf_mask_test.dir/build +make[4]: Entering directory '/build/relion-3.1.3/build' +[ 55%] Building CXX object src/apps/CMakeFiles/ctf_mask_test.dir/ctf_mask_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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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_mask_test.dir/ctf_mask_test.cpp.o -MF CMakeFiles/ctf_mask_test.dir/ctf_mask_test.cpp.o.d -o CMakeFiles/ctf_mask_test.dir/ctf_mask_test.cpp.o -c /build/relion-3.1.3/src/apps/ctf_mask_test.cpp +[ 55%] 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +[ 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +make[4]: Leaving directory '/build/relion-3.1.3/build' +[ 56%] Built target autopick +/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' +[ 56%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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/estimate_gain.cpp:27: + 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&)': /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 @@ -7560,10 +7504,33 @@ /usr/include/i386-linux-gnu/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_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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/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/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' +[ 56%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 +make[4]: Leaving directory '/build/relion-3.1.3/build' +[ 56%] Built target convert_to_tiff_mpi +/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' +[ 57%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 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, - from /build/relion-3.1.3/src/apps/flex_analyse.cpp:22: + 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/apps/ctf_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 @@ -7621,9 +7588,20 @@ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +[ 58%] 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +In file included from /usr/include/stdio.h:906, + from /usr/include/fftw3.h:50, + from /build/relion-3.1.3/src/fftw.h:49, + from /build/relion-3.1.3/src/projector.h:23: +In function 'size_t fread(void*, size_t, size_t, FILE*)', + inlined from 'int Image::readSPIDER(long int) [with T = double]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: +/usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] + 239 | return __fread_chk_warn (__ptr, sz, __size, __n, __stream); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/relion-3.1.3/src/image.h:455, - from /build/relion-3.1.3/src/displayer.h:40, - from /build/relion-3.1.3/src/displayer.cpp:21: + 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 @@ -7743,10 +7721,22 @@ /usr/include/i386-linux-gnu/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' +[ 58%] Built target autopick_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' +[ 58%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 +[ 59%] 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/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/autopicker.h:10, - from /build/relion-3.1.3/src/autopicker_mpi.h:12, - from /build/relion-3.1.3/src/apps/autopick_mpi.cpp:20: + 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 @@ -7756,13 +7746,6 @@ /usr/include/i386-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ -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: -/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 - | ^~~~~ /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 | ^~~~~~ @@ -7772,53 +7755,60 @@ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ -In file included from /usr/include/i386-linux-gnu/tiffio.h:31, - from /build/relion-3.1.3/src/image.h:57: -/usr/include/i386-linux-gnu/tiff.h:86:38: note: declared here - 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; - | ^~~~~~ /usr/include/i386-linux-gnu/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:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations] - 43 | uint32 width, length; // apparent dimensions in the file - | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -/usr/include/i386-linux-gnu/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:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ -/build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; - | ^~~~~~~~~~~~ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -/usr/include/i386-linux-gnu/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/i386-linux-gnu/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:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; - | ^~~~~~~~~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 185 | uint32 cur_width, cur_length; + | ^~~~~~~~~~ +/usr/include/i386-linux-gnu/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/i386-linux-gnu/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; - | ^~~~~~~~~~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 186 | uint16 cur_sampleFormat, cur_bitsPerSample; + | ^~~~~~~~~~~~~~~~~ /usr/include/i386-linux-gnu/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' +[ 59%] Built target ctf_refine +/usr/bin/make -f src/apps/CMakeFiles/estimate_gain.dir/build.make src/apps/CMakeFiles/estimate_gain.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/estimate_gain.dir/DependInfo.cmake --color= +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' +[ 59%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 +[ 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/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/jaz/io/star_converter.h:5, - from /build/relion-3.1.3/src/apps/convert_star.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 @@ -7876,27 +7866,78 @@ /usr/include/i386-linux-gnu/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; - | ^~~~~~~~~ +[ 59%] 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +In file included from /usr/include/stdio.h:906, + from /usr/include/i386-linux-gnu/tiffio.h:267: +In function 'size_t fread(void*, size_t, size_t, FILE*)', + inlined from 'int Image::readSPIDER(long int) [with T = double]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: +/usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] + 239 | return __fread_chk_warn (__ptr, sz, __size, __n, __stream); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +make[4]: Leaving directory '/build/relion-3.1.3/build' +[ 59%] Built target ctf_refine_mpi +/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' +[ 60%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 +make[4]: Leaving directory '/build/relion-3.1.3/build' +[ 60%] Built target align_symmetry +/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' +[ 60%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 +In file included from /usr/include/stdio.h:906, + from /usr/include/i386-linux-gnu/tiffio.h:267: +In function 'size_t fread(void*, size_t, size_t, FILE*)', + inlined from 'int Image::readSPIDER(long int) [with T = double]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: +/usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] + 239 | return __fread_chk_warn (__ptr, sz, __size, __n, __stream); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 61%] 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/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/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 + | ^~~~~ +In file included from /usr/include/i386-linux-gnu/tiffio.h:31, + from /build/relion-3.1.3/src/image.h:57: /usr/include/i386-linux-gnu/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; - | ^~~~~~~~~~ +/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/i386-linux-gnu/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; - | ^~~~~~~~~~~~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; + | ^~~~~~~~~~~~ /usr/include/i386-linux-gnu/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; - | ^~~~~~~~~~~~~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; + | ^~~~~~~~~~~~~ +/usr/include/i386-linux-gnu/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/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ @@ -7924,61 +7965,6 @@ /usr/include/i386-linux-gnu/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 -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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -[ 58%] 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 -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/convert_star.dir/convert_star.cpp.o -o ../../bin/relion_convert_star ../../lib/librelion_lib.a /usr/lib/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -[ 58%] Built target convert_to_tiff -/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= -[ 58%] 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -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' -[ 58%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 -[ 58%] 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -[ 59%] 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 59%] Built target convert_star -/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' -[ 60%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 -make[4]: Leaving directory '/build/relion-3.1.3/build' -make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 60%] Built target convert_to_tiff_mpi -[ 60%] Built target autopick -/usr/bin/make -f src/apps/CMakeFiles/helix_toolbox.dir/build.make src/apps/CMakeFiles/helix_toolbox.dir/depend -/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/helix_toolbox.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/image_handler.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/helix_toolbox.dir/build.make src/apps/CMakeFiles/helix_toolbox.dir/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' -make[4]: Entering directory '/build/relion-3.1.3/build' -[ 60%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 -[ 61%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 In file included from /usr/include/stdio.h:906, from /usr/include/c++/12/cstdio:42, from /usr/include/c++/12/ext/string_conversions.h:43, @@ -7995,23 +7981,20 @@ /usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] 239 | return __fread_chk_warn (__ptr, sz, __size, __n, __stream); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 62%] 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 62%] Built target ctf_refine -/usr/bin/make -f src/apps/CMakeFiles/import.dir/build.make src/apps/CMakeFiles/import.dir/depend +[ 61%] Built target ctf_mask_test +/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/import.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/flex_analyse.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 +/usr/bin/make -f src/apps/CMakeFiles/flex_analyse.dir/build.make src/apps/CMakeFiles/flex_analyse.dir/build make[4]: Entering directory '/build/relion-3.1.3/build' -[ 62%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 +[ 61%] Building CXX object src/apps/CMakeFiles/flex_analyse.dir/flex_analyse.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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.dir/flex_analyse.cpp.o -MF CMakeFiles/flex_analyse.dir/flex_analyse.cpp.o.d -o CMakeFiles/flex_analyse.dir/flex_analyse.cpp.o -c /build/relion-3.1.3/src/apps/flex_analyse.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/apps/../flex_analyser.h:24, - from /build/relion-3.1.3/src/apps/flex_analyse_mpi.cpp:22: + from /build/relion-3.1.3/src/apps/flex_analyse.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 @@ -8091,9 +8074,6 @@ /build/relion-3.1.3/src/numerical_recipes.h:198:26: note: declared here 198 | int *indxc, *indxr, *ipiv; | ^~~~ -[ 62%] 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In file included from /usr/include/stdio.h:906, from /usr/include/i386-linux-gnu/tiffio.h:267: In function 'size_t fread(void*, size_t, size_t, FILE*)', @@ -8101,9 +8081,61 @@ /usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] 239 | return __fread_chk_warn (__ptr, sz, __size, __n, __stream); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +make[4]: Leaving directory '/build/relion-3.1.3/build' +[ 61%] Built target ctf_toolbox +/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' +[ 61%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 +In file included from /usr/include/stdio.h:906, + from /usr/include/FL/fl_utf8.h:34, + from /usr/include/FL/Fl.H:32, + from /build/relion-3.1.3/src/displayer.h:26: +In function 'size_t fread(void*, size_t, size_t, FILE*)', + inlined from 'int Image::readSPIDER(long int) [with T = double]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: +/usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] + 239 | return __fread_chk_warn (__ptr, sz, __size, __n, __stream); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 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 +/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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +[ 63%] 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +make[4]: Leaving directory '/build/relion-3.1.3/build' +[ 63%] Built target demodulate +/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' +[ 64%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 +make[4]: Leaving directory '/build/relion-3.1.3/build' +[ 64%] Built target find_tiltpairs +/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= +make[4]: Leaving directory '/build/relion-3.1.3/build' +/usr/bin/make -f src/apps/CMakeFiles/helix_toolbox.dir/build.make src/apps/CMakeFiles/helix_toolbox.dir/build +make[4]: Entering directory '/build/relion-3.1.3/build' +[ 65%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 +[ 65%] 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/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/../helix_inimodel2d.h:29, - from /build/relion-3.1.3/src/apps/helix_inimodel2d.cpp:22: + from /build/relion-3.1.3/src/exp_model.h:24, + from /build/relion-3.1.3/src/apps/../flex_analyser.h:24, + from /build/relion-3.1.3/src/apps/flex_analyse_mpi.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 @@ -8161,32 +8193,19 @@ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -In file included from /usr/include/stdio.h:906, - from /usr/include/i386-linux-gnu/tiffio.h:267: -In function 'size_t fread(void*, size_t, size_t, FILE*)', - inlined from 'int Image::readSPIDER(long int) [with T = double]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: -/usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] - 239 | return __fread_chk_warn (__ptr, sz, __size, __n, __stream); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 62%] Built target autopick_mpi -/usr/bin/make -f src/apps/CMakeFiles/localsym.dir/build.make src/apps/CMakeFiles/localsym.dir/depend +[ 65%] Built target estimate_gain +/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/localsym.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/image_handler.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 +/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' -[ 63%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 -In file included from /usr/include/stdio.h:906, - from /usr/include/i386-linux-gnu/tiffio.h:267: -In function 'size_t fread(void*, size_t, size_t, FILE*)', - inlined from 'int Image::readSPIDER(long int) [with T = double]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: -/usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] - 239 | return __fread_chk_warn (__ptr, sz, __size, __n, __stream); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 65%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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: + from /build/relion-3.1.3/src/apps/../helix_inimodel2d.h:29, + from /build/relion-3.1.3/src/apps/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 @@ -8304,18 +8323,11 @@ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -In file included from /usr/include/stdio.h:906, - from /usr/include/fftw3.h:50, - from /build/relion-3.1.3/src/fftw.h:49, - from /build/relion-3.1.3/src/projector.h:23: -In function 'size_t fread(void*, size_t, size_t, FILE*)', - inlined from 'int Image::readSPIDER(long int) [with T = double]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: -/usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] - 239 | return __fread_chk_warn (__ptr, sz, __size, __n, __stream); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/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/jaz/obs_model.h:24, - from /build/relion-3.1.3/src/apps/import.cpp:22: + 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&)': /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 @@ -8373,32 +8385,42 @@ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +[ 66%] 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +[ 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 63%] Built target ctf_refine_mpi -/usr/bin/make -f src/apps/CMakeFiles/localsym_mpi.dir/build.make src/apps/CMakeFiles/localsym_mpi.dir/depend +[ 66%] Built target flex_analyse +/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/localsym_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/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]: 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' -[ 64%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 -[ 64%] 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -[ 65%] 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +[ 66%] Built target external_reconstruct +[ 66%] Building CXX object src/apps/CMakeFiles/import.dir/import.cpp.o +/usr/bin/make -f src/apps/CMakeFiles/localsym.dir/build.make src/apps/CMakeFiles/localsym.dir/depend +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 +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' -[ 65%] Built target helix_inimodel2d -/usr/bin/make -f src/apps/CMakeFiles/mask_create.dir/build.make src/apps/CMakeFiles/mask_create.dir/depend +/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' -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= +[ 67%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 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 +[ 67%] Built target helix_inimodel2d +/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' -[ 65%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 +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' +[ 68%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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: @@ -8459,19 +8481,66 @@ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 66%] 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 66%] Built target find_tiltpairs -/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' -[ 67%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 +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: +/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/i386-linux-gnu/tiffio.h:31, + from /build/relion-3.1.3/src/image.h:57: +/usr/include/i386-linux-gnu/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/i386-linux-gnu/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/i386-linux-gnu/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/i386-linux-gnu/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/i386-linux-gnu/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/i386-linux-gnu/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/i386-linux-gnu/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/i386-linux-gnu/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/i386-linux-gnu/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/local_symmetry.h:30, from /build/relion-3.1.3/src/local_symmetry_mpi.h:5, @@ -8533,19 +8602,35 @@ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +[ 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +[ 68%] 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 67%] Built target flex_analyse -/usr/bin/make -f src/apps/CMakeFiles/motion_refine.dir/build.make src/apps/CMakeFiles/motion_refine.dir/depend +[ 68%] Built target localsym +/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/motion_refine.dir/DependInfo.cmake --color= -[ 67%] 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 +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/motion_refine.dir/build.make src/apps/CMakeFiles/motion_refine.dir/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' -/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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -[ 68%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 +[ 68%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 +[ 68%] 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +make[4]: Leaving directory '/build/relion-3.1.3/build' +[ 68%] Built target flex_analyse_mpi +/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' +[ 69%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 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: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': @@ -8605,19 +8690,16 @@ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 69%] 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 69%] Built target localsym -/usr/bin/make -f src/apps/CMakeFiles/motion_refine_mpi.dir/build.make src/apps/CMakeFiles/motion_refine_mpi.dir/depend +[ 69%] Built target localsym_mpi +/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_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/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_mpi.dir/build.make src/apps/CMakeFiles/motion_refine_mpi.dir/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' -[ 69%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 +[ 70%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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: @@ -8740,48 +8822,41 @@ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +[ 70%] 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +[ 70%] 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 69%] 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 -[ 69%] Built target ctf_mask_test -/usr/bin/make -f src/apps/CMakeFiles/mrc2vtk.dir/build.make src/apps/CMakeFiles/mrc2vtk.dir/depend -/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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -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' -[ 69%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 -[ 69%] 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -[ 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 69%] Built target estimate_gain -/usr/bin/make -f src/apps/CMakeFiles/particle_FCC.dir/build.make src/apps/CMakeFiles/particle_FCC.dir/depend +[ 70%] 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/particle_FCC.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/motion_refine_mpi.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 +/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' -[ 70%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 -[ 70%] 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +[ 70%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 70%] Built target external_reconstruct -/usr/bin/make -f src/apps/CMakeFiles/particle_reposition.dir/build.make src/apps/CMakeFiles/particle_reposition.dir/depend +[ 70%] Built target import +/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/particle_reposition.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/mrc2vtk.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 +/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' -[ 71%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 +[ 70%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 +In file included from /usr/include/stdio.h:906, + from /usr/include/i386-linux-gnu/tiffio.h:267: +In function 'size_t fread(void*, size_t, size_t, FILE*)', + inlined from 'int Image::readSPIDER(long int) [with T = double]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: +/usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] + 239 | return __fread_chk_warn (__ptr, sz, __size, __n, __stream); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 71%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 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, @@ -8845,27 +8920,9 @@ /usr/include/i386-linux-gnu/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' -[ 71%] Built target localsym_mpi -/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= -[ 71%] 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 -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/ctf_toolbox.dir/ctf_toolbox.cpp.o -o ../../bin/relion_ctf_toolbox ../../lib/librelion_lib.a /usr/lib/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -[ 71%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 -[ 72%] 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -[ 72%] 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -[ 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 +[ 71%] 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/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&)': @@ -8925,42 +8982,39 @@ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -/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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -make[4]: Leaving directory '/build/relion-3.1.3/build' -make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 72%] Built target flex_analyse_mpi -/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' -[ 72%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 -make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 72%] Built target merge_particles -[ 72%] Built target ctf_toolbox -/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= -[ 73%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 -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' -[ 73%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 +In file included from /usr/include/stdio.h:906, + from /usr/include/i386-linux-gnu/tiffio.h:267: +In function 'size_t fread(void*, size_t, size_t, FILE*)', + inlined from 'int Image::readSPIDER(long int) [with T = double]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: +/usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] + 239 | return __fread_chk_warn (__ptr, sz, __size, __n, __stream); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 73%] Built target import -/usr/bin/make -f src/apps/CMakeFiles/particle_symmetry_expand.dir/build.make src/apps/CMakeFiles/particle_symmetry_expand.dir/depend +[ 71%] Built target motion_refine +/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_symmetry_expand.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/particle_FCC.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 +/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' -make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 74%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 +[ 72%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 +In file included from /usr/include/stdio.h:906, + from /usr/include/i386-linux-gnu/tiffio.h:267: +In function 'size_t fread(void*, size_t, size_t, FILE*)', + inlined from 'int Image::readSPIDER(long int) [with T = double]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: +/usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] + 239 | return __fread_chk_warn (__ptr, sz, __size, __n, __stream); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/stdio.h:906, + from /usr/include/c++/12/cstdio:42, + from /build/relion-3.1.3/src/args.h:48, + from /build/relion-3.1.3/src/apps/helix_toolbox.cpp:21: +In function 'size_t fread(void*, size_t, size_t, FILE*)', + inlined from 'int Image::readSPIDER(long int) [with T = double]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: +/usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] + 239 | return __fread_chk_warn (__ptr, sz, __size, __n, __stream); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': @@ -9020,15 +9074,37 @@ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 74%] Built target demodulate -/usr/bin/make -f src/apps/CMakeFiles/pipeliner.dir/build.make src/apps/CMakeFiles/pipeliner.dir/depend +[ 72%] 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +[ 72%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 +make[4]: Leaving directory '/build/relion-3.1.3/build' +[ 72%] Built target mask_create +/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/pipeliner.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/particle_reposition.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 +/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' -[ 74%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 +[ 73%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 +[ 73%] 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +make[4]: Leaving directory '/build/relion-3.1.3/build' +[ 73%] 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= +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' +[ 73%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 +[ 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/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, @@ -9091,6 +9167,9 @@ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +[ 74%] 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/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/jaz/obs_model.h:24, from /build/relion-3.1.3/src/ctf.h:50, @@ -9153,12 +9232,26 @@ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 74%] 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -[ 74%] 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +make[4]: Leaving directory '/build/relion-3.1.3/build' +[ 74%] Built target motion_refine_mpi +/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' +[ 74%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 +make[4]: Leaving directory '/build/relion-3.1.3/build' +[ 74%] Built target particle_FCC +/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' +[ 74%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 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, @@ -9222,26 +9315,12 @@ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -In file included from /usr/include/stdio.h:906, - from /usr/include/i386-linux-gnu/tiffio.h:267: -In function 'size_t fread(void*, size_t, size_t, FILE*)', - inlined from 'int Image::readSPIDER(long int) [with T = double]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: -/usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] - 239 | return __fread_chk_warn (__ptr, sz, __size, __n, __stream); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/stdio.h:906, - from /usr/include/i386-linux-gnu/tiffio.h:267: -In function 'size_t fread(void*, size_t, size_t, FILE*)', - inlined from 'int Image::readSPIDER(long int) [with T = double]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: -/usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] - 239 | return __fread_chk_warn (__ptr, sz, __size, __n, __stream); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 74%] Built target align_symmetry -/usr/bin/make -f src/apps/CMakeFiles/plot_delocalisation.dir/build.make src/apps/CMakeFiles/plot_delocalisation.dir/depend 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: + 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/../particle_subtractor.h:24, + from /build/relion-3.1.3/src/apps/particle_subtract_mpi.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 @@ -9299,19 +9378,38 @@ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +[ 75%] 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +[ 75%] 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +make[4]: Leaving directory '/build/relion-3.1.3/build' +[ 75%] Built target particle_select +/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/plot_delocalisation.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/particle_symmetry_expand.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 +/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' -[ 74%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 +[ 76%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 +make[4]: Leaving directory '/build/relion-3.1.3/build' +[ 76%] Built target helix_toolbox +/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' +[ 76%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 +[ 77%] 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/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, - from /build/relion-3.1.3/src/ml_optimiser.h:35, - from /build/relion-3.1.3/src/apps/../particle_subtractor.h:24, - from /build/relion-3.1.3/src/apps/particle_subtract_mpi.cpp:22: + 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: /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 @@ -9370,18 +9468,15 @@ 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 74%] Built target motion_refine -/usr/bin/make -f src/apps/CMakeFiles/postprocess.dir/build.make src/apps/CMakeFiles/postprocess.dir/depend +[ 77%] Built target image_handler +/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/postprocess.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/plot_delocalisation.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 +/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' -[ 74%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 -[ 74%] 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +[ 77%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 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&)': @@ -9441,27 +9536,22 @@ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 74%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 -[ 75%] 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -[ 76%] 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +[ 77%] 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 76%] Built target particle_FCC -/usr/bin/make -f src/apps/CMakeFiles/postprocess_mpi.dir/build.make src/apps/CMakeFiles/postprocess_mpi.dir/depend +[ 77%] Built target particle_symmetry_expand +/usr/bin/make -f src/apps/CMakeFiles/postprocess.dir/build.make src/apps/CMakeFiles/postprocess.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= +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_mpi.dir/build.make src/apps/CMakeFiles/postprocess_mpi.dir/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' -[ 77%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 +[ 77%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 +[ 78%] 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/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/postprocessing.h:24, from /build/relion-3.1.3/src/apps/postprocess.cpp:20: @@ -9498,15 +9588,6 @@ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -In file included from /usr/include/stdio.h:906, - from /usr/include/FL/fl_utf8.h:34, - from /usr/include/FL/Fl.H:32, - from /build/relion-3.1.3/src/displayer.h:26: -In function 'size_t fread(void*, size_t, size_t, FILE*)', - inlined from 'int Image::readSPIDER(long int) [with T = double]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: -/usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] - 239 | return __fread_chk_warn (__ptr, sz, __size, __n, __stream); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ @@ -9531,42 +9612,43 @@ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +[ 79%] 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +In file included from /usr/include/stdio.h:906, + from /usr/include/c++/12/cstdio:42, + from /build/relion-3.1.3/src/args.h:48, + from /build/relion-3.1.3/src/apps/particle_reposition.cpp:21: +In function 'size_t fread(void*, size_t, size_t, FILE*)', + inlined from 'int Image::readSPIDER(long int) [with T = double]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: +/usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] + 239 | return __fread_chk_warn (__ptr, sz, __size, __n, __stream); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 77%] Built target mrc2vtk -/usr/bin/make -f src/apps/CMakeFiles/prepare_subtomo.dir/build.make src/apps/CMakeFiles/prepare_subtomo.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/prepare_subtomo.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/relion-3.1.3/build' -/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' -[ 77%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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]: Leaving directory '/build/relion-3.1.3/build' -[ 77%] Built target particle_select -/usr/bin/make -f src/apps/CMakeFiles/preprocess.dir/build.make src/apps/CMakeFiles/preprocess.dir/depend +[ 79%] 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 /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 && /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= 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 +/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' -[ 77%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 +[ 80%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 +[ 80%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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' -[ 77%] Built target motion_refine_mpi -/usr/bin/make -f src/apps/CMakeFiles/preprocess_mpi.dir/build.make src/apps/CMakeFiles/preprocess_mpi.dir/depend +[ 80%] Built target plot_delocalisation +/usr/bin/make -f src/apps/CMakeFiles/prepare_subtomo.dir/build.make src/apps/CMakeFiles/prepare_subtomo.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/prepare_subtomo.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/prepare_subtomo.dir/build.make src/apps/CMakeFiles/prepare_subtomo.dir/build make[4]: Entering directory '/build/relion-3.1.3/build' -[ 77%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 -[ 77%] 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -[ 78%] 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +[ 80%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 +[ 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/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/postprocessing.h:24, from /build/relion-3.1.3/src/apps/postprocess_mpi.cpp:20: @@ -9627,12 +9709,11 @@ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 78%] 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/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/helix.h:30, - from /build/relion-3.1.3/src/apps/prepare_subtomo.cpp:22: + 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: /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 @@ -9690,29 +9771,9 @@ /usr/include/i386-linux-gnu/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' -make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 78%] Built target particle_symmetry_expand -[ 78%] Built target pipeliner -/usr/bin/make -f src/apps/CMakeFiles/project.dir/build.make src/apps/CMakeFiles/project.dir/depend -/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/project.dir/DependInfo.cmake --color= -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/reconstruct.dir/DependInfo.cmake --color= -/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' -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 -make[4]: Entering directory '/build/relion-3.1.3/build' -[ 79%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 -[ 79%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 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/helix.h:30, + from /build/relion-3.1.3/src/apps/prepare_subtomo.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 @@ -9771,26 +9832,34 @@ 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 79%] Built target mask_create -/usr/bin/make -f src/apps/CMakeFiles/reconstruct_mpi.dir/build.make src/apps/CMakeFiles/reconstruct_mpi.dir/depend +[ 81%] Built target particle_subtract +/usr/bin/make -f src/apps/CMakeFiles/preprocess.dir/build.make src/apps/CMakeFiles/preprocess.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= +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= 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 +/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' -[ 79%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 /usr/include/stdio.h:906, - from /usr/include/i386-linux-gnu/tiffio.h:267: -In function 'size_t fread(void*, size_t, size_t, FILE*)', - inlined from 'int Image::readSPIDER(long int) [with T = double]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: -/usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] - 239 | return __fread_chk_warn (__ptr, sz, __size, __n, __stream); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 81%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 +[ 81%] 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +[ 81%] 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +make[4]: Leaving directory '/build/relion-3.1.3/build' +[ 81%] Built target postprocess +/usr/bin/make -f src/apps/CMakeFiles/preprocess_mpi.dir/build.make src/apps/CMakeFiles/preprocess_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/preprocess_mpi.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 +make[4]: Entering directory '/build/relion-3.1.3/build' +[ 81%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 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/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 @@ -9848,20 +9917,20 @@ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 80%] 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -[ 80%] 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -[ 81%] 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +make[4]: Leaving directory '/build/relion-3.1.3/build' +[ 81%] Built target particle_subtract_mpi +/usr/bin/make -f src/apps/CMakeFiles/project.dir/build.make src/apps/CMakeFiles/project.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= +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' +[ 82%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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/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/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: /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 @@ -9919,6 +9988,22 @@ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +[ 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 +/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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +make[4]: Leaving directory '/build/relion-3.1.3/build' +[ 82%] Built target postprocess_mpi +/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/reconstruct.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 +make[4]: Entering directory '/build/relion-3.1.3/build' +[ 82%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 +[ 83%] 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/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/apps/project.cpp:21: @@ -9980,21 +10065,20 @@ 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 81%] Built target postprocess -/usr/bin/make -f src/apps/CMakeFiles/refine.dir/build.make src/apps/CMakeFiles/refine.dir/depend +[ 83%] Built target preprocess +/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/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/reconstruct_mpi.dir/DependInfo.cmake --color= 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/reconstruct_mpi.dir/build.make src/apps/CMakeFiles/reconstruct_mpi.dir/build make[4]: Entering directory '/build/relion-3.1.3/build' -[ 81%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 +[ 83%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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/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 @@ -10052,53 +10136,18 @@ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -In file included from /usr/include/stdio.h:906, - from /usr/include/c++/12/cstdio:42, - from /build/relion-3.1.3/src/args.h:48, - from /build/relion-3.1.3/src/apps/helix_toolbox.cpp:21: -In function 'size_t fread(void*, size_t, size_t, FILE*)', - inlined from 'int Image::readSPIDER(long int) [with T = double]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: -/usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] - 239 | return __fread_chk_warn (__ptr, sz, __size, __n, __stream); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 81%] Built target plot_delocalisation -/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' -[ 82%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 -make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 82%] Built target preprocess -/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' -[ 82%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 -[ 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 -/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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 82%] Built target postprocess_mpi -/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' -[ 82%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 +[ 83%] 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +[ 83%] 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/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, - 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/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 @@ -10156,12 +10205,40 @@ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 82%] 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +make[4]: Leaving directory '/build/relion-3.1.3/build' +[ 83%] Built target preprocess_mpi +/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/refine.dir/DependInfo.cmake --color= +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 +make[4]: Entering directory '/build/relion-3.1.3/build' +[ 83%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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' +[ 83%] Built target particle_reposition +/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' +[ 84%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 /usr/include/stdio.h:906, + from /usr/include/c++/12/cstdio:42, + from /build/relion-3.1.3/src/args.h:48, + from /build/relion-3.1.3/src/apps/prepare_subtomo.cpp:21: +In function 'size_t fread(void*, size_t, size_t, FILE*)', + inlined from 'int Image::readSPIDER(long int) [with T = double]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: +/usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] + 239 | return __fread_chk_warn (__ptr, sz, __size, __n, __stream); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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/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: /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 @@ -10282,28 +10359,25 @@ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -In file included from /usr/include/stdio.h:906, - from /usr/include/c++/12/cstdio:42, - from /build/relion-3.1.3/src/args.h:48, - from /build/relion-3.1.3/src/apps/particle_reposition.cpp:21: -In function 'size_t fread(void*, size_t, size_t, FILE*)', - inlined from 'int Image::readSPIDER(long int) [with T = double]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: -/usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] - 239 | return __fread_chk_warn (__ptr, sz, __size, __n, __stream); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 85%] 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 82%] Built target preprocess_mpi -/usr/bin/make -f src/apps/CMakeFiles/run_ctffind_mpi.dir/build.make src/apps/CMakeFiles/run_ctffind_mpi.dir/depend +[ 85%] Built target reconstruct +/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/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/reposition.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/reposition.dir/build.make src/apps/CMakeFiles/reposition.dir/build make[4]: Entering directory '/build/relion-3.1.3/build' -[ 83%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 +[ 85%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 +[ 86%] 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/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/apps/run_ctffind.cpp:20: + 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 @@ -10334,11 +10408,9 @@ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ -[ 84%] Linking CXX executable ../../bin/relion_reconstruct /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/reconstruct.dir/link.txt --verbose=1 /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ @@ -10363,33 +10435,28 @@ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -/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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -[ 85%] 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +make[4]: Leaving directory '/build/relion-3.1.3/build' +[ 86%] Built target reconstruct_mpi +/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' +[ 86%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 In file included from /usr/include/stdio.h:906, - from /usr/include/c++/12/cstdio:42, - from /build/relion-3.1.3/src/args.h:48, - from /build/relion-3.1.3/src/apps/prepare_subtomo.cpp:21: + from /usr/include/fftw3.h:50, + from /build/relion-3.1.3/src/fftw.h:49, + from /build/relion-3.1.3/src/projector.h:23: In function 'size_t fread(void*, size_t, size_t, FILE*)', inlined from 'int Image::readSPIDER(long int) [with T = double]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: /usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] 239 | return __fread_chk_warn (__ptr, sz, __size, __n, __stream); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 85%] Built target reconstruct -/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_motioncorr.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 -make[4]: Entering directory '/build/relion-3.1.3/build' -[ 86%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 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/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 @@ -10447,35 +10514,28 @@ /usr/include/i386-linux-gnu/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' -[ 86%] Built target particle_subtract -/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_motioncorr_mpi.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 -make[4]: Entering directory '/build/relion-3.1.3/build' [ 86%] 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 -[ 86%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 /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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 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 -[ 87%] Built target run_ctffind -/usr/bin/make -f src/apps/CMakeFiles/scheduler.dir/build.make src/apps/CMakeFiles/scheduler.dir/depend -/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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +[ 86%] Built target run_ctffind +/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/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/run_ctffind_mpi.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/run_ctffind_mpi.dir/build.make src/apps/CMakeFiles/run_ctffind_mpi.dir/build make[4]: Entering directory '/build/relion-3.1.3/build' -[ 87%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 +[ 87%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 +[ 87%] 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +[ 88%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 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/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 @@ -10533,13 +10593,23 @@ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 87%] 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +[ 89%] 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +make[4]: Leaving directory '/build/relion-3.1.3/build' +[ 89%] Built target refine +/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_motioncorr.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 +make[4]: Entering directory '/build/relion-3.1.3/build' +[ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 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/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 @@ -10598,19 +10668,21 @@ 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 87%] Built target reconstruct_mpi -/usr/bin/make -f src/apps/CMakeFiles/stack_create.dir/build.make src/apps/CMakeFiles/stack_create.dir/depend +[ 90%] Built target reposition +/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/stack_create.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/stack_create.dir/build.make src/apps/CMakeFiles/stack_create.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' -[ 88%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 +[ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 +[ 90%] 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/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/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/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 @@ -10668,39 +10740,27 @@ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 88%] Linking CXX executable ../../bin/relion_run_ctffind_mpi +[ 90%] 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -[ 88%] 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 88%] Built target particle_subtract_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 +[ 90%] Built target refine_mpi +/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' -[ 89%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 -[ 90%] 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +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' -[ 90%] Built target run_ctffind_mpi -/usr/bin/make -f src/apps/CMakeFiles/tiltpair_plot.dir/build.make src/apps/CMakeFiles/tiltpair_plot.dir/depend +/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' -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 +[ 90%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 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/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 | ^~~~~ -make[4]: Entering directory '/build/relion-3.1.3/build' In file included from /usr/include/i386-linux-gnu/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/i386-linux-gnu/tiff.h:86:38: note: declared here @@ -10754,45 +10814,39 @@ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 90%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 -[ 90%] 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +[ 90%] 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 90%] Built target run_motioncorr -/usr/bin/make -f src/apps/CMakeFiles/tomo_test.dir/build.make src/apps/CMakeFiles/tomo_test.dir/depend +[ 90%] Built target run_ctffind_mpi +/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/tomo_test.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/tomo_test.dir/build.make src/apps/CMakeFiles/tomo_test.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' -[ 90%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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/stdio.h:906, - from /usr/include/fftw3.h:50, - from /build/relion-3.1.3/src/fftw.h:49, - from /build/relion-3.1.3/src/projector.h:23: -In function 'size_t fread(void*, size_t, size_t, FILE*)', - inlined from 'int Image::readSPIDER(long int) [with T = double]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: -/usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] - 239 | return __fread_chk_warn (__ptr, sz, __size, __n, __stream); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 91%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 +[ 91%] 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 90%] Built target reposition -[ 90%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 +[ 91%] Built target run_motioncorr +/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' -[ 90%] Built target helix_toolbox -[ 91%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 -[ 92%] 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -[ 92%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 +/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' +[ 92%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 +make[4]: Leaving directory '/build/relion-3.1.3/build' +[ 92%] Built target project +/usr/bin/make -f src/apps/CMakeFiles/tiltpair_plot.dir/build.make src/apps/CMakeFiles/tiltpair_plot.dir/depend 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/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 @@ -10826,6 +10880,8 @@ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +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= /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ @@ -10850,10 +10906,13 @@ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 93%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 +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' +[ 92%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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/tiltpair_plot.cpp:25: + 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 @@ -10912,8 +10971,7 @@ 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/tomo/tomo_stack.h:25, - from /build/relion-3.1.3/src/apps/tomo_test.cpp:2: + 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 @@ -10971,24 +11029,11 @@ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 94%] 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 94%] Built target run_motioncorr_mpi -[ 94%] 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 94%] Built target image_handler -[ 94%] 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +[ 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/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/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/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 @@ -11046,10 +11091,19 @@ /usr/include/i386-linux-gnu/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' +[ 93%] Built target run_motioncorr_mpi +/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' +[ 93%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 /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/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 @@ -11107,13 +11161,13 @@ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +[ 94%] 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 94%] Built target particle_reposition -make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 94%] Built target refine -[ 94%] 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +[ 94%] Built target prepare_subtomo +[ 94%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 /usr/include/stdio.h:906, from /usr/include/i386-linux-gnu/tiffio.h:267: In function 'size_t fread(void*, size_t, size_t, FILE*)', @@ -11124,42 +11178,20 @@ [ 95%] 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -[ 95%] Linking CXX executable ../../bin/relion_scheduler +make[4]: Leaving directory '/build/relion-3.1.3/build' +[ 95%] Built target tiltpair_plot +[ 96%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 +[ 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 95%] Built target tiltpair_plot -[ 96%] Linking CXX executable ../../bin/relion_tomo_test +[ 96%] Built target scheduler +[ 97%] 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' -make[4]: Leaving directory '/build/relion-3.1.3/build' -make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 96%] Built target scheduler -[ 96%] Built target tomo_test -[ 96%] Built target refine_mpi -[ 96%] 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 96%] Built target project -[ 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 96%] Built target stack_create -[ 97%] 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 97%] Built target prepare_subtomo -In file included from /usr/include/stdio.h:906, - from /usr/include/i386-linux-gnu/tiffio.h:267: -In function 'size_t fread(void*, size_t, size_t, FILE*)', - inlined from 'int Image::readSPIDER(long int) [with T = double]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: -/usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] - 239 | return __fread_chk_warn (__ptr, sz, __size, __n, __stream); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 97%] Built target tomo_test [ 97%] 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 @@ -11173,24 +11205,29 @@ 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]: 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]: 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/manualpick.dir/build.make src/apps/CMakeFiles/manualpick.dir/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/manualpick.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/relion.dir/build.make src/apps/CMakeFiles/relion.dir/build -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 -/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' make[4]: Entering directory '/build/relion-3.1.3/build' +/usr/bin/make -f src/apps/CMakeFiles/relion.dir/build.make src/apps/CMakeFiles/relion.dir/build +[ 97%] Building CXX object src/apps/CMakeFiles/manualpick.dir/manualpick.cpp.o make[4]: Entering directory '/build/relion-3.1.3/build' +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 [ 97%] Building CXX object src/apps/CMakeFiles/display.dir/display.cpp.o -[ 97%] Building CXX object src/apps/CMakeFiles/relion.dir/maingui.cpp.o -[ 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 +[ 97%] 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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -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 +[ 97%] 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +make[4]: Leaving directory '/build/relion-3.1.3/build' +[ 97%] Built target stack_create In file included from /build/relion-3.1.3/src/image.h:455, 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&)': @@ -11371,17 +11408,19 @@ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 97%] 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 98%] 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gui_lib.a /usr/lib/i386-linux-gnu/libfltk_images.so /usr/lib/i386-linux-gnu/libfltk_forms.so /usr/lib/i386-linux-gnu/libfltk.so -lX11 -lm -ltiff ../../lib/librelion_lib.a -lfftw3f -lfftw3 -ltiff [ 99%] 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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gui_lib.a /usr/lib/i386-linux-gnu/libfltk_images.so /usr/lib/i386-linux-gnu/libfltk_forms.so /usr/lib/i386-linux-gnu/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 star_handler +In file included from /usr/include/stdio.h:906, + from /usr/include/i386-linux-gnu/tiffio.h:267: +In function 'size_t fread(void*, size_t, size_t, FILE*)', + inlined from 'int Image::readSPIDER(long int) [with T = double]' at /build/relion-3.1.3/src/rwSPIDER.h:133:15: +/usr/include/i386-linux-gnu/bits/stdio2.h:239:29: warning: call to '__fread_chk_warn' declared with attribute warning: fread called with bigger size * nmemb than length of destination buffer [-Wattribute-warning] + 239 | return __fread_chk_warn (__ptr, sz, __size, __n, __stream); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/relion-3.1.3/build' [ 99%] Built target display make[4]: Leaving directory '/build/relion-3.1.3/build' @@ -11391,6 +11430,11 @@ /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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gui_lib.a /usr/lib/i386-linux-gnu/libfltk_images.so /usr/lib/i386-linux-gnu/libfltk_forms.so /usr/lib/i386-linux-gnu/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 relion +[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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +make[4]: Leaving directory '/build/relion-3.1.3/build' +[100%] Built target star_handler make[3]: Leaving directory '/build/relion-3.1.3/build' /usr/bin/cmake -E cmake_progress_start /build/relion-3.1.3/build/CMakeFiles 0 make[2]: Leaving directory '/build/relion-3.1.3/build' @@ -11970,71 +12014,71 @@ /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_ctf_refine --- 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_plot_delocalisation --- 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_scheduler +-- 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_import +-- 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_particle_subtract -- 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_ctf_refine_mpi --- 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_manualpick --- 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_printtable --- 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_star_datablock_stack --- 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_find_tiltpairs --- 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_ctf_refine -- 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_particle_subtract --- 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_run_ctffind +-- 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_image_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_display +-- 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_convert_to_tiff --- 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_particle_reposition --- 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_convert_to_tiff_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_mrc2vtk +-- 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_plot_delocalisation +-- 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_ctf_mask_test +-- 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_convert_star +-- 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_external_reconstruct --- 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_tiltpair_plot +-- 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_ctf_toolbox --- 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_demodulate --- 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 -- 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 +-- 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_merge_particles --- 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_reposition +-- 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_postprocess -- 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_mask_create +-- 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_autopick_mpi +-- 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_star_datablock_ctfdat +-- 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_star_datablock_singlefiles +-- 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_reconstruct_mpi -- 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_localsym_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_run_motioncorr --- 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_run_ctffind --- 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_display --- 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_postprocess --- 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_helix_inimodel2d --- 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_image_handler --- 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_refine_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_convert_star --- 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_tomo_test +-- 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_postprocess_mpi +-- 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_reposition +-- 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_motion_refine +-- 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_project +-- 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_localsym --- 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_ctf_mask_test --- 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_tomo_test --- 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_flex_analyse +-- 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 +-- 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_refine_mpi +-- 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_preprocess +-- 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_mask_create +-- 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_ctf_refine_mpi -- 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 @@ -12118,23 +12162,24 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'relion' in '../relion_3.1.3-3_i386.deb'. dpkg-deb: building package 'relion-dbgsym' in '../relion-dbgsym_3.1.3-3_i386.deb'. -dpkg-deb: building package 'relion-gui' in '../relion-gui_3.1.3-3_i386.deb'. dpkg-deb: building package 'relion-gui-dbgsym' in '../relion-gui-dbgsym_3.1.3-3_i386.deb'. +dpkg-deb: building package 'relion' in '../relion_3.1.3-3_i386.deb'. +dpkg-deb: building package 'relion-gui' in '../relion-gui_3.1.3-3_i386.deb'. dpkg-genbuildinfo --build=binary -O../relion_3.1.3-3_i386.buildinfo dpkg-genchanges --build=binary -O../relion_3.1.3-3_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . 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/14116/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/14116/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/104210 and its subdirectories -I: Current time: Tue May 28 18:48:33 -12 2024 -I: pbuilder-time-stamp: 1716965313 +I: removing directory /srv/workspace/pbuilder/14116 and its subdirectories +I: Current time: Thu Apr 27 14:42:17 +14 2023 +I: pbuilder-time-stamp: 1682556137