Diff of the two buildlogs: -- --- b1/build.log 2021-06-22 06:56:51.846523381 +0000 +++ b2/build.log 2021-06-22 07:45:53.355559057 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Jul 25 01:13:01 -12 2022 -I: pbuilder-time-stamp: 1658754781 +I: Current time: Tue Jun 22 20:57:01 +14 2021 +I: pbuilder-time-stamp: 1624345021 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration @@ -17,8 +17,8 @@ I: copying [./relion_3.1.0-4.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig.UWupU3xK/trustedkeys.kbx': General error -gpgv: Signature made Wed Oct 7 02:36:44 2020 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.RTofqYdv/trustedkeys.kbx': General error +gpgv: Signature made Thu Oct 8 04:36:44 2020 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -28,137 +28,171 @@ dpkg-source: info: unpacking relion_3.1.0-4.debian.tar.xz I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/52110/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/21607/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 +Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' +Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' +Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' +Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by 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/21607/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/21607/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,-fixfilepath parallel=18' - DISTRIBUTION='' - HOME='/root' - HOST_ARCH='i386' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") + BASH_VERSION='5.1.4(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,-fixfilepath parallel=10' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - INVOCATION_ID='a6d962679054447ab53e38b25a6a3024' - 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='52110' - PS1='# ' - PS2='> ' + INVOCATION_ID=54e6d8cf21e046e6891a7dd7aaa42e3f + 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=21607 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/tmp.4wiMpvkHix/pbuilderrc_LqQ7 --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.4wiMpvkHix/b1 --logfile b1/build.log relion_3.1.0-4.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/tmp.4wiMpvkHix/pbuilderrc_vnlc --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.4wiMpvkHix/b2 --logfile b2/build.log --extrapackages usrmerge relion_3.1.0-4.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 4.19.0-17-amd64 #1 SMP Debian 4.19.194-1 (2021-06-10) x86_64 GNU/Linux + Linux i-capture-the-hostname 4.19.0-17-686-pae #1 SMP Debian 4.19.194-1 (2021-06-10) i686 GNU/Linux I: ls -l /bin - total 5776 - -rwxr-xr-x 1 root root 1367848 Feb 24 2021 bash - -rwxr-xr-x 3 root root 38280 Jul 20 2020 bunzip2 - -rwxr-xr-x 3 root root 38280 Jul 20 2020 bzcat - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep - -rwxr-xr-x 3 root root 38280 Jul 20 2020 bzip2 - -rwxr-xr-x 1 root root 17768 Jul 20 2020 bzip2recover - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore - -rwxr-xr-x 1 root root 38824 Sep 22 2020 cat - -rwxr-xr-x 1 root root 71624 Sep 22 2020 chgrp - -rwxr-xr-x 1 root root 67528 Sep 22 2020 chmod - -rwxr-xr-x 1 root root 75752 Sep 22 2020 chown - -rwxr-xr-x 1 root root 157960 Sep 22 2020 cp - -rwxr-xr-x 1 root root 128724 Dec 10 2020 dash - -rwxr-xr-x 1 root root 124904 Sep 22 2020 date - -rwxr-xr-x 1 root root 92172 Sep 22 2020 dd - -rwxr-xr-x 1 root root 100752 Sep 22 2020 df - -rwxr-xr-x 1 root root 153964 Sep 22 2020 dir - -rwxr-xr-x 1 root root 83644 Feb 7 2021 dmesg - lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname - -rwxr-xr-x 1 root root 34664 Sep 22 2020 echo - -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep - -rwxr-xr-x 1 root root 34664 Sep 22 2020 false - -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep - -rwxr-xr-x 1 root root 71928 Feb 7 2021 findmnt - -rwsr-xr-x 1 root root 30112 Feb 26 2021 fusermount - -rwxr-xr-x 1 root root 210488 Nov 9 2020 grep - -rwxr-xr-x 2 root root 2346 Mar 2 2021 gunzip - -rwxr-xr-x 1 root root 6376 Mar 2 2021 gzexe - -rwxr-xr-x 1 root root 100952 Mar 2 2021 gzip - -rwxr-xr-x 1 root root 21916 Nov 6 2019 hostname - -rwxr-xr-x 1 root root 83980 Sep 22 2020 ln - -rwxr-xr-x 1 root root 55572 Feb 7 2020 login - -rwxr-xr-x 1 root root 153964 Sep 22 2020 ls - -rwxr-xr-x 1 root root 153124 Feb 7 2021 lsblk - -rwxr-xr-x 1 root root 96328 Sep 22 2020 mkdir - -rwxr-xr-x 1 root root 79912 Sep 22 2020 mknod - -rwxr-xr-x 1 root root 47048 Sep 22 2020 mktemp - -rwxr-xr-x 1 root root 58920 Feb 7 2021 more - -rwsr-xr-x 1 root root 50720 Feb 7 2021 mount - -rwxr-xr-x 1 root root 13856 Feb 7 2021 mountpoint - -rwxr-xr-x 1 root root 157996 Sep 22 2020 mv - lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 18 2021 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 38824 Sep 22 2020 pwd - lrwxrwxrwx 1 root root 4 Feb 24 2021 rbash -> bash - -rwxr-xr-x 1 root root 46984 Sep 22 2020 readlink - -rwxr-xr-x 1 root root 75720 Sep 22 2020 rm - -rwxr-xr-x 1 root root 46984 Sep 22 2020 rmdir - -rwxr-xr-x 1 root root 22292 Sep 27 2020 run-parts - -rwxr-xr-x 1 root root 125036 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Jul 23 03:46 sh -> dash - -rwxr-xr-x 1 root root 34696 Sep 22 2020 sleep - -rwxr-xr-x 1 root root 83880 Sep 22 2020 stty - -rwsr-xr-x 1 root root 79396 Feb 7 2021 su - -rwxr-xr-x 1 root root 34696 Sep 22 2020 sync - -rwxr-xr-x 1 root root 602584 Feb 16 2021 tar - -rwxr-xr-x 1 root root 13860 Sep 27 2020 tempfile - -rwxr-xr-x 1 root root 108520 Sep 22 2020 touch - -rwxr-xr-x 1 root root 34664 Sep 22 2020 true - -rwxr-xr-x 1 root root 17768 Feb 26 2021 ulockmgr_server - -rwsr-xr-x 1 root root 30236 Feb 7 2021 umount - -rwxr-xr-x 1 root root 34664 Sep 22 2020 uname - -rwxr-xr-x 2 root root 2346 Mar 2 2021 uncompress - -rwxr-xr-x 1 root root 153964 Sep 22 2020 vdir - -rwxr-xr-x 1 root root 63024 Feb 7 2021 wdctl - lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Mar 2 2021 zcat - -rwxr-xr-x 1 root root 1678 Mar 2 2021 zcmp - -rwxr-xr-x 1 root root 5880 Mar 2 2021 zdiff - -rwxr-xr-x 1 root root 29 Mar 2 2021 zegrep - -rwxr-xr-x 1 root root 29 Mar 2 2021 zfgrep - -rwxr-xr-x 1 root root 2081 Mar 2 2021 zforce - -rwxr-xr-x 1 root root 7585 Mar 2 2021 zgrep - -rwxr-xr-x 1 root root 2206 Mar 2 2021 zless - -rwxr-xr-x 1 root root 1842 Mar 2 2021 zmore - -rwxr-xr-x 1 root root 4553 Mar 2 2021 znew -I: user script /srv/workspace/pbuilder/52110/tmp/hooks/D02_print_environment finished + total 5780 + -rwxr-xr-x 1 root root 1367848 Feb 25 10:57 bash + -rwxr-xr-x 3 root root 38280 Jul 21 2020 bunzip2 + -rwxr-xr-x 3 root root 38280 Jul 21 2020 bzcat + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep + -rwxr-xr-x 3 root root 38280 Jul 21 2020 bzip2 + -rwxr-xr-x 1 root root 17768 Jul 21 2020 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore + -rwxr-xr-x 1 root root 38824 Sep 23 2020 cat + -rwxr-xr-x 1 root root 71624 Sep 23 2020 chgrp + -rwxr-xr-x 1 root root 67528 Sep 23 2020 chmod + -rwxr-xr-x 1 root root 75752 Sep 23 2020 chown + -rwxr-xr-x 1 root root 157960 Sep 23 2020 cp + -rwxr-xr-x 1 root root 128724 Dec 11 2020 dash + -rwxr-xr-x 1 root root 124904 Sep 23 2020 date + -rwxr-xr-x 1 root root 92172 Sep 23 2020 dd + -rwxr-xr-x 1 root root 100752 Sep 23 2020 df + -rwxr-xr-x 1 root root 153964 Sep 23 2020 dir + -rwxr-xr-x 1 root root 83644 Feb 8 04:38 dmesg + lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname + -rwxr-xr-x 1 root root 34664 Sep 23 2020 echo + -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep + -rwxr-xr-x 1 root root 34664 Sep 23 2020 false + -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep + -rwxr-xr-x 1 root root 71928 Feb 8 04:38 findmnt + -rwsr-xr-x 1 root root 30112 Feb 27 06:12 fusermount + -rwxr-xr-x 1 root root 210488 Nov 10 2020 grep + -rwxr-xr-x 2 root root 2346 Mar 3 13:30 gunzip + -rwxr-xr-x 1 root root 6376 Mar 3 13:30 gzexe + -rwxr-xr-x 1 root root 100952 Mar 3 13:30 gzip + -rwxr-xr-x 1 root root 21916 Nov 8 2019 hostname + -rwxr-xr-x 1 root root 83980 Sep 23 2020 ln + -rwxr-xr-x 1 root root 55572 Feb 8 2020 login + -rwxr-xr-x 1 root root 153964 Sep 23 2020 ls + -rwxr-xr-x 1 root root 153124 Feb 8 04:38 lsblk + -rwxr-xr-x 1 root root 96328 Sep 23 2020 mkdir + -rwxr-xr-x 1 root root 79912 Sep 23 2020 mknod + -rwxr-xr-x 1 root root 47048 Sep 23 2020 mktemp + -rwxr-xr-x 1 root root 58920 Feb 8 04:38 more + -rwsr-xr-x 1 root root 50720 Feb 8 04:38 mount + -rwxr-xr-x 1 root root 13856 Feb 8 04:38 mountpoint + -rwxr-xr-x 1 root root 157996 Sep 23 2020 mv + lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 19 05:38 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 38824 Sep 23 2020 pwd + lrwxrwxrwx 1 root root 4 Feb 25 10:57 rbash -> bash + -rwxr-xr-x 1 root root 46984 Sep 23 2020 readlink + -rwxr-xr-x 1 root root 75720 Sep 23 2020 rm + -rwxr-xr-x 1 root root 46984 Sep 23 2020 rmdir + -rwxr-xr-x 1 root root 22292 Sep 28 2020 run-parts + -rwxr-xr-x 1 root root 125036 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Jun 22 20:59 sh -> bash + lrwxrwxrwx 1 root root 4 Jun 20 23:25 sh.distrib -> dash + -rwxr-xr-x 1 root root 34696 Sep 23 2020 sleep + -rwxr-xr-x 1 root root 83880 Sep 23 2020 stty + -rwsr-xr-x 1 root root 79396 Feb 8 04:38 su + -rwxr-xr-x 1 root root 34696 Sep 23 2020 sync + -rwxr-xr-x 1 root root 602584 Feb 17 23:55 tar + -rwxr-xr-x 1 root root 13860 Sep 28 2020 tempfile + -rwxr-xr-x 1 root root 108520 Sep 23 2020 touch + -rwxr-xr-x 1 root root 34664 Sep 23 2020 true + -rwxr-xr-x 1 root root 17768 Feb 27 06:12 ulockmgr_server + -rwsr-xr-x 1 root root 30236 Feb 8 04:38 umount + -rwxr-xr-x 1 root root 34664 Sep 23 2020 uname + -rwxr-xr-x 2 root root 2346 Mar 3 13:30 uncompress + -rwxr-xr-x 1 root root 153964 Sep 23 2020 vdir + -rwxr-xr-x 1 root root 63024 Feb 8 04:38 wdctl + lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Mar 3 13:30 zcat + -rwxr-xr-x 1 root root 1678 Mar 3 13:30 zcmp + -rwxr-xr-x 1 root root 5880 Mar 3 13:30 zdiff + -rwxr-xr-x 1 root root 29 Mar 3 13:30 zegrep + -rwxr-xr-x 1 root root 29 Mar 3 13:30 zfgrep + -rwxr-xr-x 1 root root 2081 Mar 3 13:30 zforce + -rwxr-xr-x 1 root root 7585 Mar 3 13:30 zgrep + -rwxr-xr-x 1 root root 2206 Mar 3 13:30 zless + -rwxr-xr-x 1 root root 1842 Mar 3 13:30 zmore + -rwxr-xr-x 1 root root 4553 Mar 3 13:30 znew +I: user script /srv/workspace/pbuilder/21607/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -381,7 +415,7 @@ Get: 173 http://deb.debian.org/debian bullseye/main i386 libtiff5 i386 4.2.0-1 [305 kB] Get: 174 http://deb.debian.org/debian bullseye/main i386 libtiffxx5 i386 4.2.0-1 [129 kB] Get: 175 http://deb.debian.org/debian bullseye/main i386 libtiff-dev i386 4.2.0-1 [438 kB] -Fetched 108 MB in 2s (68.7 MB/s) +Fetched 108 MB in 23s (4768 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 19675 files and directories currently installed.) @@ -1101,8 +1135,44 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +The following additional packages will be installed: + libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl +The following NEW packages will be installed: + libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl usrmerge +0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. +Need to get 59.5 kB of archives. +After this operation, 157 kB of additional disk space will be used. +Get:1 http://deb.debian.org/debian bullseye/main i386 libnumber-compare-perl all 0.03-1.1 [6956 B] +Get:2 http://deb.debian.org/debian bullseye/main i386 libtext-glob-perl all 0.11-1 [8888 B] +Get:3 http://deb.debian.org/debian bullseye/main i386 libfile-find-rule-perl all 0.34-1 [30.6 kB] +Get:4 http://deb.debian.org/debian bullseye/main i386 usrmerge all 25 [13.0 kB] +debconf: delaying package configuration, since apt-utils is not installed +Fetched 59.5 kB in 0s (888 kB/s) +Selecting previously unselected package libnumber-compare-perl. +(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 ... 29409 files and directories currently installed.) +Preparing to unpack .../libnumber-compare-perl_0.03-1.1_all.deb ... +Unpacking libnumber-compare-perl (0.03-1.1) ... +Selecting previously unselected package libtext-glob-perl. +Preparing to unpack .../libtext-glob-perl_0.11-1_all.deb ... +Unpacking libtext-glob-perl (0.11-1) ... +Selecting previously unselected package libfile-find-rule-perl. +Preparing to unpack .../libfile-find-rule-perl_0.34-1_all.deb ... +Unpacking libfile-find-rule-perl (0.34-1) ... +Selecting previously unselected package usrmerge. +Preparing to unpack .../archives/usrmerge_25_all.deb ... +Unpacking usrmerge (25) ... +Setting up libtext-glob-perl (0.11-1) ... +Setting up libnumber-compare-perl (0.03-1.1) ... +Setting up libfile-find-rule-perl (0.34-1) ... +Setting up usrmerge (25) ... +The system has been successfully converted. +Processing triggers for man-db (2.9.4-2) ... +Not building database; man-db/auto-update is not 'true'. I: Building the package -I: Running cd /build/relion-3.1.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b +I: Running cd /build/relion-3.1.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package relion dpkg-buildpackage: info: source version 3.1.0-4 dpkg-buildpackage: info: source distribution unstable @@ -1125,7 +1195,7 @@ mkdir /build/relion-3.1.0/build cd /build/relion-3.1.0/build; \ CC=gcc CXX=g++ cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_SKIP_RPATH=TRUE -DDoublePrec_GPU=ON -DGUI=ON -DCUDA=OFF /build/relion-3.1.0;\ -make -j18; DESTDIR=/build/relion-3.1.0/debian/tmp/cli make install +make -j10; DESTDIR=/build/relion-3.1.0/debian/tmp/cli make install CMake Warning (dev) at /usr/share/cmake-3.18/Modules/CMakeDetermineCompilerId.cmake:72 (if): Policy CMP0054 is not set: Only interpret if() arguments as variables or keywords when unquoted. Run "cmake --help-policy CMP0054" for policy @@ -1221,9 +1291,9 @@ make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/relion-3.1.0/build' make -f CMakeFiles/copy_scripts.dir/build.make CMakeFiles/copy_scripts.dir/depend -make -f src/apps/CMakeFiles/relion_lib.dir/build.make src/apps/CMakeFiles/relion_lib.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0 /build/relion-3.1.0/build /build/relion-3.1.0/build /build/relion-3.1.0/build/CMakeFiles/copy_scripts.dir/DependInfo.cmake --color= +make -f src/apps/CMakeFiles/relion_lib.dir/build.make src/apps/CMakeFiles/relion_lib.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/relion_lib.dir/DependInfo.cmake --color= Scanning dependencies of target copy_scripts @@ -1244,59 +1314,41 @@ make -f src/apps/CMakeFiles/relion_lib.dir/build.make src/apps/CMakeFiles/relion_lib.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' [ 0%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/__/macros.cpp.o +[ 0%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/args.cpp.o +cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/__/macros.cpp.o -c /build/relion-3.1.0/build/macros.cpp [ 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-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/CPlot2D.cpp.o -c /build/relion-3.1.0/src/CPlot2D.cpp -[ 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 -cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/__/macros.cpp.o -c /build/relion-3.1.0/build/macros.cpp -[ 2%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/autopicker_mpi.cpp.o -[ 3%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/fftw.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/args.cpp.o -c /build/relion-3.1.0/src/args.cpp -cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/assembly.cpp.o -c /build/relion-3.1.0/src/assembly.cpp -[ 4%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/backprojector.cpp.o -[ 5%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/error.cpp.o -[ 5%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/complex.cpp.o -[ 6%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ctffind_runner.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.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/autopicker.cpp.o -c /build/relion-3.1.0/src/autopicker.cpp -[ 6%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ctffind_runner_mpi.cpp.o +[ 3%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/backprojector.cpp.o +cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/assembly.cpp.o -c /build/relion-3.1.0/src/assembly.cpp +[ 3%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/autopicker_mpi.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/autopicker_mpi.cpp.o -c /build/relion-3.1.0/src/autopicker_mpi.cpp -[ 6%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ctf.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/backprojector.cpp.o -c /build/relion-3.1.0/src/backprojector.cpp +[ 3%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/complex.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/complex.cpp.o -c /build/relion-3.1.0/src/complex.cpp +[ 4%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ctffind_runner.cpp.o +[ 4%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ctf.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/ctf.cpp.o -c /build/relion-3.1.0/src/ctf.cpp -[ 6%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/euler.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/ctffind_runner.cpp.o -c /build/relion-3.1.0/src/ctffind_runner.cpp -[ 6%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/exp_model.cpp.o +[ 4%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ctffind_runner_mpi.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/ctffind_runner_mpi.cpp.o -c /build/relion-3.1.0/src/ctffind_runner_mpi.cpp -[ 6%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/filename.cpp.o +[ 5%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/error.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/error.cpp.o -c /build/relion-3.1.0/src/error.cpp +[ 5%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/euler.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/euler.cpp.o -c /build/relion-3.1.0/src/euler.cpp +[ 5%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/exp_model.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/exp_model.cpp.o -c /build/relion-3.1.0/src/exp_model.cpp +[ 6%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/fftw.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/fftw.cpp.o -c /build/relion-3.1.0/src/fftw.cpp +[ 6%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/filename.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/filename.cpp.o -c /build/relion-3.1.0/src/filename.cpp [ 7%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/flex_analyser.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/flex_analyser.cpp.o -c /build/relion-3.1.0/src/flex_analyser.cpp [ 7%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/funcs.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/funcs.cpp.o -c /build/relion-3.1.0/src/funcs.cpp -[ 7%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/healpix_sampling.cpp.o -cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/healpix_sampling.cpp.o -c /build/relion-3.1.0/src/healpix_sampling.cpp -[ 8%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/helix.cpp.o -cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/helix.cpp.o -c /build/relion-3.1.0/src/helix.cpp -[ 8%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/helix_inimodel2d.cpp.o -cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/helix_inimodel2d.cpp.o -c /build/relion-3.1.0/src/helix_inimodel2d.cpp -[ 8%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/image.cpp.o -cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/image.cpp.o -c /build/relion-3.1.0/src/image.cpp -[ 9%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/local_symmetry.cpp.o -cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/local_symmetry.cpp.o -c /build/relion-3.1.0/src/local_symmetry.cpp -[ 9%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/local_symmetry_mpi.cpp.o -cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/local_symmetry_mpi.cpp.o -c /build/relion-3.1.0/src/local_symmetry_mpi.cpp -[ 10%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/mask.cpp.o -cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/mask.cpp.o -c /build/relion-3.1.0/src/mask.cpp -[ 10%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/matrix1d.cpp.o -cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/matrix1d.cpp.o -c /build/relion-3.1.0/src/matrix1d.cpp -[ 10%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/matrix2d.cpp.o -cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/matrix2d.cpp.o -c /build/relion-3.1.0/src/matrix2d.cpp /build/relion-3.1.0/src/CPlot2D.cpp: In member function 'void CPlot2D::ComputeLabelTickSpacing(double, double, double*, double*, double*, int, std::string)': /build/relion-3.1.0/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); @@ -1316,6 +1368,24 @@ /build/relion-3.1.0/src/CPlot2D.cpp:733:16: note: 'sprintf' output between 5 and 14 bytes into a destination of size 10 733 | sprintf(m_cXAxisLabelFormat,"%%.%df",nfrac); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 7%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/healpix_sampling.cpp.o +cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/healpix_sampling.cpp.o -c /build/relion-3.1.0/src/healpix_sampling.cpp +[ 8%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/helix.cpp.o +cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/helix.cpp.o -c /build/relion-3.1.0/src/helix.cpp +[ 8%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/helix_inimodel2d.cpp.o +cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/helix_inimodel2d.cpp.o -c /build/relion-3.1.0/src/helix_inimodel2d.cpp +[ 8%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/image.cpp.o +cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/image.cpp.o -c /build/relion-3.1.0/src/image.cpp +[ 9%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/local_symmetry.cpp.o +cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/local_symmetry.cpp.o -c /build/relion-3.1.0/src/local_symmetry.cpp +[ 9%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/local_symmetry_mpi.cpp.o +cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/local_symmetry_mpi.cpp.o -c /build/relion-3.1.0/src/local_symmetry_mpi.cpp +[ 10%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/mask.cpp.o +cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/mask.cpp.o -c /build/relion-3.1.0/src/mask.cpp +[ 10%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/matrix1d.cpp.o +cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/matrix1d.cpp.o -c /build/relion-3.1.0/src/matrix1d.cpp +[ 10%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/matrix2d.cpp.o +cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/matrix2d.cpp.o -c /build/relion-3.1.0/src/matrix2d.cpp [ 11%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/memory.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/memory.cpp.o -c /build/relion-3.1.0/src/memory.cpp [ 11%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/metadata_container.cpp.o @@ -1328,9 +1398,9 @@ cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/micrograph_model.cpp.o -c /build/relion-3.1.0/src/micrograph_model.cpp [ 13%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ml_model.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/ml_model.cpp.o -c /build/relion-3.1.0/src/ml_model.cpp +[ 13%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ml_optimiser_mpi.cpp.o [ 13%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ml_optimiser.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/ml_optimiser.cpp.o -c /build/relion-3.1.0/src/ml_optimiser.cpp -[ 13%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ml_optimiser_mpi.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/ml_optimiser_mpi.cpp.o -c /build/relion-3.1.0/src/ml_optimiser_mpi.cpp [ 14%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/motioncorr_runner.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/motioncorr_runner.cpp.o -c /build/relion-3.1.0/src/motioncorr_runner.cpp @@ -1452,10 +1522,10 @@ cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/optimization/lbfgs.cpp.o -c /build/relion-3.1.0/src/jaz/optimization/lbfgs.cpp [ 36%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/nelder_mead.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/optimization/nelder_mead.cpp.o -c /build/relion-3.1.0/src/jaz/optimization/nelder_mead.cpp -[ 36%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/aberration_estimator.cpp.o -cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/ctf/aberration_estimator.cpp.o -c /build/relion-3.1.0/src/jaz/ctf/aberration_estimator.cpp [ 37%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/optimization.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/optimization/optimization.cpp.o -c /build/relion-3.1.0/src/jaz/optimization/optimization.cpp +[ 37%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/aberration_estimator.cpp.o +cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/ctf/aberration_estimator.cpp.o -c /build/relion-3.1.0/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-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/ctf/bfactor_refiner.cpp.o -c /build/relion-3.1.0/src/jaz/ctf/bfactor_refiner.cpp [ 38%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/ctf_refiner.cpp.o @@ -1477,13 +1547,13 @@ [ 41%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/modular_ctf_optimisation.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/ctf/modular_ctf_optimisation.cpp.o -c /build/relion-3.1.0/src/jaz/ctf/modular_ctf_optimisation.cpp [ 41%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_estimator.cpp.o -[ 41%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_helper.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_estimator.cpp.o -c /build/relion-3.1.0/src/jaz/ctf/tilt_estimator.cpp +[ 41%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_helper.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_helper.cpp.o -c /build/relion-3.1.0/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-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/motion/alignment_set.cpp.o -c /build/relion-3.1.0/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-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/motion/frame_recombiner.cpp.o -c /build/relion-3.1.0/src/jaz/motion/frame_recombiner.cpp +[ 42%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/alignment_set.cpp.o +cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/motion/alignment_set.cpp.o -c /build/relion-3.1.0/src/jaz/motion/alignment_set.cpp [ 43%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/gp_motion_fit.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/motion/gp_motion_fit.cpp.o -c /build/relion-3.1.0/src/jaz/motion/gp_motion_fit.cpp [ 43%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_estimator.cpp.o @@ -1507,8 +1577,8 @@ [ 46%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/img_proc/filter_helper.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/img_proc/filter_helper.cpp.o -c /build/relion-3.1.0/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-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/img_proc/image_op.cpp.o -c /build/relion-3.1.0/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-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/img_proc/image_op.cpp.o -c /build/relion-3.1.0/src/jaz/img_proc/image_op.cpp cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/tomo/backprojection_helper.cpp.o -c /build/relion-3.1.0/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-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/tomo/imod_helper.cpp.o -c /build/relion-3.1.0/src/jaz/tomo/imod_helper.cpp @@ -1525,8 +1595,8 @@ [ 50%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevd3.c.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c99 -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevd3.c.o -c /build/relion-3.1.0/src/jaz/d3x3/dsyevd3.c [ 50%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevh3.c.o -cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c99 -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevh3.c.o -c /build/relion-3.1.0/src/jaz/d3x3/dsyevh3.c [ 51%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevj3.c.o +cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c99 -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevh3.c.o -c /build/relion-3.1.0/src/jaz/d3x3/dsyevh3.c cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c99 -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevj3.c.o -c /build/relion-3.1.0/src/jaz/d3x3/dsyevj3.c [ 51%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevq3.c.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c99 -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevq3.c.o -c /build/relion-3.1.0/src/jaz/d3x3/dsyevq3.c @@ -1550,258 +1620,298 @@ make -f src/apps/CMakeFiles/plot_delocalisation.dir/build.make src/apps/CMakeFiles/plot_delocalisation.dir/depend make -f src/apps/CMakeFiles/postprocess_mpi.dir/build.make src/apps/CMakeFiles/postprocess_mpi.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' +cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/image_handler.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/particle_FCC.dir/DependInfo.cmake --color= make -f src/apps/CMakeFiles/helix_toolbox.dir/build.make src/apps/CMakeFiles/helix_toolbox.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' -cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/image_handler.dir/DependInfo.cmake --color= -make -f src/apps/CMakeFiles/preprocess_mpi.dir/build.make src/apps/CMakeFiles/preprocess_mpi.dir/depend -make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/plot_delocalisation.dir/DependInfo.cmake --color= -make -f src/apps/CMakeFiles/helix_inimodel2d.dir/build.make src/apps/CMakeFiles/helix_inimodel2d.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/postprocess_mpi.dir/DependInfo.cmake --color= +make -f src/apps/CMakeFiles/preprocess_mpi.dir/build.make src/apps/CMakeFiles/preprocess_mpi.dir/depend +make -f src/apps/CMakeFiles/helix_inimodel2d.dir/build.make src/apps/CMakeFiles/helix_inimodel2d.dir/depend +make -f src/apps/CMakeFiles/find_tiltpairs.dir/build.make src/apps/CMakeFiles/find_tiltpairs.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/helix_toolbox.dir/DependInfo.cmake --color= -make -f src/apps/CMakeFiles/find_tiltpairs.dir/build.make src/apps/CMakeFiles/find_tiltpairs.dir/depend make -f src/apps/CMakeFiles/localsym.dir/build.make src/apps/CMakeFiles/localsym.dir/depend +make -f src/apps/CMakeFiles/relion_gui_lib.dir/build.make src/apps/CMakeFiles/relion_gui_lib.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/preprocess_mpi.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/relion-3.1.0/build' +cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/localsym.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/helix_inimodel2d.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/find_tiltpairs.dir/DependInfo.cmake --color= -make -f src/apps/CMakeFiles/relion_gui_lib.dir/build.make src/apps/CMakeFiles/relion_gui_lib.dir/depend -make -f src/apps/CMakeFiles/localsym_mpi.dir/build.make src/apps/CMakeFiles/localsym_mpi.dir/depend -make[4]: Entering directory '/build/relion-3.1.0/build' -cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/localsym.dir/DependInfo.cmake --color= -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-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/relion_gui_lib.dir/DependInfo.cmake --color= -make -f src/apps/CMakeFiles/prepare_subtomo.dir/build.make src/apps/CMakeFiles/prepare_subtomo.dir/depend -make -f src/apps/CMakeFiles/particle_subtract_mpi.dir/build.make src/apps/CMakeFiles/particle_subtract_mpi.dir/depend -make -f src/apps/CMakeFiles/external_reconstruct.dir/build.make src/apps/CMakeFiles/external_reconstruct.dir/depend -make[4]: Entering directory '/build/relion-3.1.0/build' -cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/localsym_mpi.dir/DependInfo.cmake --color= -make -f src/apps/CMakeFiles/import.dir/build.make src/apps/CMakeFiles/import.dir/depend -make[4]: Entering directory '/build/relion-3.1.0/build' -cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/flex_analyse_mpi.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/relion-3.1.0/build' -cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/prepare_subtomo.dir/DependInfo.cmake --color= -make -f src/apps/CMakeFiles/flex_analyse.dir/build.make src/apps/CMakeFiles/flex_analyse.dir/depend -make[4]: Entering directory '/build/relion-3.1.0/build' -cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/external_reconstruct.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/relion-3.1.0/build' -cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/particle_subtract_mpi.dir/DependInfo.cmake --color= -make -f src/apps/CMakeFiles/autopick.dir/build.make src/apps/CMakeFiles/autopick.dir/depend -make[4]: Entering directory '/build/relion-3.1.0/build' -cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/import.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/relion-3.1.0/build' -cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/flex_analyse.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/relion-3.1.0/build' -cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/autopick.dir/DependInfo.cmake --color= Scanning dependencies of target find_tiltpairs make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/find_tiltpairs.dir/build.make src/apps/CMakeFiles/find_tiltpairs.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' -Scanning dependencies of target postprocess_mpi -Scanning dependencies of target helix_toolbox -make[4]: Leaving directory '/build/relion-3.1.0/build' Scanning dependencies of target helix_inimodel2d -Scanning dependencies of target particle_FCC -Scanning dependencies of target plot_delocalisation -make[4]: Leaving directory '/build/relion-3.1.0/build' -make -f src/apps/CMakeFiles/postprocess_mpi.dir/build.make src/apps/CMakeFiles/postprocess_mpi.dir/build -make -f src/apps/CMakeFiles/helix_toolbox.dir/build.make src/apps/CMakeFiles/helix_toolbox.dir/build -make[4]: Leaving directory '/build/relion-3.1.0/build' +Scanning dependencies of target localsym make[4]: Leaving directory '/build/relion-3.1.0/build' make[4]: Leaving directory '/build/relion-3.1.0/build' -make -f src/apps/CMakeFiles/particle_FCC.dir/build.make src/apps/CMakeFiles/particle_FCC.dir/build -make -f src/apps/CMakeFiles/plot_delocalisation.dir/build.make src/apps/CMakeFiles/plot_delocalisation.dir/build make -f src/apps/CMakeFiles/helix_inimodel2d.dir/build.make src/apps/CMakeFiles/helix_inimodel2d.dir/build -Scanning dependencies of target image_handler -make[4]: Entering directory '/build/relion-3.1.0/build' -make[4]: Entering directory '/build/relion-3.1.0/build' +Scanning dependencies of target helix_toolbox +make[4]: Leaving directory '/build/relion-3.1.0/build' +Scanning dependencies of target particle_FCC make[4]: Leaving directory '/build/relion-3.1.0/build' make[4]: Entering directory '/build/relion-3.1.0/build' +make -f src/apps/CMakeFiles/particle_FCC.dir/build.make src/apps/CMakeFiles/particle_FCC.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' +make -f src/apps/CMakeFiles/helix_toolbox.dir/build.make src/apps/CMakeFiles/helix_toolbox.dir/build +[ 54%] Building CXX object src/apps/CMakeFiles/find_tiltpairs.dir/find_tiltpairs.cpp.o make[4]: Entering directory '/build/relion-3.1.0/build' -make -f src/apps/CMakeFiles/image_handler.dir/build.make src/apps/CMakeFiles/image_handler.dir/build -Scanning dependencies of target localsym -Scanning dependencies of target external_reconstruct -Scanning dependencies of target prepare_subtomo +make -f src/apps/CMakeFiles/localsym.dir/build.make src/apps/CMakeFiles/localsym.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' +cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/find_tiltpairs.dir/find_tiltpairs.cpp.o -c /build/relion-3.1.0/src/apps/find_tiltpairs.cpp +Scanning dependencies of target plot_delocalisation make[4]: Leaving directory '/build/relion-3.1.0/build' +make -f src/apps/CMakeFiles/plot_delocalisation.dir/build.make src/apps/CMakeFiles/plot_delocalisation.dir/build +make[4]: Entering directory '/build/relion-3.1.0/build' +Scanning dependencies of target image_handler +Scanning dependencies of target postprocess_mpi make[4]: Leaving directory '/build/relion-3.1.0/build' -make -f src/apps/CMakeFiles/localsym.dir/build.make src/apps/CMakeFiles/localsym.dir/build make[4]: Leaving directory '/build/relion-3.1.0/build' -make -f src/apps/CMakeFiles/prepare_subtomo.dir/build.make src/apps/CMakeFiles/prepare_subtomo.dir/build +make -f src/apps/CMakeFiles/image_handler.dir/build.make src/apps/CMakeFiles/image_handler.dir/build +[ 55%] Building CXX object src/apps/CMakeFiles/helix_inimodel2d.dir/helix_inimodel2d.cpp.o +cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/helix_inimodel2d.dir/helix_inimodel2d.cpp.o -c /build/relion-3.1.0/src/apps/helix_inimodel2d.cpp +make -f src/apps/CMakeFiles/postprocess_mpi.dir/build.make src/apps/CMakeFiles/postprocess_mpi.dir/build Scanning dependencies of target preprocess_mpi -make -f src/apps/CMakeFiles/external_reconstruct.dir/build.make src/apps/CMakeFiles/external_reconstruct.dir/build -make[4]: Leaving directory '/build/relion-3.1.0/build' -make -f src/apps/CMakeFiles/preprocess_mpi.dir/build.make src/apps/CMakeFiles/preprocess_mpi.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' +make[4]: Leaving directory '/build/relion-3.1.0/build' make[4]: Entering directory '/build/relion-3.1.0/build' +make -f src/apps/CMakeFiles/preprocess_mpi.dir/build.make src/apps/CMakeFiles/preprocess_mpi.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' -[ 54%] Building CXX object src/apps/CMakeFiles/find_tiltpairs.dir/find_tiltpairs.cpp.o +[ 56%] Building CXX object src/apps/CMakeFiles/plot_delocalisation.dir/plot_delocalisation.cpp.o +[ 57%] Building CXX object src/apps/CMakeFiles/helix_toolbox.dir/helix_toolbox.cpp.o +cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/plot_delocalisation.dir/plot_delocalisation.cpp.o -c /build/relion-3.1.0/src/apps/plot_delocalisation.cpp +[ 58%] Building CXX object src/apps/CMakeFiles/localsym.dir/localsym.cpp.o +cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/localsym.dir/localsym.cpp.o -c /build/relion-3.1.0/src/apps/localsym.cpp +[ 56%] Building CXX object src/apps/CMakeFiles/particle_FCC.dir/particle_FCC.cpp.o +cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/particle_FCC.dir/particle_FCC.cpp.o -c /build/relion-3.1.0/src/apps/particle_FCC.cpp +cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/helix_toolbox.dir/helix_toolbox.cpp.o -c /build/relion-3.1.0/src/apps/helix_toolbox.cpp +Scanning dependencies of target relion_gui_lib +make[4]: Leaving directory '/build/relion-3.1.0/build' +make -f src/apps/CMakeFiles/relion_gui_lib.dir/build.make src/apps/CMakeFiles/relion_gui_lib.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' -cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/find_tiltpairs.dir/find_tiltpairs.cpp.o -c /build/relion-3.1.0/src/apps/find_tiltpairs.cpp -Scanning dependencies of target flex_analyse_mpi -Scanning dependencies of target import +[ 58%] Building CXX object src/apps/CMakeFiles/image_handler.dir/image_handler.cpp.o +[ 59%] Building CXX object src/apps/CMakeFiles/postprocess_mpi.dir/postprocess_mpi.cpp.o +cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/image_handler.dir/image_handler.cpp.o -c /build/relion-3.1.0/src/apps/image_handler.cpp +[ 60%] Building CXX object src/apps/CMakeFiles/preprocess_mpi.dir/preprocess_mpi.cpp.o +cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/postprocess_mpi.dir/postprocess_mpi.cpp.o -c /build/relion-3.1.0/src/apps/postprocess_mpi.cpp +[ 60%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/displayer.cpp.o +cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/preprocess_mpi.dir/preprocess_mpi.cpp.o -c /build/relion-3.1.0/src/apps/preprocess_mpi.cpp +cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_gui_lib.dir/__/displayer.cpp.o -c /build/relion-3.1.0/src/displayer.cpp +[ 60%] Linking CXX executable ../../bin/relion_localsym +cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/localsym.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 +[ 60%] Linking CXX executable ../../bin/relion_helix_inimodel2d +cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/helix_inimodel2d.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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-3.1.0/build' +[ 60%] Built target helix_inimodel2d +make -f src/apps/CMakeFiles/localsym_mpi.dir/build.make src/apps/CMakeFiles/localsym_mpi.dir/depend +make[4]: Entering directory '/build/relion-3.1.0/build' +cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/localsym_mpi.dir/DependInfo.cmake --color= +[ 60%] Linking CXX executable ../../bin/relion_particle_FCC +cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/particle_FCC.dir/link.txt --verbose=1 Scanning dependencies of target localsym_mpi make[4]: Leaving directory '/build/relion-3.1.0/build' -make -f src/apps/CMakeFiles/flex_analyse_mpi.dir/build.make src/apps/CMakeFiles/flex_analyse_mpi.dir/build -make -f src/apps/CMakeFiles/import.dir/build.make src/apps/CMakeFiles/import.dir/build -make[4]: Leaving directory '/build/relion-3.1.0/build' -Scanning dependencies of target flex_analyse make -f src/apps/CMakeFiles/localsym_mpi.dir/build.make src/apps/CMakeFiles/localsym_mpi.dir/build -[ 55%] Building CXX object src/apps/CMakeFiles/postprocess_mpi.dir/postprocess_mpi.cpp.o +/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 +make[4]: Entering directory '/build/relion-3.1.0/build' +[ 61%] Building CXX object src/apps/CMakeFiles/localsym_mpi.dir/localsym_mpi.cpp.o +cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/localsym_mpi.dir/localsym_mpi.cpp.o -c /build/relion-3.1.0/src/apps/localsym_mpi.cpp make[4]: Leaving directory '/build/relion-3.1.0/build' -[ 56%] Building CXX object src/apps/CMakeFiles/helix_toolbox.dir/helix_toolbox.cpp.o -[ 57%] Building CXX object src/apps/CMakeFiles/particle_FCC.dir/particle_FCC.cpp.o -make -f src/apps/CMakeFiles/flex_analyse.dir/build.make src/apps/CMakeFiles/flex_analyse.dir/build +[ 61%] Built target localsym +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-3.1.0/build' -Scanning dependencies of target autopick -[ 57%] Building CXX object src/apps/CMakeFiles/plot_delocalisation.dir/plot_delocalisation.cpp.o -cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/postprocess_mpi.dir/postprocess_mpi.cpp.o -c /build/relion-3.1.0/src/apps/postprocess_mpi.cpp -[ 58%] Building CXX object src/apps/CMakeFiles/helix_inimodel2d.dir/helix_inimodel2d.cpp.o +cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/flex_analyse_mpi.dir/DependInfo.cmake --color= +Scanning dependencies of target flex_analyse_mpi +make[4]: Leaving directory '/build/relion-3.1.0/build' +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-3.1.0/build' -cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/helix_toolbox.dir/helix_toolbox.cpp.o -c /build/relion-3.1.0/src/apps/helix_toolbox.cpp +[ 61%] Building CXX object src/apps/CMakeFiles/flex_analyse_mpi.dir/flex_analyse_mpi.cpp.o +cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/flex_analyse_mpi.dir/flex_analyse_mpi.cpp.o -c /build/relion-3.1.0/src/apps/flex_analyse_mpi.cpp +[ 61%] Linking CXX executable ../../bin/relion_preprocess_mpi +cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/preprocess_mpi.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 +[ 61%] Linking CXX executable ../../bin/relion_postprocess_mpi +cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/postprocess_mpi.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 +[ 61%] Linking CXX executable ../../bin/relion_plot_delocalisation +cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/plot_delocalisation.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 make[4]: Leaving directory '/build/relion-3.1.0/build' -cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/particle_FCC.dir/particle_FCC.cpp.o -c /build/relion-3.1.0/src/apps/particle_FCC.cpp -cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/plot_delocalisation.dir/plot_delocalisation.cpp.o -c /build/relion-3.1.0/src/apps/plot_delocalisation.cpp -make -f src/apps/CMakeFiles/autopick.dir/build.make src/apps/CMakeFiles/autopick.dir/build +[ 61%] Built target particle_FCC +make -f src/apps/CMakeFiles/prepare_subtomo.dir/build.make src/apps/CMakeFiles/prepare_subtomo.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' +cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/prepare_subtomo.dir/DependInfo.cmake --color= +Scanning dependencies of target prepare_subtomo +make[4]: Leaving directory '/build/relion-3.1.0/build' +make -f src/apps/CMakeFiles/prepare_subtomo.dir/build.make src/apps/CMakeFiles/prepare_subtomo.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' -[ 58%] Building CXX object src/apps/CMakeFiles/image_handler.dir/image_handler.cpp.o -cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/image_handler.dir/image_handler.cpp.o -c /build/relion-3.1.0/src/apps/image_handler.cpp -cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/helix_inimodel2d.dir/helix_inimodel2d.cpp.o -c /build/relion-3.1.0/src/apps/helix_inimodel2d.cpp -Scanning dependencies of target relion_gui_lib -[ 59%] Building CXX object src/apps/CMakeFiles/localsym.dir/localsym.cpp.o +[ 61%] Building CXX object src/apps/CMakeFiles/prepare_subtomo.dir/prepare_subtomo.cpp.o +cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/prepare_subtomo.dir/prepare_subtomo.cpp.o -c /build/relion-3.1.0/src/apps/prepare_subtomo.cpp +make[4]: Leaving directory '/build/relion-3.1.0/build' +[ 61%] Built target postprocess_mpi +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-3.1.0/build' +cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/particle_subtract_mpi.dir/DependInfo.cmake --color= Scanning dependencies of target particle_subtract_mpi +make[4]: Leaving directory '/build/relion-3.1.0/build' +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-3.1.0/build' -cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/localsym.dir/localsym.cpp.o -c /build/relion-3.1.0/src/apps/localsym.cpp +[ 62%] Building CXX object src/apps/CMakeFiles/particle_subtract_mpi.dir/particle_subtract_mpi.cpp.o +cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/particle_subtract_mpi.dir/particle_subtract_mpi.cpp.o -c /build/relion-3.1.0/src/apps/particle_subtract_mpi.cpp make[4]: Leaving directory '/build/relion-3.1.0/build' -[ 59%] Building CXX object src/apps/CMakeFiles/prepare_subtomo.dir/prepare_subtomo.cpp.o +[ 62%] Built target preprocess_mpi +make -f src/apps/CMakeFiles/external_reconstruct.dir/build.make src/apps/CMakeFiles/external_reconstruct.dir/depend +make[4]: Entering directory '/build/relion-3.1.0/build' +cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/external_reconstruct.dir/DependInfo.cmake --color= +Scanning dependencies of target external_reconstruct make[4]: Leaving directory '/build/relion-3.1.0/build' -[ 60%] Building CXX object src/apps/CMakeFiles/external_reconstruct.dir/external_reconstruct.cpp.o -[ 61%] Building CXX object src/apps/CMakeFiles/preprocess_mpi.dir/preprocess_mpi.cpp.o -cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/prepare_subtomo.dir/prepare_subtomo.cpp.o -c /build/relion-3.1.0/src/apps/prepare_subtomo.cpp -make -f src/apps/CMakeFiles/relion_gui_lib.dir/build.make src/apps/CMakeFiles/relion_gui_lib.dir/build +make -f src/apps/CMakeFiles/external_reconstruct.dir/build.make src/apps/CMakeFiles/external_reconstruct.dir/build +make[4]: Entering directory '/build/relion-3.1.0/build' +[ 63%] Building CXX object src/apps/CMakeFiles/external_reconstruct.dir/external_reconstruct.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/external_reconstruct.dir/external_reconstruct.cpp.o -c /build/relion-3.1.0/src/apps/external_reconstruct.cpp -cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/preprocess_mpi.dir/preprocess_mpi.cpp.o -c /build/relion-3.1.0/src/apps/preprocess_mpi.cpp +make[4]: Leaving directory '/build/relion-3.1.0/build' +[ 63%] Built target plot_delocalisation +make -f src/apps/CMakeFiles/import.dir/build.make src/apps/CMakeFiles/import.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' -make -f src/apps/CMakeFiles/particle_subtract_mpi.dir/build.make src/apps/CMakeFiles/particle_subtract_mpi.dir/build -[ 61%] Building CXX object src/apps/CMakeFiles/import.dir/import.cpp.o -[ 61%] Building CXX object src/apps/CMakeFiles/flex_analyse.dir/flex_analyse.cpp.o +cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/import.dir/DependInfo.cmake --color= +Scanning dependencies of target import +make[4]: Leaving directory '/build/relion-3.1.0/build' +make -f src/apps/CMakeFiles/import.dir/build.make src/apps/CMakeFiles/import.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' +[ 63%] Building CXX object src/apps/CMakeFiles/import.dir/import.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/import.dir/import.cpp.o -c /build/relion-3.1.0/src/apps/import.cpp -[ 61%] Building CXX object src/apps/CMakeFiles/flex_analyse_mpi.dir/flex_analyse_mpi.cpp.o +[ 63%] Linking CXX executable ../../bin/relion_find_tiltpairs +cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/find_tiltpairs.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 +[ 63%] Linking CXX executable ../../bin/relion_localsym_mpi +cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/localsym_mpi.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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-3.1.0/build' +[ 63%] Built target find_tiltpairs +make -f src/apps/CMakeFiles/flex_analyse.dir/build.make src/apps/CMakeFiles/flex_analyse.dir/depend +make[4]: Entering directory '/build/relion-3.1.0/build' +cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/flex_analyse.dir/DependInfo.cmake --color= +Scanning dependencies of target flex_analyse +make[4]: Leaving directory '/build/relion-3.1.0/build' +make -f src/apps/CMakeFiles/flex_analyse.dir/build.make src/apps/CMakeFiles/flex_analyse.dir/build +make[4]: Entering directory '/build/relion-3.1.0/build' +[ 63%] Building CXX object src/apps/CMakeFiles/flex_analyse.dir/flex_analyse.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/flex_analyse.dir/flex_analyse.cpp.o -c /build/relion-3.1.0/src/apps/flex_analyse.cpp -[ 62%] Building CXX object src/apps/CMakeFiles/localsym_mpi.dir/localsym_mpi.cpp.o -cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/localsym_mpi.dir/localsym_mpi.cpp.o -c /build/relion-3.1.0/src/apps/localsym_mpi.cpp -cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/flex_analyse_mpi.dir/flex_analyse_mpi.cpp.o -c /build/relion-3.1.0/src/apps/flex_analyse_mpi.cpp -[ 63%] Building CXX object src/apps/CMakeFiles/autopick.dir/autopick.cpp.o +make[4]: Leaving directory '/build/relion-3.1.0/build' +[ 63%] Built target localsym_mpi +make -f src/apps/CMakeFiles/autopick.dir/build.make src/apps/CMakeFiles/autopick.dir/depend +make[4]: Entering directory '/build/relion-3.1.0/build' +cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/autopick.dir/DependInfo.cmake --color= +Scanning dependencies of target autopick +make[4]: Leaving directory '/build/relion-3.1.0/build' +make -f src/apps/CMakeFiles/autopick.dir/build.make src/apps/CMakeFiles/autopick.dir/build +make[4]: Entering directory '/build/relion-3.1.0/build' +[ 64%] Building CXX object src/apps/CMakeFiles/autopick.dir/autopick.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/autopick.dir/autopick.cpp.o -c /build/relion-3.1.0/src/apps/autopick.cpp -[ 63%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/displayer.cpp.o -[ 64%] Building CXX object src/apps/CMakeFiles/particle_subtract_mpi.dir/particle_subtract_mpi.cpp.o -cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_gui_lib.dir/__/displayer.cpp.o -c /build/relion-3.1.0/src/displayer.cpp -cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/particle_subtract_mpi.dir/particle_subtract_mpi.cpp.o -c /build/relion-3.1.0/src/apps/particle_subtract_mpi.cpp -[ 64%] Linking CXX executable ../../bin/relion_localsym -cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/localsym.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 -[ 64%] Linking CXX executable ../../bin/relion_helix_inimodel2d -cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/helix_inimodel2d.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 -[ 64%] Linking CXX executable ../../bin/relion_autopick -cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/autopick.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 +[ 64%] Linking CXX executable ../../bin/relion_flex_analyse_mpi +cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/flex_analyse_mpi.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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-3.1.0/build' -[ 64%] Built target helix_inimodel2d +[ 64%] Built target flex_analyse_mpi +[ 64%] Linking CXX executable ../../bin/relion_import make -f src/apps/CMakeFiles/convert_to_tiff.dir/build.make src/apps/CMakeFiles/convert_to_tiff.dir/depend +cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/import.dir/link.txt --verbose=1 make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/convert_to_tiff.dir/DependInfo.cmake --color= +/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 Scanning dependencies of target convert_to_tiff make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/convert_to_tiff.dir/build.make src/apps/CMakeFiles/convert_to_tiff.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' [ 64%] Building CXX object src/apps/CMakeFiles/convert_to_tiff.dir/convert_to_tiff.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/convert_to_tiff.dir/convert_to_tiff.cpp.o -c /build/relion-3.1.0/src/apps/convert_to_tiff.cpp -[ 64%] Linking CXX executable ../../bin/relion_localsym_mpi -cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/localsym_mpi.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 +[ 64%] Linking CXX executable ../../bin/relion_autopick +cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/autopick.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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-3.1.0/build' -[ 64%] Built target localsym +[ 64%] Built target import 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-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/ctf_refine_mpi.dir/DependInfo.cmake --color= +[ 65%] Linking CXX executable ../../bin/relion_flex_analyse +cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/flex_analyse.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 Scanning dependencies of target ctf_refine_mpi make[4]: Leaving directory '/build/relion-3.1.0/build' 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-3.1.0/build' -[ 64%] Building CXX object src/apps/CMakeFiles/ctf_refine_mpi.dir/ctf_refine_mpi.cpp.o +[ 65%] Building CXX object src/apps/CMakeFiles/ctf_refine_mpi.dir/ctf_refine_mpi.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/ctf_refine_mpi.dir/ctf_refine_mpi.cpp.o -c /build/relion-3.1.0/src/apps/ctf_refine_mpi.cpp -[ 64%] Linking CXX executable ../../bin/relion_preprocess_mpi -cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/preprocess_mpi.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 +[ 65%] Linking CXX executable ../../bin/relion_convert_to_tiff +cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/convert_to_tiff.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 +[ 65%] Linking CXX executable ../../bin/relion_external_reconstruct +cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/external_reconstruct.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/relion-3.1.0/build' -[ 64%] Linking CXX executable ../../bin/relion_particle_FCC -cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/particle_FCC.dir/link.txt --verbose=1 -[ 64%] Built target autopick +/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 +[ 65%] Built target autopick make -f src/apps/CMakeFiles/merge_particles.dir/build.make src/apps/CMakeFiles/merge_particles.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/merge_particles.dir/DependInfo.cmake --color= -/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 Scanning dependencies of target merge_particles make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/merge_particles.dir/build.make src/apps/CMakeFiles/merge_particles.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' -[ 65%] Building CXX object src/apps/CMakeFiles/merge_particles.dir/merge_particles.cpp.o +[ 66%] Building CXX object src/apps/CMakeFiles/merge_particles.dir/merge_particles.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/merge_particles.dir/merge_particles.cpp.o -c /build/relion-3.1.0/src/apps/merge_particles.cpp -[ 65%] Linking CXX executable ../../bin/relion_postprocess_mpi -cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/postprocess_mpi.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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-3.1.0/build' -[ 65%] Built target localsym_mpi +[ 66%] Built target external_reconstruct make -f src/apps/CMakeFiles/mask_create.dir/build.make src/apps/CMakeFiles/mask_create.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/mask_create.dir/DependInfo.cmake --color= -Scanning dependencies of target mask_create make[4]: Leaving directory '/build/relion-3.1.0/build' -make -f src/apps/CMakeFiles/mask_create.dir/build.make src/apps/CMakeFiles/mask_create.dir/build -make[4]: Entering directory '/build/relion-3.1.0/build' -[ 65%] Building CXX object src/apps/CMakeFiles/mask_create.dir/mask_create.cpp.o -cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/mask_create.dir/mask_create.cpp.o -c /build/relion-3.1.0/src/apps/mask_create.cpp -[ 65%] Linking CXX executable ../../bin/relion_convert_to_tiff -cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/convert_to_tiff.dir/link.txt --verbose=1 -make[4]: Leaving directory '/build/relion-3.1.0/build' -/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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-3.1.0/build' -[ 65%] Built target preprocess_mpi +[ 66%] Built target convert_to_tiff make -f src/apps/CMakeFiles/project.dir/build.make src/apps/CMakeFiles/project.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/project.dir/DependInfo.cmake --color= -[ 65%] Linking CXX executable ../../bin/relion_plot_delocalisation -cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/plot_delocalisation.dir/link.txt --verbose=1 -[ 65%] Built target postprocess_mpi -make -f src/apps/CMakeFiles/ctf_mask_test.dir/build.make src/apps/CMakeFiles/ctf_mask_test.dir/depend +Scanning dependencies of target mask_create +make[4]: Leaving directory '/build/relion-3.1.0/build' +make -f src/apps/CMakeFiles/mask_create.dir/build.make src/apps/CMakeFiles/mask_create.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' -cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/ctf_mask_test.dir/DependInfo.cmake --color= -/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 Scanning dependencies of target project make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/project.dir/build.make src/apps/CMakeFiles/project.dir/build +[ 66%] Building CXX object src/apps/CMakeFiles/mask_create.dir/mask_create.cpp.o make[4]: Entering directory '/build/relion-3.1.0/build' +cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/mask_create.dir/mask_create.cpp.o -c /build/relion-3.1.0/src/apps/mask_create.cpp +[ 67%] Building CXX object src/apps/CMakeFiles/project.dir/project.cpp.o +cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/project.dir/project.cpp.o -c /build/relion-3.1.0/src/apps/project.cpp +[ 67%] Linking CXX executable ../../bin/relion_particle_subtract_mpi +cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/particle_subtract_mpi.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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-3.1.0/build' +[ 67%] Built target flex_analyse +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-3.1.0/build' +cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/ctf_mask_test.dir/DependInfo.cmake --color= Scanning dependencies of target ctf_mask_test make[4]: Leaving directory '/build/relion-3.1.0/build' 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-3.1.0/build' -[ 66%] Building CXX object src/apps/CMakeFiles/project.dir/project.cpp.o -cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/project.dir/project.cpp.o -c /build/relion-3.1.0/src/apps/project.cpp -[ 66%] Building CXX object src/apps/CMakeFiles/ctf_mask_test.dir/ctf_mask_test.cpp.o +[ 67%] Building CXX object src/apps/CMakeFiles/ctf_mask_test.dir/ctf_mask_test.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/ctf_mask_test.dir/ctf_mask_test.cpp.o -c /build/relion-3.1.0/src/apps/ctf_mask_test.cpp +[ 67%] Linking CXX executable ../../bin/relion_merge_particles +cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/merge_particles.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 +[ 67%] Linking CXX executable ../../bin/relion_ctf_refine_mpi +cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/ctf_refine_mpi.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 make[4]: Leaving directory '/build/relion-3.1.0/build' -[ 66%] Built target particle_FCC +[ 67%] Built target particle_subtract_mpi make -f src/apps/CMakeFiles/preprocess.dir/build.make src/apps/CMakeFiles/preprocess.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/preprocess.dir/DependInfo.cmake --color= @@ -1809,10 +1919,13 @@ make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/preprocess.dir/build.make src/apps/CMakeFiles/preprocess.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' -[ 66%] Building CXX object src/apps/CMakeFiles/preprocess.dir/preprocess.cpp.o +[ 67%] Building CXX object src/apps/CMakeFiles/preprocess.dir/preprocess.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/preprocess.dir/preprocess.cpp.o -c /build/relion-3.1.0/src/apps/preprocess.cpp +[ 67%] Linking CXX executable ../../bin/relion_helix_toolbox +cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/helix_toolbox.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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-3.1.0/build' -[ 66%] Built target convert_to_tiff +[ 67%] Built target merge_particles make -f src/apps/CMakeFiles/convert_star.dir/build.make src/apps/CMakeFiles/convert_star.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/convert_star.dir/DependInfo.cmake --color= @@ -1820,10 +1933,13 @@ make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/convert_star.dir/build.make src/apps/CMakeFiles/convert_star.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' -[ 66%] Building CXX object src/apps/CMakeFiles/convert_star.dir/convert_star.cpp.o +[ 67%] Building CXX object src/apps/CMakeFiles/convert_star.dir/convert_star.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/convert_star.dir/convert_star.cpp.o -c /build/relion-3.1.0/src/apps/convert_star.cpp +[ 68%] Linking CXX executable ../../bin/relion_image_handler +cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/image_handler.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/relion-3.1.0/build' -[ 66%] Built target plot_delocalisation +/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 +[ 68%] Built target helix_toolbox make -f src/apps/CMakeFiles/demodulate.dir/build.make src/apps/CMakeFiles/demodulate.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/demodulate.dir/DependInfo.cmake --color= @@ -1831,72 +1947,71 @@ make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/demodulate.dir/build.make src/apps/CMakeFiles/demodulate.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' -[ 66%] Building CXX object src/apps/CMakeFiles/demodulate.dir/demodulate.cpp.o +[ 68%] Building CXX object src/apps/CMakeFiles/demodulate.dir/demodulate.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/demodulate.dir/demodulate.cpp.o -c /build/relion-3.1.0/src/apps/demodulate.cpp -[ 66%] Linking CXX executable ../../bin/relion_flex_analyse_mpi -cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/flex_analyse_mpi.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 -[ 67%] Linking CXX executable ../../bin/relion_flex_analyse -cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/flex_analyse.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 -[ 67%] Linking CXX executable ../../bin/relion_import -cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/import.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 -[ 67%] Linking CXX executable ../../bin/relion_merge_particles -cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/merge_particles.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 -[ 67%] Linking CXX executable ../../bin/relion_find_tiltpairs -cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/find_tiltpairs.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 +[ 69%] Linking CXX executable ../../bin/relion_convert_star +cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/convert_star.dir/link.txt --verbose=1 +[ 69%] Linking CXX executable ../../bin/relion_preprocess +cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/preprocess.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 +/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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-3.1.0/build' -[ 67%] Built target find_tiltpairs +[ 69%] Built target image_handler make -f src/apps/CMakeFiles/motion_refine.dir/build.make src/apps/CMakeFiles/motion_refine.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/motion_refine.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/relion-3.1.0/build' -[ 67%] Built target merge_particles -make -f src/apps/CMakeFiles/tomo_test.dir/build.make src/apps/CMakeFiles/tomo_test.dir/depend Scanning dependencies of target motion_refine -make[4]: Entering directory '/build/relion-3.1.0/build' -cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/tomo_test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/motion_refine.dir/build.make src/apps/CMakeFiles/motion_refine.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' -[ 67%] Building CXX object src/apps/CMakeFiles/motion_refine.dir/motion_refine.cpp.o +[ 69%] Building CXX object src/apps/CMakeFiles/motion_refine.dir/motion_refine.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/motion_refine.dir/motion_refine.cpp.o -c /build/relion-3.1.0/src/apps/motion_refine.cpp +make[4]: Leaving directory '/build/relion-3.1.0/build' +[ 69%] Built target ctf_refine_mpi +make -f src/apps/CMakeFiles/tomo_test.dir/build.make src/apps/CMakeFiles/tomo_test.dir/depend +make[4]: Entering directory '/build/relion-3.1.0/build' +cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/tomo_test.dir/DependInfo.cmake --color= Scanning dependencies of target tomo_test make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/tomo_test.dir/build.make src/apps/CMakeFiles/tomo_test.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' -make[4]: Leaving directory '/build/relion-3.1.0/build' -[ 67%] Building CXX object src/apps/CMakeFiles/tomo_test.dir/tomo_test.cpp.o +[ 69%] Building CXX object src/apps/CMakeFiles/tomo_test.dir/tomo_test.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/tomo_test.dir/tomo_test.cpp.o -c /build/relion-3.1.0/src/apps/tomo_test.cpp -[ 67%] Linking CXX executable ../../bin/relion_ctf_refine_mpi -cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/ctf_refine_mpi.dir/link.txt --verbose=1 -[ 67%] Built target flex_analyse_mpi +[ 70%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/gui_entries.cpp.o +cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_gui_lib.dir/__/gui_entries.cpp.o -c /build/relion-3.1.0/src/gui_entries.cpp +make[4]: Leaving directory '/build/relion-3.1.0/build' +[ 70%] Built target convert_star make -f src/apps/CMakeFiles/scheduler.dir/build.make src/apps/CMakeFiles/scheduler.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/scheduler.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/relion-3.1.0/build' -/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 -[ 67%] Built target import -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-3.1.0/build' -cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/convert_to_tiff_mpi.dir/DependInfo.cmake --color= Scanning dependencies of target scheduler make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/scheduler.dir/build.make src/apps/CMakeFiles/scheduler.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' -[ 67%] Building CXX object src/apps/CMakeFiles/scheduler.dir/scheduler.cpp.o +[ 70%] Building CXX object src/apps/CMakeFiles/scheduler.dir/scheduler.cpp.o +[ 71%] Linking CXX executable ../../bin/relion_ctf_mask_test cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/scheduler.dir/scheduler.cpp.o -c /build/relion-3.1.0/src/apps/scheduler.cpp +cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/ctf_mask_test.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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-3.1.0/build' +[ 71%] Built target preprocess +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-3.1.0/build' +cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/convert_to_tiff_mpi.dir/DependInfo.cmake --color= Scanning dependencies of target convert_to_tiff_mpi make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/convert_to_tiff_mpi.dir/build.make src/apps/CMakeFiles/convert_to_tiff_mpi.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' -[ 68%] Building CXX object src/apps/CMakeFiles/convert_to_tiff_mpi.dir/convert_to_tiff_mpi.cpp.o +[ 72%] Building CXX object src/apps/CMakeFiles/convert_to_tiff_mpi.dir/convert_to_tiff_mpi.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/convert_to_tiff_mpi.dir/convert_to_tiff_mpi.cpp.o -c /build/relion-3.1.0/src/apps/convert_to_tiff_mpi.cpp +[ 72%] Linking CXX executable ../../bin/relion_mask_create +cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/mask_create.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 +[ 73%] Linking CXX executable ../../bin/relion_motion_refine +cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/motion_refine.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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-3.1.0/build' -[ 68%] Built target flex_analyse +[ 73%] Built target ctf_mask_test 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-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/motion_refine_mpi.dir/DependInfo.cmake --color= @@ -1904,19 +2019,10 @@ make[4]: Leaving directory '/build/relion-3.1.0/build' 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-3.1.0/build' -[ 68%] Building CXX object src/apps/CMakeFiles/motion_refine_mpi.dir/motion_refine_mpi.cpp.o +[ 73%] Building CXX object src/apps/CMakeFiles/motion_refine_mpi.dir/motion_refine_mpi.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/motion_refine_mpi.dir/motion_refine_mpi.cpp.o -c /build/relion-3.1.0/src/apps/motion_refine_mpi.cpp -[ 68%] Linking CXX executable ../../bin/relion_preprocess -cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/preprocess.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 -[ 69%] Linking CXX executable ../../bin/relion_convert_star -cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/convert_star.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 -[ 69%] Linking CXX executable ../../bin/relion_external_reconstruct -cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/external_reconstruct.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 make[4]: Leaving directory '/build/relion-3.1.0/build' -[ 69%] Built target preprocess +[ 73%] Built target mask_create make -f src/apps/CMakeFiles/mrc2vtk.dir/build.make src/apps/CMakeFiles/mrc2vtk.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/mrc2vtk.dir/DependInfo.cmake --color= @@ -1924,32 +2030,49 @@ make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/mrc2vtk.dir/build.make src/apps/CMakeFiles/mrc2vtk.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' -[ 69%] Building CXX object src/apps/CMakeFiles/mrc2vtk.dir/mrc2vtk.cpp.o +[ 73%] Building CXX object src/apps/CMakeFiles/mrc2vtk.dir/mrc2vtk.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/mrc2vtk.dir/mrc2vtk.cpp.o -c /build/relion-3.1.0/src/apps/mrc2vtk.cpp +[ 73%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/gui_jobwindow.cpp.o +cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_gui_lib.dir/__/gui_jobwindow.cpp.o -c /build/relion-3.1.0/src/gui_jobwindow.cpp +[ 73%] Linking CXX executable ../../bin/relion_convert_to_tiff_mpi +cd /build/relion-3.1.0/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 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 +[ 73%] Linking CXX executable ../../bin/relion_project +cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/project.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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-3.1.0/build' -make[4]: Leaving directory '/build/relion-3.1.0/build' -[ 69%] Built target external_reconstruct +[ 73%] Built target motion_refine make -f src/apps/CMakeFiles/particle_reposition.dir/build.make src/apps/CMakeFiles/particle_reposition.dir/depend +make[4]: Leaving directory '/build/relion-3.1.0/build' make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/particle_reposition.dir/DependInfo.cmake --color= -[ 69%] Built target convert_star +[ 73%] Built target convert_to_tiff_mpi make -f src/apps/CMakeFiles/particle_select.dir/build.make src/apps/CMakeFiles/particle_select.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/particle_select.dir/DependInfo.cmake --color= Scanning dependencies of target particle_reposition +Scanning dependencies of target particle_select +make[4]: Leaving directory '/build/relion-3.1.0/build' make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/particle_reposition.dir/build.make src/apps/CMakeFiles/particle_reposition.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' -Scanning dependencies of target particle_select -make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/particle_select.dir/build.make src/apps/CMakeFiles/particle_select.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' -[ 69%] Building CXX object src/apps/CMakeFiles/particle_reposition.dir/particle_reposition.cpp.o +[ 73%] Building CXX object src/apps/CMakeFiles/particle_reposition.dir/particle_reposition.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/particle_reposition.dir/particle_reposition.cpp.o -c /build/relion-3.1.0/src/apps/particle_reposition.cpp -[ 69%] Building CXX object src/apps/CMakeFiles/particle_select.dir/particle_select.cpp.o -make[4]: Leaving directory '/build/relion-3.1.0/build' +[ 73%] Building CXX object src/apps/CMakeFiles/particle_select.dir/particle_select.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/particle_select.dir/particle_select.cpp.o -c /build/relion-3.1.0/src/apps/particle_select.cpp -[ 69%] Built target ctf_refine_mpi +[ 74%] Linking CXX executable ../../bin/relion_tomo_test +cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/tomo_test.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 +[ 75%] Linking CXX executable ../../bin/relion_demodulate +cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/demodulate.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 +[ 76%] Linking CXX executable ../../bin/relion_prepare_subtomo +cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/prepare_subtomo.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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-3.1.0/build' +[ 76%] Built target project make -f src/apps/CMakeFiles/particle_subtract.dir/build.make src/apps/CMakeFiles/particle_subtract.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/particle_subtract.dir/DependInfo.cmake --color= @@ -1957,67 +2080,55 @@ make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/particle_subtract.dir/build.make src/apps/CMakeFiles/particle_subtract.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' -[ 69%] Building CXX object src/apps/CMakeFiles/particle_subtract.dir/particle_subtract.cpp.o +[ 76%] Building CXX object src/apps/CMakeFiles/particle_subtract.dir/particle_subtract.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/particle_subtract.dir/particle_subtract.cpp.o -c /build/relion-3.1.0/src/apps/particle_subtract.cpp -[ 69%] Linking CXX executable ../../bin/relion_convert_to_tiff_mpi -cd /build/relion-3.1.0/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 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 -[ 69%] Linking CXX executable ../../bin/relion_particle_subtract_mpi -cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/particle_subtract_mpi.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 +[ 77%] Linking CXX executable ../../bin/relion_motion_refine_mpi +cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/motion_refine_mpi.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 +[ 77%] Linking CXX executable ../../bin/relion_scheduler +cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/scheduler.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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-3.1.0/build' make[4]: Leaving directory '/build/relion-3.1.0/build' -[ 69%] Built target convert_to_tiff_mpi +[ 77%] Built target tomo_test make -f src/apps/CMakeFiles/ctf_refine.dir/build.make src/apps/CMakeFiles/ctf_refine.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/ctf_refine.dir/DependInfo.cmake --color= -Scanning dependencies of target ctf_refine -make[4]: Leaving directory '/build/relion-3.1.0/build' -make -f src/apps/CMakeFiles/ctf_refine.dir/build.make src/apps/CMakeFiles/ctf_refine.dir/build -make[4]: Entering directory '/build/relion-3.1.0/build' -[ 69%] Building CXX object src/apps/CMakeFiles/ctf_refine.dir/ctf_refine.cpp.o -cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/ctf_refine.dir/ctf_refine.cpp.o -c /build/relion-3.1.0/src/apps/ctf_refine.cpp -[ 70%] Linking CXX executable ../../bin/relion_motion_refine -cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/motion_refine.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 -[ 70%] Linking CXX executable ../../bin/relion_mask_create -cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/mask_create.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 -make[4]: Leaving directory '/build/relion-3.1.0/build' -[ 70%] Built target particle_subtract_mpi +[ 77%] Built target prepare_subtomo 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-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/particle_symmetry_expand.dir/DependInfo.cmake --color= Scanning dependencies of target particle_symmetry_expand make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/particle_symmetry_expand.dir/build.make src/apps/CMakeFiles/particle_symmetry_expand.dir/build +Scanning dependencies of target ctf_refine +make[4]: Leaving directory '/build/relion-3.1.0/build' +make -f src/apps/CMakeFiles/ctf_refine.dir/build.make src/apps/CMakeFiles/ctf_refine.dir/build +make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Entering directory '/build/relion-3.1.0/build' -[ 70%] Building CXX object src/apps/CMakeFiles/particle_symmetry_expand.dir/particle_symmetry_expand.cpp.o -cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/particle_symmetry_expand.dir/particle_symmetry_expand.cpp.o -c /build/relion-3.1.0/src/apps/particle_symmetry_expand.cpp -[ 71%] Linking CXX executable ../../bin/relion_particle_select -cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/particle_select.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 -[ 72%] Linking CXX executable ../../bin/relion_ctf_mask_test -cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/ctf_mask_test.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 -[ 73%] Linking CXX executable ../../bin/relion_motion_refine_mpi -cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/motion_refine_mpi.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 -[ 73%] Linking CXX executable ../../bin/relion_mrc2vtk -cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/mrc2vtk.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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-3.1.0/build' -[ 73%] Built target motion_refine +[ 77%] Building CXX object src/apps/CMakeFiles/ctf_refine.dir/ctf_refine.cpp.o +cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/ctf_refine.dir/ctf_refine.cpp.o -c /build/relion-3.1.0/src/apps/ctf_refine.cpp +[ 77%] Building CXX object src/apps/CMakeFiles/particle_symmetry_expand.dir/particle_symmetry_expand.cpp.o +cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/particle_symmetry_expand.dir/particle_symmetry_expand.cpp.o -c /build/relion-3.1.0/src/apps/particle_symmetry_expand.cpp +[ 77%] Built target demodulate make -f src/apps/CMakeFiles/postprocess.dir/build.make src/apps/CMakeFiles/postprocess.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/postprocess.dir/DependInfo.cmake --color= +[ 77%] Linking CXX executable ../../bin/relion_mrc2vtk +cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/mrc2vtk.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 Scanning dependencies of target postprocess make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/postprocess.dir/build.make src/apps/CMakeFiles/postprocess.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' -[ 74%] Building CXX object src/apps/CMakeFiles/postprocess.dir/postprocess.cpp.o +[ 78%] Building CXX object src/apps/CMakeFiles/postprocess.dir/postprocess.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/postprocess.dir/postprocess.cpp.o -c /build/relion-3.1.0/src/apps/postprocess.cpp +[ 79%] Linking CXX executable ../../bin/relion_particle_select +cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/particle_select.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 make[4]: Leaving directory '/build/relion-3.1.0/build' -[ 74%] Built target mask_create +[ 79%] Built target mrc2vtk make -f src/apps/CMakeFiles/reconstruct.dir/build.make src/apps/CMakeFiles/reconstruct.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/reconstruct.dir/DependInfo.cmake --color= @@ -2025,32 +2136,32 @@ make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/reconstruct.dir/build.make src/apps/CMakeFiles/reconstruct.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' -[ 74%] Building CXX object src/apps/CMakeFiles/reconstruct.dir/reconstruct.cpp.o +[ 79%] Building CXX object src/apps/CMakeFiles/reconstruct.dir/reconstruct.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/reconstruct.dir/reconstruct.cpp.o -c /build/relion-3.1.0/src/apps/reconstruct.cpp make[4]: Leaving directory '/build/relion-3.1.0/build' -[ 74%] Built target mrc2vtk +[ 79%] Built target scheduler make -f src/apps/CMakeFiles/reconstruct_mpi.dir/build.make src/apps/CMakeFiles/reconstruct_mpi.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/reconstruct_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' -[ 74%] Built target particle_select +[ 79%] Built target particle_select make -f src/apps/CMakeFiles/ctf_toolbox.dir/build.make src/apps/CMakeFiles/ctf_toolbox.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/ctf_toolbox.dir/DependInfo.cmake --color= -Scanning dependencies of target reconstruct_mpi -make[4]: Leaving directory '/build/relion-3.1.0/build' -make -f src/apps/CMakeFiles/reconstruct_mpi.dir/build.make src/apps/CMakeFiles/reconstruct_mpi.dir/build -make[4]: Entering directory '/build/relion-3.1.0/build' -[ 74%] Building CXX object src/apps/CMakeFiles/reconstruct_mpi.dir/reconstruct_mpi.cpp.o -cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/reconstruct_mpi.dir/reconstruct_mpi.cpp.o -c /build/relion-3.1.0/src/apps/reconstruct_mpi.cpp Scanning dependencies of target ctf_toolbox make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/ctf_toolbox.dir/build.make src/apps/CMakeFiles/ctf_toolbox.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' -[ 75%] Building CXX object src/apps/CMakeFiles/ctf_toolbox.dir/ctf_toolbox.cpp.o +[ 80%] Building CXX object src/apps/CMakeFiles/ctf_toolbox.dir/ctf_toolbox.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/ctf_toolbox.dir/ctf_toolbox.cpp.o -c /build/relion-3.1.0/src/apps/ctf_toolbox.cpp +Scanning dependencies of target reconstruct_mpi +make[4]: Leaving directory '/build/relion-3.1.0/build' +make -f src/apps/CMakeFiles/reconstruct_mpi.dir/build.make src/apps/CMakeFiles/reconstruct_mpi.dir/build +make[4]: Entering directory '/build/relion-3.1.0/build' +[ 80%] Building CXX object src/apps/CMakeFiles/reconstruct_mpi.dir/reconstruct_mpi.cpp.o +cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/reconstruct_mpi.dir/reconstruct_mpi.cpp.o -c /build/relion-3.1.0/src/apps/reconstruct_mpi.cpp make[4]: Leaving directory '/build/relion-3.1.0/build' -[ 75%] Built target ctf_mask_test +[ 80%] Built target motion_refine_mpi make -f src/apps/CMakeFiles/refine.dir/build.make src/apps/CMakeFiles/refine.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/refine.dir/DependInfo.cmake --color= @@ -2058,16 +2169,16 @@ make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/refine.dir/build.make src/apps/CMakeFiles/refine.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' -[ 76%] Building CXX object src/apps/CMakeFiles/refine.dir/refine.cpp.o +[ 81%] Building CXX object src/apps/CMakeFiles/refine.dir/refine.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/refine.dir/refine.cpp.o -c /build/relion-3.1.0/src/apps/refine.cpp -[ 77%] Linking CXX executable ../../bin/relion_ctf_refine +[ 81%] Linking CXX executable ../../bin/relion_postprocess +cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/postprocess.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 +[ 82%] Linking CXX executable ../../bin/relion_ctf_refine cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/ctf_refine.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 -[ 78%] Linking CXX executable ../../bin/relion_demodulate -cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/demodulate.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 make[4]: Leaving directory '/build/relion-3.1.0/build' -[ 78%] Built target motion_refine_mpi +[ 82%] Built target postprocess make -f src/apps/CMakeFiles/refine_mpi.dir/build.make src/apps/CMakeFiles/refine_mpi.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/refine_mpi.dir/DependInfo.cmake --color= @@ -2075,16 +2186,16 @@ make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/refine_mpi.dir/build.make src/apps/CMakeFiles/refine_mpi.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' -[ 79%] Building CXX object src/apps/CMakeFiles/refine_mpi.dir/refine_mpi.cpp.o +[ 83%] Building CXX object src/apps/CMakeFiles/refine_mpi.dir/refine_mpi.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/refine_mpi.dir/refine_mpi.cpp.o -c /build/relion-3.1.0/src/apps/refine_mpi.cpp -[ 79%] Linking CXX executable ../../bin/relion_scheduler -cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/scheduler.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 -[ 80%] Linking CXX executable ../../bin/relion_tomo_test -cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/tomo_test.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 +[ 84%] Linking CXX executable ../../bin/relion_particle_symmetry_expand +cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/particle_symmetry_expand.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 +[ 85%] Linking CXX executable ../../bin/relion_reconstruct +cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/reconstruct.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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-3.1.0/build' -[ 80%] Built target demodulate +[ 85%] Built target particle_symmetry_expand make -f src/apps/CMakeFiles/estimate_gain.dir/build.make src/apps/CMakeFiles/estimate_gain.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/estimate_gain.dir/DependInfo.cmake --color= @@ -2092,10 +2203,10 @@ make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/estimate_gain.dir/build.make src/apps/CMakeFiles/estimate_gain.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' -[ 80%] Building CXX object src/apps/CMakeFiles/estimate_gain.dir/estimate_gain.cpp.o +[ 85%] Building CXX object src/apps/CMakeFiles/estimate_gain.dir/estimate_gain.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/estimate_gain.dir/estimate_gain.cpp.o -c /build/relion-3.1.0/src/apps/estimate_gain.cpp make[4]: Leaving directory '/build/relion-3.1.0/build' -[ 80%] Built target ctf_refine +[ 85%] Built target ctf_refine make -f src/apps/CMakeFiles/autopick_mpi.dir/build.make src/apps/CMakeFiles/autopick_mpi.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/autopick_mpi.dir/DependInfo.cmake --color= @@ -2103,10 +2214,18 @@ make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/autopick_mpi.dir/build.make src/apps/CMakeFiles/autopick_mpi.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' -[ 80%] Building CXX object src/apps/CMakeFiles/autopick_mpi.dir/autopick_mpi.cpp.o +[ 85%] Building CXX object src/apps/CMakeFiles/autopick_mpi.dir/autopick_mpi.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/autopick_mpi.dir/autopick_mpi.cpp.o -c /build/relion-3.1.0/src/apps/autopick_mpi.cpp +[ 86%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/gui_mainwindow.cpp.o +cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_gui_lib.dir/__/gui_mainwindow.cpp.o -c /build/relion-3.1.0/src/gui_mainwindow.cpp +[ 86%] Linking CXX executable ../../bin/relion_particle_subtract +cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/particle_subtract.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 +[ 86%] Linking CXX executable ../../bin/relion_reconstruct_mpi +cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/reconstruct_mpi.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 make[4]: Leaving directory '/build/relion-3.1.0/build' -[ 80%] Built target tomo_test +[ 86%] Built target reconstruct make -f src/apps/CMakeFiles/run_motioncorr.dir/build.make src/apps/CMakeFiles/run_motioncorr.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/run_motioncorr.dir/DependInfo.cmake --color= @@ -2114,92 +2233,80 @@ make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/run_motioncorr.dir/build.make src/apps/CMakeFiles/run_motioncorr.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' -[ 81%] Building CXX object src/apps/CMakeFiles/run_motioncorr.dir/run_motioncorr.cpp.o +[ 87%] Building CXX object src/apps/CMakeFiles/run_motioncorr.dir/run_motioncorr.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/run_motioncorr.dir/run_motioncorr.cpp.o -c /build/relion-3.1.0/src/apps/run_motioncorr.cpp +[ 87%] Linking CXX executable ../../bin/relion_refine +cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/refine.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 make[4]: Leaving directory '/build/relion-3.1.0/build' -[ 81%] Built target scheduler +[ 87%] Built target reconstruct_mpi make -f src/apps/CMakeFiles/align_symmetry.dir/build.make src/apps/CMakeFiles/align_symmetry.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/align_symmetry.dir/DependInfo.cmake --color= -Scanning dependencies of target align_symmetry -make[4]: Leaving directory '/build/relion-3.1.0/build' -make -f src/apps/CMakeFiles/align_symmetry.dir/build.make src/apps/CMakeFiles/align_symmetry.dir/build -make[4]: Entering directory '/build/relion-3.1.0/build' -[ 81%] Building CXX object src/apps/CMakeFiles/align_symmetry.dir/align_symmetry.cpp.o -cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/align_symmetry.dir/align_symmetry.cpp.o -c /build/relion-3.1.0/src/apps/align_symmetry.cpp -[ 82%] Linking CXX executable ../../bin/relion_particle_symmetry_expand -cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/particle_symmetry_expand.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 -[ 82%] Linking CXX executable ../../bin/relion_postprocess -cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/postprocess.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 make[4]: Leaving directory '/build/relion-3.1.0/build' -[ 82%] Built target particle_symmetry_expand +[ 87%] Built target particle_subtract make -f src/apps/CMakeFiles/reposition.dir/build.make src/apps/CMakeFiles/reposition.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/reposition.dir/DependInfo.cmake --color= +Scanning dependencies of target align_symmetry +make[4]: Leaving directory '/build/relion-3.1.0/build' Scanning dependencies of target reposition make[4]: Leaving directory '/build/relion-3.1.0/build' +make -f src/apps/CMakeFiles/align_symmetry.dir/build.make src/apps/CMakeFiles/align_symmetry.dir/build make -f src/apps/CMakeFiles/reposition.dir/build.make src/apps/CMakeFiles/reposition.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' -[ 82%] Building CXX object src/apps/CMakeFiles/reposition.dir/reposition.cpp.o +make[4]: Entering directory '/build/relion-3.1.0/build' +[ 87%] Building CXX object src/apps/CMakeFiles/align_symmetry.dir/align_symmetry.cpp.o +cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/align_symmetry.dir/align_symmetry.cpp.o -c /build/relion-3.1.0/src/apps/align_symmetry.cpp +[ 87%] Building CXX object src/apps/CMakeFiles/reposition.dir/reposition.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/reposition.dir/reposition.cpp.o -c /build/relion-3.1.0/src/apps/reposition.cpp +[ 88%] Linking CXX executable ../../bin/relion_autopick_mpi +cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/autopick_mpi.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 +[ 88%] Linking CXX executable ../../bin/relion_run_motioncorr +cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/run_motioncorr.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 +[ 88%] Linking CXX executable ../../bin/relion_ctf_toolbox +cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/ctf_toolbox.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 +[ 89%] Linking CXX executable ../../bin/relion_particle_reposition +cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/particle_reposition.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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-3.1.0/build' -[ 83%] Linking CXX executable ../../bin/relion_reconstruct -cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/reconstruct.dir/link.txt --verbose=1 -[ 83%] Built target postprocess +[ 89%] Built target run_motioncorr make -f src/apps/CMakeFiles/run_ctffind.dir/build.make src/apps/CMakeFiles/run_ctffind.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/run_ctffind.dir/DependInfo.cmake --color= -/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 Scanning dependencies of target run_ctffind make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/run_ctffind.dir/build.make src/apps/CMakeFiles/run_ctffind.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' -[ 83%] Building CXX object src/apps/CMakeFiles/run_ctffind.dir/run_ctffind.cpp.o +[ 89%] Building CXX object src/apps/CMakeFiles/run_ctffind.dir/run_ctffind.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/run_ctffind.dir/run_ctffind.cpp.o -c /build/relion-3.1.0/src/apps/run_ctffind.cpp -[ 83%] Linking CXX executable ../../bin/relion_particle_subtract -cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/particle_subtract.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 -[ 83%] Linking CXX executable ../../bin/relion_run_motioncorr -cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/run_motioncorr.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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-3.1.0/build' -[ 83%] Built target reconstruct +[ 89%] Built target ctf_toolbox 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-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/run_ctffind_mpi.dir/DependInfo.cmake --color= Scanning dependencies of target run_ctffind_mpi make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/run_ctffind_mpi.dir/build.make src/apps/CMakeFiles/run_ctffind_mpi.dir/build +make[4]: Leaving directory '/build/relion-3.1.0/build' make[4]: Entering directory '/build/relion-3.1.0/build' -[ 84%] Building CXX object src/apps/CMakeFiles/run_ctffind_mpi.dir/run_ctffind_mpi.cpp.o +[ 90%] Building CXX object src/apps/CMakeFiles/run_ctffind_mpi.dir/run_ctffind_mpi.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/run_ctffind_mpi.dir/run_ctffind_mpi.cpp.o -c /build/relion-3.1.0/src/apps/run_ctffind_mpi.cpp -make[4]: Leaving directory '/build/relion-3.1.0/build' -[ 84%] Built target run_motioncorr -[ 84%] Linking CXX executable ../../bin/relion_reconstruct_mpi +[ 90%] Built target autopick_mpi make -f src/apps/CMakeFiles/run_motioncorr_mpi.dir/build.make src/apps/CMakeFiles/run_motioncorr_mpi.dir/depend -cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/reconstruct_mpi.dir/link.txt --verbose=1 make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/run_motioncorr_mpi.dir/DependInfo.cmake --color= -/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 Scanning dependencies of target run_motioncorr_mpi make[4]: Leaving directory '/build/relion-3.1.0/build' 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-3.1.0/build' -[ 84%] Building CXX object src/apps/CMakeFiles/run_motioncorr_mpi.dir/run_motioncorr_mpi.cpp.o +[ 90%] Building CXX object src/apps/CMakeFiles/run_motioncorr_mpi.dir/run_motioncorr_mpi.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/run_motioncorr_mpi.dir/run_motioncorr_mpi.cpp.o -c /build/relion-3.1.0/src/apps/run_motioncorr_mpi.cpp -[ 84%] Linking CXX executable ../../bin/relion_helix_toolbox -cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/helix_toolbox.dir/link.txt --verbose=1 -[ 84%] Linking CXX executable ../../bin/relion_project -cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/project.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 -/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 -[ 85%] Linking CXX executable ../../bin/relion_autopick_mpi -cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/autopick_mpi.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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-3.1.0/build' -[ 85%] Built target particle_subtract +[ 90%] Built target refine make -f src/apps/CMakeFiles/stack_create.dir/build.make src/apps/CMakeFiles/stack_create.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/stack_create.dir/DependInfo.cmake --color= @@ -2207,13 +2314,13 @@ make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/stack_create.dir/build.make src/apps/CMakeFiles/stack_create.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' -[ 86%] Building CXX object src/apps/CMakeFiles/stack_create.dir/stack_create.cpp.o +[ 91%] Building CXX object src/apps/CMakeFiles/stack_create.dir/stack_create.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/stack_create.dir/stack_create.cpp.o -c /build/relion-3.1.0/src/apps/stack_create.cpp -[ 86%] Linking CXX executable ../../bin/relion_run_ctffind -cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/run_ctffind.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 +[ 91%] Linking CXX executable ../../bin/relion_refine_mpi +cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/refine_mpi.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 make[4]: Leaving directory '/build/relion-3.1.0/build' -[ 86%] Built target helix_toolbox +[ 91%] Built target particle_reposition make -f src/apps/CMakeFiles/star_handler.dir/build.make src/apps/CMakeFiles/star_handler.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/star_handler.dir/DependInfo.cmake --color= @@ -2221,107 +2328,65 @@ make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/star_handler.dir/build.make src/apps/CMakeFiles/star_handler.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' -[ 87%] Building CXX object src/apps/CMakeFiles/star_handler.dir/star_handler.cpp.o +[ 92%] Building CXX object src/apps/CMakeFiles/star_handler.dir/star_handler.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/star_handler.dir/star_handler.cpp.o -c /build/relion-3.1.0/src/apps/star_handler.cpp +[ 92%] Linking CXX executable ../../bin/relion_run_ctffind +cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/run_ctffind.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 +[ 92%] Linking CXX executable ../../bin/relion_estimate_gain +cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/estimate_gain.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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]: Leaving directory '/build/relion-3.1.0/build' -[ 87%] Built target reconstruct_mpi +[ 92%] Built target estimate_gain make -f src/apps/CMakeFiles/tiltpair_plot.dir/build.make src/apps/CMakeFiles/tiltpair_plot.dir/depend +make[4]: Leaving directory '/build/relion-3.1.0/build' make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/tiltpair_plot.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/relion-3.1.0/build' -[ 87%] Built target project +[ 92%] Built target run_ctffind +[ 92%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/manualpicker.cpp.o +cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_gui_lib.dir/__/manualpicker.cpp.o -c /build/relion-3.1.0/src/manualpicker.cpp Scanning dependencies of target tiltpair_plot make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/tiltpair_plot.dir/build.make src/apps/CMakeFiles/tiltpair_plot.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' -[ 88%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/gui_entries.cpp.o -cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_gui_lib.dir/__/gui_entries.cpp.o -c /build/relion-3.1.0/src/gui_entries.cpp -[ 88%] Building CXX object src/apps/CMakeFiles/tiltpair_plot.dir/tiltpair_plot.cpp.o +[ 92%] Building CXX object src/apps/CMakeFiles/tiltpair_plot.dir/tiltpair_plot.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/tiltpair_plot.dir/tiltpair_plot.cpp.o -c /build/relion-3.1.0/src/apps/tiltpair_plot.cpp make[4]: Leaving directory '/build/relion-3.1.0/build' -[ 88%] Built target autopick_mpi -[ 88%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/gui_jobwindow.cpp.o -cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_gui_lib.dir/__/gui_jobwindow.cpp.o -c /build/relion-3.1.0/src/gui_jobwindow.cpp -make[4]: Leaving directory '/build/relion-3.1.0/build' -[ 88%] Built target run_ctffind -[ 89%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/gui_mainwindow.cpp.o -cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_gui_lib.dir/__/gui_mainwindow.cpp.o -c /build/relion-3.1.0/src/gui_mainwindow.cpp -[ 90%] Linking CXX executable ../../bin/relion_image_handler -cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/image_handler.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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-3.1.0/build' -[ 90%] Built target image_handler -[ 90%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/manualpicker.cpp.o -cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_gui_lib.dir/__/manualpicker.cpp.o -c /build/relion-3.1.0/src/manualpicker.cpp -[ 90%] Linking CXX executable ../../bin/relion_refine -cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/refine.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 -[ 90%] Linking CXX executable ../../bin/relion_run_ctffind_mpi +[ 92%] Built target refine_mpi +[ 92%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/cxxutils.cc.o +cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/cxxutils.cc.o -c /build/relion-3.1.0/src/Healpix_2.15a/cxxutils.cc +[ 93%] Linking CXX executable ../../bin/relion_reposition +cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/reposition.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 +[ 93%] Linking CXX executable ../../bin/relion_run_ctffind_mpi cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/run_ctffind_mpi.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 -[ 91%] Linking CXX executable ../../bin/relion_particle_reposition -cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/particle_reposition.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 -[ 91%] Linking CXX executable ../../bin/relion_ctf_toolbox -cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/ctf_toolbox.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 -[ 92%] Linking CXX executable ../../bin/relion_run_motioncorr_mpi +[ 94%] Linking CXX executable ../../bin/relion_run_motioncorr_mpi cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/run_motioncorr_mpi.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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%] Linking CXX executable ../../bin/relion_estimate_gain -cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/estimate_gain.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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]: Leaving directory '/build/relion-3.1.0/build' -make[4]: Leaving directory '/build/relion-3.1.0/build' -[ 92%] Built target run_ctffind_mpi -[ 92%] Built target ctf_toolbox -[ 92%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/cxxutils.cc.o -cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/cxxutils.cc.o -c /build/relion-3.1.0/src/Healpix_2.15a/cxxutils.cc -[ 93%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/healpix_base.cc.o +[ 94%] Built target reposition +[ 95%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/healpix_base.cc.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/healpix_base.cc.o -c /build/relion-3.1.0/src/Healpix_2.15a/healpix_base.cc -[ 94%] Linking CXX executable ../../bin/relion_reposition -cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/reposition.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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-3.1.0/build' -[ 94%] Built target run_motioncorr_mpi make[4]: Leaving directory '/build/relion-3.1.0/build' -[ 94%] Built target refine +[ 95%] Built target run_ctffind_mpi make[4]: Leaving directory '/build/relion-3.1.0/build' -[ 94%] Built target estimate_gain -make[4]: Leaving directory '/build/relion-3.1.0/build' -[ 94%] Built target particle_reposition -[ 94%] Linking CXX executable ../../bin/relion_refine_mpi -cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/refine_mpi.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 -[ 95%] Linking CXX executable ../../bin/relion_tiltpair_plot +[ 95%] Built target run_motioncorr_mpi +[ 96%] Linking CXX executable ../../bin/relion_tiltpair_plot cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiltpair_plot.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 -make[4]: Leaving directory '/build/relion-3.1.0/build' -[ 95%] Built target reposition -make[4]: Leaving directory '/build/relion-3.1.0/build' -[ 95%] Built target tiltpair_plot -[ 96%] Linking CXX executable ../../bin/relion_prepare_subtomo -cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/prepare_subtomo.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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-3.1.0/build' -[ 96%] Built target prepare_subtomo -make[4]: Leaving directory '/build/relion-3.1.0/build' -[ 96%] Built target refine_mpi [ 96%] Linking CXX executable ../../bin/relion_align_symmetry cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/align_symmetry.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 make[4]: Leaving directory '/build/relion-3.1.0/build' +[ 96%] Built target tiltpair_plot +make[4]: Leaving directory '/build/relion-3.1.0/build' [ 96%] Built target align_symmetry [ 96%] Linking CXX executable ../../bin/relion_stack_create cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/stack_create.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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-3.1.0/build' [ 96%] Built target stack_create -[ 96%] Linking CXX executable ../../bin/relion_star_handler -cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/star_handler.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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-3.1.0/build' -[ 96%] Built target star_handler [ 96%] Linking CXX static library ../../lib/librelion_gui_lib.a cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -P CMakeFiles/relion_gui_lib.dir/cmake_clean_target.cmake cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/relion_gui_lib.dir/link.txt --verbose=1 @@ -2332,61 +2397,66 @@ make -f src/apps/CMakeFiles/display.dir/build.make src/apps/CMakeFiles/display.dir/depend make -f src/apps/CMakeFiles/manualpick.dir/build.make src/apps/CMakeFiles/manualpick.dir/depend make -f src/apps/CMakeFiles/maingui.dir/build.make src/apps/CMakeFiles/maingui.dir/depend -make -f src/apps/CMakeFiles/pipeliner.dir/build.make src/apps/CMakeFiles/pipeliner.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/display.dir/DependInfo.cmake --color= +make -f src/apps/CMakeFiles/pipeliner.dir/build.make src/apps/CMakeFiles/pipeliner.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/manualpick.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/maingui.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/pipeliner.dir/DependInfo.cmake --color= -Scanning dependencies of target manualpick -Scanning dependencies of target maingui -make[4]: Leaving directory '/build/relion-3.1.0/build' -make -f src/apps/CMakeFiles/manualpick.dir/build.make src/apps/CMakeFiles/manualpick.dir/build -make[4]: Leaving directory '/build/relion-3.1.0/build' -make -f src/apps/CMakeFiles/maingui.dir/build.make src/apps/CMakeFiles/maingui.dir/build Scanning dependencies of target pipeliner -make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/pipeliner.dir/build.make src/apps/CMakeFiles/pipeliner.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' -make[4]: Entering directory '/build/relion-3.1.0/build' +[ 96%] Building CXX object src/apps/CMakeFiles/pipeliner.dir/pipeliner.cpp.o +cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/pipeliner.dir/pipeliner.cpp.o -c /build/relion-3.1.0/src/apps/pipeliner.cpp +Scanning dependencies of target maingui Scanning dependencies of target display +Scanning dependencies of target manualpick +make[4]: Leaving directory '/build/relion-3.1.0/build' +make[4]: Leaving directory '/build/relion-3.1.0/build' make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/display.dir/build.make src/apps/CMakeFiles/display.dir/build +make -f src/apps/CMakeFiles/manualpick.dir/build.make src/apps/CMakeFiles/manualpick.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' -[ 96%] Building CXX object src/apps/CMakeFiles/manualpick.dir/manualpick.cpp.o +make -f src/apps/CMakeFiles/maingui.dir/build.make src/apps/CMakeFiles/maingui.dir/build +make[4]: Entering directory '/build/relion-3.1.0/build' +make[4]: Entering directory '/build/relion-3.1.0/build' +[ 96%] Building CXX object src/apps/CMakeFiles/display.dir/display.cpp.o [ 96%] Building CXX object src/apps/CMakeFiles/maingui.dir/maingui.cpp.o -cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/manualpick.dir/manualpick.cpp.o -c /build/relion-3.1.0/src/apps/manualpick.cpp cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/maingui.dir/maingui.cpp.o -c /build/relion-3.1.0/src/apps/maingui.cpp -[ 96%] Building CXX object src/apps/CMakeFiles/pipeliner.dir/pipeliner.cpp.o -cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/pipeliner.dir/pipeliner.cpp.o -c /build/relion-3.1.0/src/apps/pipeliner.cpp -[ 96%] Building CXX object src/apps/CMakeFiles/display.dir/display.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/display.dir/display.cpp.o -c /build/relion-3.1.0/src/apps/display.cpp -[ 97%] Linking CXX executable ../../bin/relion_display -cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/display.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 +[ 96%] Building CXX object src/apps/CMakeFiles/manualpick.dir/manualpick.cpp.o +cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/manualpick.dir/manualpick.cpp.o -c /build/relion-3.1.0/src/apps/manualpick.cpp +[ 98%] Linking CXX executable ../../bin/relion_display [ 98%] Linking CXX executable ../../bin/relion_manualpick +cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/display.dir/link.txt --verbose=1 cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/manualpick.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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-3.1.0/build' [ 99%] Linking CXX executable ../../bin/relion_maingui cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/maingui.dir/link.txt --verbose=1 -[ 99%] Built target display /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/maingui.dir/maingui.cpp.o -o ../../bin/relion_maingui ../../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-3.1.0/build' -[ 99%] Built target manualpick +[ 99%] Linking CXX executable ../../bin/relion_star_handler +cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/star_handler.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 [100%] Linking CXX executable ../../bin/relion_pipeliner cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/pipeliner.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 ../../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-3.1.0/build' +[100%] Built target manualpick +make[4]: Leaving directory '/build/relion-3.1.0/build' +[100%] Built target display +make[4]: Leaving directory '/build/relion-3.1.0/build' +[100%] Built target star_handler +make[4]: Leaving directory '/build/relion-3.1.0/build' +[100%] Built target pipeliner cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E copy /build/relion-3.1.0/build/bin/relion_maingui /build/relion-3.1.0/build/bin/relion cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E copy /build/relion-3.1.0/build/bin/relion_qsub.csh /build/relion-3.1.0/build/bin/qsub.csh make[4]: Leaving directory '/build/relion-3.1.0/build' [100%] Built target maingui -make[4]: Leaving directory '/build/relion-3.1.0/build' -[100%] Built target pipeliner make[3]: Leaving directory '/build/relion-3.1.0/build' /usr/bin/cmake -E cmake_progress_start /build/relion-3.1.0/build/CMakeFiles 0 make[2]: Leaving directory '/build/relion-3.1.0/build' @@ -2960,73 +3030,73 @@ /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin --- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_ctf_refine --- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_autopick_mpi --- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_plot_delocalisation --- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_motion_refine +-- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_scheduler +-- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_star_loopheader +-- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_import +-- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_qsub.csh +-- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_particle_subtract -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_particle_FCC --- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_ctf_refine_mpi --- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_run_motioncorr_mpi --- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_manualpick --- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_star_handler --- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_star_printtable --- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_stack_create --- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_star_datablock_stack --- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_mrc2vtk --- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_find_tiltpairs --- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_pipeliner +-- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_ctf_refine -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_particle_subtract_mpi --- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_particle_subtract --- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_preprocess +-- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_run_ctffind +-- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_estimate_gain +-- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/qsub.csh +-- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_image_handler +-- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_particle_symmetry_expand +-- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_display +-- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_star_plottable -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_convert_to_tiff --- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_refine --- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_particle_reposition --- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_helix_toolbox --- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_convert_to_tiff_mpi --- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_project +-- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_mrc2vtk +-- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_prepare_subtomo +-- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_plot_delocalisation +-- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_star_datablock_stack +-- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_ctf_mask_test +-- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_helix_inimodel2d +-- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_convert_star +-- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_reposition -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_external_reconstruct --- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_estimate_gain --- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_tiltpair_plot +-- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_preprocess_mpi -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_ctf_toolbox --- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_prepare_subtomo --- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_demodulate --- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_motion_refine_mpi +-- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_autopick -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_particle_select --- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion +-- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_run_ctffind_mpi -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_merge_particles --- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_star_datablock_singlefiles --- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_reposition +-- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_refine +-- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_postprocess -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_flex_analyse_mpi --- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_mask_create +-- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_convert_to_tiff_mpi +-- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_autopick_mpi +-- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_run_motioncorr_mpi +-- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_star_datablock_ctfdat +-- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_flex_analyse +-- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_star_datablock_singlefiles +-- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_motion_refine_mpi +-- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_reconstruct_mpi -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_align_symmetry -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_localsym_mpi --- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_star_datablock_ctfdat --- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_run_motioncorr --- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_star_loopheader --- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_run_ctffind --- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_star_plottable --- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_display --- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_scheduler --- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_postprocess --- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_autopick --- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_helix_inimodel2d --- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_reconstruct --- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_image_handler --- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_qsub.csh --- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_refine_mpi --- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_run_ctffind_mpi --- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/qsub.csh --- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_convert_star --- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_import +-- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion +-- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_tomo_test +-- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_helix_toolbox -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_postprocess_mpi +-- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_star_handler +-- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_particle_reposition +-- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_manualpick +-- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_motion_refine +-- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_tiltpair_plot +-- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_project +-- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_stack_create -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_localsym --- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_reconstruct_mpi --- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_ctf_mask_test --- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_particle_symmetry_expand +-- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_pipeliner +-- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_star_printtable +-- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_demodulate +-- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_refine_mpi +-- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_run_motioncorr +-- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_preprocess +-- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_reconstruct +-- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_mask_create +-- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_find_tiltpairs +-- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_ctf_refine_mpi -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_maingui --- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_tomo_test --- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_preprocess_mpi --- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_flex_analyse -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_align_symmetry -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_autopick -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_autopick_mpi @@ -3119,22 +3189,24 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'relion' in '../relion_3.1.0-4_i386.deb'. +dpkg-deb: building package 'relion-gui-dbgsym' in '../relion-gui-dbgsym_3.1.0-4_i386.deb'. dpkg-deb: building package 'relion-dbgsym' in '../relion-dbgsym_3.1.0-4_i386.deb'. +dpkg-deb: building package 'relion' in '../relion_3.1.0-4_i386.deb'. dpkg-deb: building package 'relion-gui' in '../relion-gui_3.1.0-4_i386.deb'. -dpkg-deb: building package 'relion-gui-dbgsym' in '../relion-gui-dbgsym_3.1.0-4_i386.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../relion_3.1.0-4_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) I: copying local configuration +I: user script /srv/workspace/pbuilder/21607/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/21607/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/52110 and its subdirectories -I: Current time: Mon Jul 25 01:19:51 -12 2022 -I: pbuilder-time-stamp: 1658755191 +I: removing directory /srv/workspace/pbuilder/21607 and its subdirectories +I: Current time: Tue Jun 22 21:45:52 +14 2021 +I: pbuilder-time-stamp: 1624347952