Diff of the two buildlogs: -- --- b1/build.log 2024-12-26 04:46:23.052366485 +0000 +++ b2/build.log 2024-12-26 05:01:59.013588285 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Jan 27 23:04:19 -12 2026 -I: pbuilder-time-stamp: 1769598259 +I: Current time: Thu Dec 26 18:46:27 +14 2024 +I: pbuilder-time-stamp: 1735188387 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -29,52 +29,84 @@ dpkg-source: info: applying typos.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/4041426/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1072322/tmp/hooks/D01_modify_environment starting +debug: Running on ionos11-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Dec 26 04:46 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/1072322/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1072322/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='af690eaf0cd34c2283df7cdd8a86816d' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='4041426' - PS1='# ' - PS2='> ' + INVOCATION_ID=6ac4416ef61b4161a1cf86555457b124 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=1072322 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.j9asK8vu/pbuilderrc_VW4P --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.j9asK8vu/b1 --logfile b1/build.log relion_3.1.3-4.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://213.165.73.152:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.j9asK8vu/pbuilderrc_kid2 --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.j9asK8vu/b2 --logfile b2/build.log relion_3.1.3-4.dsc' + SUDO_GID=111 + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://46.16.76.132:3128 I: uname -a - Linux ionos15-amd64 6.11.10+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.10-1~bpo12+1 (2024-12-19) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-28-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.119-1 (2024-11-22) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/4041426/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1072322/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -371,7 +403,7 @@ Get: 247 http://deb.debian.org/debian trixie/main amd64 libtiffxx6 amd64 4.5.1+git230720-5 [149 kB] Get: 248 http://deb.debian.org/debian trixie/main amd64 libtiff-dev amd64 4.5.1+git230720-5 [463 kB] Get: 249 http://deb.debian.org/debian trixie/main amd64 mpi-default-dev amd64 1.17 [3148 B] -Fetched 195 MB in 9s (22.4 MB/s) +Fetched 195 MB in 39s (4941 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-minimal:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19966 files and directories currently installed.) @@ -1183,8 +1215,8 @@ Setting up tzdata (2024b-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Wed Jan 28 11:05:05 UTC 2026. -Universal Time is now: Wed Jan 28 11:05:05 UTC 2026. +Local time is now: Thu Dec 26 04:51:04 UTC 2024. +Universal Time is now: Thu Dec 26 04:51:04 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libxcb-present0:amd64 (1.17.0-2+b1) ... @@ -1411,7 +1443,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/relion-3.1.3/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../relion_3.1.3-4_source.changes +I: user script /srv/workspace/pbuilder/1072322/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/1072322/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/relion-3.1.3/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../relion_3.1.3-4_source.changes dpkg-buildpackage: info: source package relion dpkg-buildpackage: info: source version 3.1.3-4 dpkg-buildpackage: info: source distribution unstable @@ -1517,8 +1553,8 @@ -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") --- Configuring done (3.0s) --- Generating done (0.2s) +-- Configuring done (12.8s) +-- Generating done (0.4s) CMake Warning: Manually-specified variables were not used by the project: @@ -1529,7 +1565,7 @@ make[1]: Leaving directory '/build/reproducible-path/relion-3.1.3' debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/relion-3.1.3' -/usr/bin/make -j42 -C build +/usr/bin/make -j20 -C build make[2]: Entering directory '/build/reproducible-path/relion-3.1.3/build' /usr/bin/cmake -S/build/reproducible-path/relion-3.1.3 -B/build/reproducible-path/relion-3.1.3/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/relion-3.1.3/build/CMakeFiles /build/reproducible-path/relion-3.1.3/build//CMakeFiles/progress.marks @@ -1549,115 +1585,62 @@ /usr/bin/make -f src/apps/CMakeFiles/relion_lib.dir/build.make src/apps/CMakeFiles/relion_lib.dir/build make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' /usr/bin/cmake -E copy /build/reproducible-path/relion-3.1.3/scripts/star_plottable /build/reproducible-path/relion-3.1.3/build/bin/relion_star_plottable -[ 0%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/assembly.cpp.o [ 1%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/CPlot2D.cpp.o [ 1%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/__/macros.cpp.o -[ 1%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/complex.cpp.o -[ 1%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/args.cpp.o -[ 1%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ctffind_runner_mpi.cpp.o -[ 1%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ctf.cpp.o -[ 1%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/autopicker_mpi.cpp.o +[ 2%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/args.cpp.o [ 2%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/autopicker.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/CPlot2D.cpp.o -MF CMakeFiles/relion_lib.dir/__/CPlot2D.cpp.o.d -o CMakeFiles/relion_lib.dir/__/CPlot2D.cpp.o -c /build/reproducible-path/relion-3.1.3/src/CPlot2D.cpp +[ 2%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/autopicker_mpi.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/__/macros.cpp.o -MF CMakeFiles/relion_lib.dir/__/__/macros.cpp.o.d -o CMakeFiles/relion_lib.dir/__/__/macros.cpp.o -c /build/reproducible-path/relion-3.1.3/build/macros.cpp +[ 2%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/assembly.cpp.o +[ 3%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/backprojector.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/CPlot2D.cpp.o -MF CMakeFiles/relion_lib.dir/__/CPlot2D.cpp.o.d -o CMakeFiles/relion_lib.dir/__/CPlot2D.cpp.o -c /build/reproducible-path/relion-3.1.3/src/CPlot2D.cpp cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/args.cpp.o -MF CMakeFiles/relion_lib.dir/__/args.cpp.o.d -o CMakeFiles/relion_lib.dir/__/args.cpp.o -c /build/reproducible-path/relion-3.1.3/src/args.cpp -[ 2%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/flex_analyser.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/assembly.cpp.o -MF CMakeFiles/relion_lib.dir/__/assembly.cpp.o.d -o CMakeFiles/relion_lib.dir/__/assembly.cpp.o -c /build/reproducible-path/relion-3.1.3/src/assembly.cpp -[ 3%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/backprojector.cpp.o +[ 3%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/complex.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/autopicker.cpp.o -MF CMakeFiles/relion_lib.dir/__/autopicker.cpp.o.d -o CMakeFiles/relion_lib.dir/__/autopicker.cpp.o -c /build/reproducible-path/relion-3.1.3/src/autopicker.cpp -[ 4%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ctffind_runner.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/autopicker_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/autopicker_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/autopicker_mpi.cpp.o -c /build/reproducible-path/relion-3.1.3/src/autopicker_mpi.cpp +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/backprojector.cpp.o -MF CMakeFiles/relion_lib.dir/__/backprojector.cpp.o.d -o CMakeFiles/relion_lib.dir/__/backprojector.cpp.o -c /build/reproducible-path/relion-3.1.3/src/backprojector.cpp +/usr/bin/cmake -E copy /build/reproducible-path/relion-3.1.3/scripts/star_loopheader /build/reproducible-path/relion-3.1.3/build/bin/relion_star_loopheader cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/complex.cpp.o -MF CMakeFiles/relion_lib.dir/__/complex.cpp.o.d -o CMakeFiles/relion_lib.dir/__/complex.cpp.o -c /build/reproducible-path/relion-3.1.3/src/complex.cpp +[ 3%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ctf.cpp.o +[ 4%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ctffind_runner.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/ctf.cpp.o -MF CMakeFiles/relion_lib.dir/__/ctf.cpp.o.d -o CMakeFiles/relion_lib.dir/__/ctf.cpp.o -c /build/reproducible-path/relion-3.1.3/src/ctf.cpp -[ 5%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/exp_model.cpp.o -[ 5%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/euler.cpp.o -[ 6%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/fftw.cpp.o -[ 6%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/error.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/backprojector.cpp.o -MF CMakeFiles/relion_lib.dir/__/backprojector.cpp.o.d -o CMakeFiles/relion_lib.dir/__/backprojector.cpp.o -c /build/reproducible-path/relion-3.1.3/src/backprojector.cpp -[ 6%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/filename.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/flex_analyser.cpp.o -MF CMakeFiles/relion_lib.dir/__/flex_analyser.cpp.o.d -o CMakeFiles/relion_lib.dir/__/flex_analyser.cpp.o -c /build/reproducible-path/relion-3.1.3/src/flex_analyser.cpp +[ 4%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ctffind_runner_mpi.cpp.o +[ 4%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/error.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/ctffind_runner.cpp.o -MF CMakeFiles/relion_lib.dir/__/ctffind_runner.cpp.o.d -o CMakeFiles/relion_lib.dir/__/ctffind_runner.cpp.o -c /build/reproducible-path/relion-3.1.3/src/ctffind_runner.cpp -/usr/bin/cmake -E copy /build/reproducible-path/relion-3.1.3/scripts/star_loopheader /build/reproducible-path/relion-3.1.3/build/bin/relion_star_loopheader cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/ctffind_runner_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/ctffind_runner_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/ctffind_runner_mpi.cpp.o -c /build/reproducible-path/relion-3.1.3/src/ctffind_runner_mpi.cpp cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/error.cpp.o -MF CMakeFiles/relion_lib.dir/__/error.cpp.o.d -o CMakeFiles/relion_lib.dir/__/error.cpp.o -c /build/reproducible-path/relion-3.1.3/src/error.cpp -[ 6%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/healpix_sampling.cpp.o -[ 7%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/image.cpp.o -[ 7%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/helix_inimodel2d.cpp.o +[ 5%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/euler.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/euler.cpp.o -MF CMakeFiles/relion_lib.dir/__/euler.cpp.o.d -o CMakeFiles/relion_lib.dir/__/euler.cpp.o -c /build/reproducible-path/relion-3.1.3/src/euler.cpp -[ 8%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/funcs.cpp.o -[ 8%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/helix.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/exp_model.cpp.o -MF CMakeFiles/relion_lib.dir/__/exp_model.cpp.o.d -o CMakeFiles/relion_lib.dir/__/exp_model.cpp.o -c /build/reproducible-path/relion-3.1.3/src/exp_model.cpp +/usr/bin/cmake -E copy /build/reproducible-path/relion-3.1.3/scripts/star_datablock_stack /build/reproducible-path/relion-3.1.3/build/bin/relion_star_datablock_stack +[ 6%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/fftw.cpp.o +[ 6%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/flex_analyser.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/fftw.cpp.o -MF CMakeFiles/relion_lib.dir/__/fftw.cpp.o.d -o CMakeFiles/relion_lib.dir/__/fftw.cpp.o -c /build/reproducible-path/relion-3.1.3/src/fftw.cpp +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/flex_analyser.cpp.o -MF CMakeFiles/relion_lib.dir/__/flex_analyser.cpp.o.d -o CMakeFiles/relion_lib.dir/__/flex_analyser.cpp.o -c /build/reproducible-path/relion-3.1.3/src/flex_analyser.cpp +[ 6%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/exp_model.cpp.o +[ 6%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/filename.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/exp_model.cpp.o -MF CMakeFiles/relion_lib.dir/__/exp_model.cpp.o.d -o CMakeFiles/relion_lib.dir/__/exp_model.cpp.o -c /build/reproducible-path/relion-3.1.3/src/exp_model.cpp +/usr/bin/cmake -E copy /build/reproducible-path/relion-3.1.3/scripts/star_datablock_singlefiles /build/reproducible-path/relion-3.1.3/build/bin/relion_star_datablock_singlefiles cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/filename.cpp.o -MF CMakeFiles/relion_lib.dir/__/filename.cpp.o.d -o CMakeFiles/relion_lib.dir/__/filename.cpp.o -c /build/reproducible-path/relion-3.1.3/src/filename.cpp -[ 9%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/local_symmetry.cpp.o +[ 7%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/funcs.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/funcs.cpp.o -MF CMakeFiles/relion_lib.dir/__/funcs.cpp.o.d -o CMakeFiles/relion_lib.dir/__/funcs.cpp.o -c /build/reproducible-path/relion-3.1.3/src/funcs.cpp +/usr/bin/cmake -E copy /build/reproducible-path/relion-3.1.3/scripts/star_datablock_ctfdat /build/reproducible-path/relion-3.1.3/build/bin/relion_star_datablock_ctfdat +/usr/bin/cmake -E copy /build/reproducible-path/relion-3.1.3/scripts/qsub.csh /build/reproducible-path/relion-3.1.3/build/bin/relion_qsub.csh +[ 7%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/healpix_sampling.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/healpix_sampling.cpp.o -MF CMakeFiles/relion_lib.dir/__/healpix_sampling.cpp.o.d -o CMakeFiles/relion_lib.dir/__/healpix_sampling.cpp.o -c /build/reproducible-path/relion-3.1.3/src/healpix_sampling.cpp -[ 9%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/local_symmetry_mpi.cpp.o -[ 10%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/memory.cpp.o +[ 7%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/helix.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/helix.cpp.o -MF CMakeFiles/relion_lib.dir/__/helix.cpp.o.d -o CMakeFiles/relion_lib.dir/__/helix.cpp.o -c /build/reproducible-path/relion-3.1.3/src/helix.cpp -[ 11%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/matrix1d.cpp.o -[ 11%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/mask.cpp.o -[ 11%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/metadata_container.cpp.o +make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' +[ 7%] Built target copy_scripts +[ 8%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/helix_inimodel2d.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/helix_inimodel2d.cpp.o -MF CMakeFiles/relion_lib.dir/__/helix_inimodel2d.cpp.o.d -o CMakeFiles/relion_lib.dir/__/helix_inimodel2d.cpp.o -c /build/reproducible-path/relion-3.1.3/src/helix_inimodel2d.cpp -[ 11%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/matrix2d.cpp.o +[ 8%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/image.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 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src/apps/CMakeFiles/relion_lib.dir/__/local_symmetry.cpp.o -MF CMakeFiles/relion_lib.dir/__/local_symmetry.cpp.o.d -o CMakeFiles/relion_lib.dir/__/local_symmetry.cpp.o -c /build/reproducible-path/relion-3.1.3/src/local_symmetry.cpp -[ 11%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/micrograph_model.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/local_symmetry_mpi.cpp.o -MF 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/build/reproducible-path/relion-3.1.3/src/mpi.cpp -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/multidim_array.cpp.o -MF CMakeFiles/relion_lib.dir/__/multidim_array.cpp.o.d -o CMakeFiles/relion_lib.dir/__/multidim_array.cpp.o -c /build/reproducible-path/relion-3.1.3/src/multidim_array.cpp -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/particle_subtractor.cpp.o -MF CMakeFiles/relion_lib.dir/__/particle_subtractor.cpp.o.d -o CMakeFiles/relion_lib.dir/__/particle_subtractor.cpp.o -c /build/reproducible-path/relion-3.1.3/src/particle_subtractor.cpp -[ 16%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/parallel.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/parallel.cpp.o -MF CMakeFiles/relion_lib.dir/__/parallel.cpp.o.d -o CMakeFiles/relion_lib.dir/__/parallel.cpp.o -c /build/reproducible-path/relion-3.1.3/src/parallel.cpp -[ 16%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/numerical_recipes.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/numerical_recipes.cpp.o -MF CMakeFiles/relion_lib.dir/__/numerical_recipes.cpp.o.d -o CMakeFiles/relion_lib.dir/__/numerical_recipes.cpp.o -c /build/reproducible-path/relion-3.1.3/src/numerical_recipes.cpp -/usr/bin/cmake -E copy /build/reproducible-path/relion-3.1.3/scripts/star_datablock_ctfdat /build/reproducible-path/relion-3.1.3/build/bin/relion_star_datablock_ctfdat -/usr/bin/cmake -E copy /build/reproducible-path/relion-3.1.3/scripts/qsub.csh /build/reproducible-path/relion-3.1.3/build/bin/relion_qsub.csh -make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -[ 16%] Built target copy_scripts -[ 16%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/pipeline_control.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/pipeline_control.cpp.o -MF CMakeFiles/relion_lib.dir/__/pipeline_control.cpp.o.d -o CMakeFiles/relion_lib.dir/__/pipeline_control.cpp.o -c /build/reproducible-path/relion-3.1.3/src/pipeline_control.cpp -[ 17%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/pipeline_jobs.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/pipeline_jobs.cpp.o -MF CMakeFiles/relion_lib.dir/__/pipeline_jobs.cpp.o.d -o CMakeFiles/relion_lib.dir/__/pipeline_jobs.cpp.o -c /build/reproducible-path/relion-3.1.3/src/pipeline_jobs.cpp -[ 17%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/pipeliner.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/pipeliner.cpp.o -MF CMakeFiles/relion_lib.dir/__/pipeliner.cpp.o.d -o CMakeFiles/relion_lib.dir/__/pipeliner.cpp.o -c /build/reproducible-path/relion-3.1.3/src/pipeliner.cpp -[ 17%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/postprocessing.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/postprocessing.cpp.o -MF CMakeFiles/relion_lib.dir/__/postprocessing.cpp.o.d -o CMakeFiles/relion_lib.dir/__/postprocessing.cpp.o -c /build/reproducible-path/relion-3.1.3/src/postprocessing.cpp -[ 18%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/preprocessing.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/preprocessing.cpp.o -MF CMakeFiles/relion_lib.dir/__/preprocessing.cpp.o.d -o CMakeFiles/relion_lib.dir/__/preprocessing.cpp.o -c /build/reproducible-path/relion-3.1.3/src/preprocessing.cpp -[ 18%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/preprocessing_mpi.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/preprocessing_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/preprocessing_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/preprocessing_mpi.cpp.o -c /build/reproducible-path/relion-3.1.3/src/preprocessing_mpi.cpp -[ 18%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/projector.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/projector.cpp.o -MF CMakeFiles/relion_lib.dir/__/projector.cpp.o.d -o CMakeFiles/relion_lib.dir/__/projector.cpp.o -c /build/reproducible-path/relion-3.1.3/src/projector.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/projector.h:25, - from /build/reproducible-path/relion-3.1.3/src/backprojector.h:33, - from /build/reproducible-path/relion-3.1.3/src/backprojector.cpp:27: + from /build/reproducible-path/relion-3.1.3/src/autopicker.h:10, + from /build/reproducible-path/relion-3.1.3/src/autopicker.cpp:20: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -1776,8 +1759,9 @@ 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/helix.h:30, - from /build/reproducible-path/relion-3.1.3/src/helix.cpp:22: + from /build/reproducible-path/relion-3.1.3/src/autopicker.h:10, + from /build/reproducible-path/relion-3.1.3/src/autopicker_mpi.h:12, + from /build/reproducible-path/relion-3.1.3/src/autopicker_mpi.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -1836,7 +1820,8 @@ 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/micrograph_model.cpp:23: + from /build/reproducible-path/relion-3.1.3/src/exp_model.h:24, + from /build/reproducible-path/relion-3.1.3/src/exp_model.cpp:20: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -1870,18 +1855,6 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/helix_inimodel2d.h:29, - from /build/reproducible-path/relion-3.1.3/src/helix_inimodel2d.cpp:22: -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] - 43 | uint32 width, length; // apparent dimensions in the file - | ^~~~~ -In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, - from /build/reproducible-path/relion-3.1.3/src/image.h:57: -/usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here - 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; - | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ @@ -1906,16 +1879,9 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations] - 43 | uint32 width, length; // apparent dimensions in the file - | ^~~~~~ -/usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here - 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; - | ^~~~~~ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/exp_model.h:24, - from /build/reproducible-path/relion-3.1.3/src/flex_analyser.h:24, - from /build/reproducible-path/relion-3.1.3/src/flex_analyser.cpp:21: + from /build/reproducible-path/relion-3.1.3/src/helix.h:30, + from /build/reproducible-path/relion-3.1.3/src/helix.cpp:22: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -1925,24 +1891,6 @@ /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; - | ^~~~~~~~~~~~ -/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; - | ^~~~~~~~~~~~~ -/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; - | ^~~~~~~~~~~~~~ -/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ @@ -1991,34 +1939,10 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] - 185 | uint32 cur_width, cur_length; - | ^~~~~~~~~ -/usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here - 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] - 185 | uint32 cur_width, cur_length; - | ^~~~~~~~~~ -/usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here - 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 186 | uint16 cur_sampleFormat, cur_bitsPerSample; - | ^~~~~~~~~~~~~~~~ -/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 186 | uint16 cur_sampleFormat, cur_bitsPerSample; - | ^~~~~~~~~~~~~~~~~ -/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/ctffind_runner.h:31, - from /build/reproducible-path/relion-3.1.3/src/ctffind_runner_mpi.h:25, - from /build/reproducible-path/relion-3.1.3/src/ctffind_runner_mpi.cpp:20: + from /build/reproducible-path/relion-3.1.3/src/projector.h:25, + from /build/reproducible-path/relion-3.1.3/src/backprojector.h:33, + from /build/reproducible-path/relion-3.1.3/src/backprojector.cpp:27: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -2064,13 +1988,6 @@ /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ -In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/exp_model.h:24, - from /build/reproducible-path/relion-3.1.3/src/exp_model.cpp:20: -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] - 43 | uint32 width, length; // apparent dimensions in the file - | ^~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ @@ -2083,6 +2000,14 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, + from /build/reproducible-path/relion-3.1.3/src/helix.h:30, + from /build/reproducible-path/relion-3.1.3/src/healpix_sampling.h:31, + from /build/reproducible-path/relion-3.1.3/src/healpix_sampling.cpp:20: +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 43 | uint32 width, length; // apparent dimensions in the file + | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here @@ -2137,9 +2062,7 @@ 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/autopicker.h:10, - from /build/reproducible-path/relion-3.1.3/src/autopicker_mpi.h:12, - from /build/reproducible-path/relion-3.1.3/src/autopicker_mpi.cpp:21: + from /build/reproducible-path/relion-3.1.3/src/image.cpp:20: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -2173,10 +2096,33 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 185 | uint32 cur_width, cur_length; + | ^~~~~~~~~ +/usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here + 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 185 | uint32 cur_width, cur_length; + | ^~~~~~~~~~ +/usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here + 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 186 | uint16 cur_sampleFormat, cur_bitsPerSample; + | ^~~~~~~~~~~~~~~~ +/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 186 | uint16 cur_sampleFormat, cur_bitsPerSample; + | ^~~~~~~~~~~~~~~~~ +/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/jaz/obs_model.h:24, - from /build/reproducible-path/relion-3.1.3/src/ctf.h:50, - from /build/reproducible-path/relion-3.1.3/src/ctf.cpp:45: + from /build/reproducible-path/relion-3.1.3/src/local_symmetry.h:30, + from /build/reproducible-path/relion-3.1.3/src/local_symmetry.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -2234,48 +2180,12 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] - 185 | uint32 cur_width, cur_length; - | ^~~~~~~~~ -/usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here - 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] - 185 | uint32 cur_width, cur_length; - | ^~~~~~~~~~ -/usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here - 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 186 | uint16 cur_sampleFormat, cur_bitsPerSample; - | ^~~~~~~~~~~~~~~~ -/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 186 | uint16 cur_sampleFormat, cur_bitsPerSample; - | ^~~~~~~~~~~~~~~~~ -/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ -In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/autopicker.h:10, - from /build/reproducible-path/relion-3.1.3/src/autopicker.cpp:20: -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] - 43 | uint32 width, length; // apparent dimensions in the file - | ^~~~~ -In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, - from /build/reproducible-path/relion-3.1.3/src/image.h:57: -/usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here - 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; - | ^~~~~~ +[ 9%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/local_symmetry_mpi.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/local_symmetry_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/local_symmetry_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/local_symmetry_mpi.cpp.o -c /build/reproducible-path/relion-3.1.3/src/local_symmetry_mpi.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/projector.h:25, - from /build/reproducible-path/relion-3.1.3/src/ml_model.h:23, - from /build/reproducible-path/relion-3.1.3/src/ml_optimiser.h:35, - from /build/reproducible-path/relion-3.1.3/src/particle_subtractor.h:24, - from /build/reproducible-path/relion-3.1.3/src/particle_subtractor.cpp:21: + from /build/reproducible-path/relion-3.1.3/src/exp_model.h:24, + from /build/reproducible-path/relion-3.1.3/src/flex_analyser.h:24, + from /build/reproducible-path/relion-3.1.3/src/flex_analyser.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -2309,35 +2219,34 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations] - 43 | uint32 width, length; // apparent dimensions in the file - | ^~~~~~ +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 185 | uint32 cur_width, cur_length; + | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 19%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/reconstructor.cpp.o -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; - | ^~~~~~~~~~~~ -/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 185 | uint32 cur_width, cur_length; + | ^~~~~~~~~~ +/usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here + 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; - | ^~~~~~~~~~~~~ +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 186 | uint16 cur_sampleFormat, cur_bitsPerSample; + | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; - | ^~~~~~~~~~~~~~ +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 186 | uint16 cur_sampleFormat, cur_bitsPerSample; + | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/reconstructor.cpp.o -MF CMakeFiles/relion_lib.dir/__/reconstructor.cpp.o.d -o CMakeFiles/relion_lib.dir/__/reconstructor.cpp.o -c /build/reproducible-path/relion-3.1.3/src/reconstructor.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/motioncorr_runner.h:32, - from /build/reproducible-path/relion-3.1.3/src/motioncorr_runner.cpp:22: + from /build/reproducible-path/relion-3.1.3/src/jaz/obs_model.h:24, + from /build/reproducible-path/relion-3.1.3/src/ctf.h:50, + from /build/reproducible-path/relion-3.1.3/src/ctf.cpp:45: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -2356,6 +2265,21 @@ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ +/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; + | ^~~~~~~~~~~~~ +/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; + | ^~~~~~~~~~~~~~ +/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ @@ -2374,51 +2298,49 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; - | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] - 185 | uint32 cur_width, cur_length; - | ^~~~~~~~~ +In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, + from /build/reproducible-path/relion-3.1.3/src/helix_inimodel2d.h:29, + from /build/reproducible-path/relion-3.1.3/src/helix_inimodel2d.cpp:22: +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 43 | uint32 width, length; // apparent dimensions in the file + | ^~~~~ +In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, + from /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ -/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] - 185 | uint32 cur_width, cur_length; - | ^~~~~~~~~~ +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 43 | uint32 width, length; // apparent dimensions in the file + | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; - | ^~~~~~~~~~~~~~ + | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 186 | uint16 cur_sampleFormat, cur_bitsPerSample; - | ^~~~~~~~~~~~~~~~ +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; + | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 186 | uint16 cur_sampleFormat, cur_bitsPerSample; - | ^~~~~~~~~~~~~~~~~ +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; + | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +[ 9%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/mask.cpp.o /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ @@ -2443,10 +2365,11 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/mask.cpp.o -MF CMakeFiles/relion_lib.dir/__/mask.cpp.o.d -o CMakeFiles/relion_lib.dir/__/mask.cpp.o -c /build/reproducible-path/relion-3.1.3/src/mask.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/local_symmetry.h:30, - from /build/reproducible-path/relion-3.1.3/src/local_symmetry_mpi.h:5, - from /build/reproducible-path/relion-3.1.3/src/local_symmetry_mpi.cpp:1: + from /build/reproducible-path/relion-3.1.3/src/ctffind_runner.h:31, + from /build/reproducible-path/relion-3.1.3/src/ctffind_runner_mpi.h:25, + from /build/reproducible-path/relion-3.1.3/src/ctffind_runner_mpi.cpp:20: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -2504,10 +2427,18 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +[ 10%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/matrix1d.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/matrix1d.cpp.o -MF CMakeFiles/relion_lib.dir/__/matrix1d.cpp.o.d -o CMakeFiles/relion_lib.dir/__/matrix1d.cpp.o -c /build/reproducible-path/relion-3.1.3/src/matrix1d.cpp +[ 10%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/matrix2d.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/matrix2d.cpp.o -MF CMakeFiles/relion_lib.dir/__/matrix2d.cpp.o.d -o CMakeFiles/relion_lib.dir/__/matrix2d.cpp.o -c /build/reproducible-path/relion-3.1.3/src/matrix2d.cpp +[ 11%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/memory.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/memory.cpp.o -MF CMakeFiles/relion_lib.dir/__/memory.cpp.o.d -o CMakeFiles/relion_lib.dir/__/memory.cpp.o -c /build/reproducible-path/relion-3.1.3/src/memory.cpp +[ 11%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/metadata_container.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/metadata_container.cpp.o -MF CMakeFiles/relion_lib.dir/__/metadata_container.cpp.o.d -o CMakeFiles/relion_lib.dir/__/metadata_container.cpp.o -c /build/reproducible-path/relion-3.1.3/src/metadata_container.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/motioncorr_runner.h:32, - from /build/reproducible-path/relion-3.1.3/src/motioncorr_runner_mpi.h:25, - from /build/reproducible-path/relion-3.1.3/src/motioncorr_runner_mpi.cpp:20: + from /build/reproducible-path/relion-3.1.3/src/local_symmetry.h:30, + from /build/reproducible-path/relion-3.1.3/src/local_symmetry_mpi.h:5, + from /build/reproducible-path/relion-3.1.3/src/local_symmetry_mpi.cpp:1: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -2565,8 +2496,22 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +[ 11%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/metadata_label.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/metadata_label.cpp.o -MF CMakeFiles/relion_lib.dir/__/metadata_label.cpp.o.d -o CMakeFiles/relion_lib.dir/__/metadata_label.cpp.o -c /build/reproducible-path/relion-3.1.3/src/metadata_label.cpp +[ 12%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/metadata_table.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/metadata_table.cpp.o -MF CMakeFiles/relion_lib.dir/__/metadata_table.cpp.o.d -o CMakeFiles/relion_lib.dir/__/metadata_table.cpp.o -c /build/reproducible-path/relion-3.1.3/src/metadata_table.cpp +[ 12%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/micrograph_model.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/micrograph_model.cpp.o -MF CMakeFiles/relion_lib.dir/__/micrograph_model.cpp.o.d -o CMakeFiles/relion_lib.dir/__/micrograph_model.cpp.o -c /build/reproducible-path/relion-3.1.3/src/micrograph_model.cpp +[ 12%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ml_model.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/ml_model.cpp.o -MF CMakeFiles/relion_lib.dir/__/ml_model.cpp.o.d -o CMakeFiles/relion_lib.dir/__/ml_model.cpp.o -c /build/reproducible-path/relion-3.1.3/src/ml_model.cpp +[ 13%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ml_optimiser.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/ml_optimiser.cpp.o -MF CMakeFiles/relion_lib.dir/__/ml_optimiser.cpp.o.d -o CMakeFiles/relion_lib.dir/__/ml_optimiser.cpp.o -c /build/reproducible-path/relion-3.1.3/src/ml_optimiser.cpp +[ 13%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ml_optimiser_mpi.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/ml_optimiser_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/ml_optimiser_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/ml_optimiser_mpi.cpp.o -c /build/reproducible-path/relion-3.1.3/src/ml_optimiser_mpi.cpp +[ 14%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/motioncorr_runner.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/motioncorr_runner.cpp.o -MF CMakeFiles/relion_lib.dir/__/motioncorr_runner.cpp.o.d -o CMakeFiles/relion_lib.dir/__/motioncorr_runner.cpp.o -c /build/reproducible-path/relion-3.1.3/src/motioncorr_runner.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/image.cpp:20: + from /build/reproducible-path/relion-3.1.3/src/micrograph_model.cpp:23: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -2625,10 +2570,8 @@ 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/projector.h:25, - from /build/reproducible-path/relion-3.1.3/src/ml_model.h:23, - from /build/reproducible-path/relion-3.1.3/src/ml_optimiser.h:35, - from /build/reproducible-path/relion-3.1.3/src/ml_optimiser.cpp:44: + from /build/reproducible-path/relion-3.1.3/src/motioncorr_runner.h:32, + from /build/reproducible-path/relion-3.1.3/src/motioncorr_runner.cpp:22: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -2662,12 +2605,34 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 185 | uint32 cur_width, cur_length; + | ^~~~~~~~~ +/usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here + 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 185 | uint32 cur_width, cur_length; + | ^~~~~~~~~~ +/usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here + 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 186 | uint16 cur_sampleFormat, cur_bitsPerSample; + | ^~~~~~~~~~~~~~~~ +/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 186 | uint16 cur_sampleFormat, cur_bitsPerSample; + | ^~~~~~~~~~~~~~~~~ +/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/projector.h:25, from /build/reproducible-path/relion-3.1.3/src/ml_model.h:23, - from /build/reproducible-path/relion-3.1.3/src/ml_optimiser.h:35, - from /build/reproducible-path/relion-3.1.3/src/ml_optimiser_mpi.h:24, - from /build/reproducible-path/relion-3.1.3/src/ml_optimiser_mpi.cpp:20: + from /build/reproducible-path/relion-3.1.3/src/ml_model.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -2701,6 +2666,7 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +[ 14%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/motioncorr_runner_mpi.cpp.o /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ @@ -2725,34 +2691,15 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] - 185 | uint32 cur_width, cur_length; - | ^~~~~~~~~ -/usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here - 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] - 185 | uint32 cur_width, cur_length; - | ^~~~~~~~~~ -/usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here - 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 186 | uint16 cur_sampleFormat, cur_bitsPerSample; - | ^~~~~~~~~~~~~~~~ -/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 186 | uint16 cur_sampleFormat, cur_bitsPerSample; - | ^~~~~~~~~~~~~~~~~ -/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/motioncorr_runner_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/motioncorr_runner_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/motioncorr_runner_mpi.cpp.o -c /build/reproducible-path/relion-3.1.3/src/motioncorr_runner_mpi.cpp +[ 14%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/mpi.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/mpi.cpp.o -c /build/reproducible-path/relion-3.1.3/src/mpi.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/helix.h:30, - from /build/reproducible-path/relion-3.1.3/src/healpix_sampling.h:31, - from /build/reproducible-path/relion-3.1.3/src/healpix_sampling.cpp:20: + from /build/reproducible-path/relion-3.1.3/src/projector.h:25, + from /build/reproducible-path/relion-3.1.3/src/ml_model.h:23, + from /build/reproducible-path/relion-3.1.3/src/ml_optimiser.h:35, + from /build/reproducible-path/relion-3.1.3/src/ml_optimiser_mpi.h:24, + from /build/reproducible-path/relion-3.1.3/src/ml_optimiser_mpi.cpp:20: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -2813,7 +2760,8 @@ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/projector.h:25, from /build/reproducible-path/relion-3.1.3/src/ml_model.h:23, - from /build/reproducible-path/relion-3.1.3/src/ml_model.cpp:21: + from /build/reproducible-path/relion-3.1.3/src/ml_optimiser.h:35, + from /build/reproducible-path/relion-3.1.3/src/ml_optimiser.cpp:44: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -2871,26 +2819,12 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 19%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/reconstructor_mpi.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/reconstructor_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/reconstructor_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/reconstructor_mpi.cpp.o -c /build/reproducible-path/relion-3.1.3/src/reconstructor_mpi.cpp -In file included from /build/reproducible-path/relion-3.1.3/src/numerical_recipes.h:48, - from /build/reproducible-path/relion-3.1.3/src/numerical_recipes.cpp:49: -In function 'void free_Tvector(T*&, int, int) [with T = double]', - inlined from 'void mnbrak(double*, double*, double*, double*, double*, double*, double (*)(double*, void*), void*, int, double*, double*)' at /build/reproducible-path/relion-3.1.3/src/numerical_recipes.cpp:561:17: -/build/reproducible-path/relion-3.1.3/src/memory.h:74:13: warning: 'void free(void*)' called on pointer 'xt' with nonzero offset 8 [-Wfree-nonheap-object] - 74 | free((char*)(v + nl)); - | ~~~~^~~~~~~~~~~~~~~~~ -/build/reproducible-path/relion-3.1.3/src/numerical_recipes.cpp: In function 'void mnbrak(double*, double*, double*, double*, double*, double*, double (*)(double*, void*), void*, int, double*, double*)': -/build/reproducible-path/relion-3.1.3/src/numerical_recipes.cpp:499:13: note: declared here - 499 | RFLOAT *xt=NULL; - | ^~ -[ 20%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/renderEER.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/renderEER.cpp.o -MF CMakeFiles/relion_lib.dir/__/renderEER.cpp.o.d -o CMakeFiles/relion_lib.dir/__/renderEER.cpp.o -c /build/reproducible-path/relion-3.1.3/src/renderEER.cpp -[ 20%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/scheduler.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/scheduler.cpp.o -MF CMakeFiles/relion_lib.dir/__/scheduler.cpp.o.d -o CMakeFiles/relion_lib.dir/__/scheduler.cpp.o -c /build/reproducible-path/relion-3.1.3/src/scheduler.cpp +[ 15%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/multidim_array.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/multidim_array.cpp.o -MF CMakeFiles/relion_lib.dir/__/multidim_array.cpp.o.d -o CMakeFiles/relion_lib.dir/__/multidim_array.cpp.o -c /build/reproducible-path/relion-3.1.3/src/multidim_array.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/local_symmetry.h:30, - from /build/reproducible-path/relion-3.1.3/src/local_symmetry.cpp:21: + from /build/reproducible-path/relion-3.1.3/src/motioncorr_runner.h:32, + from /build/reproducible-path/relion-3.1.3/src/motioncorr_runner_mpi.h:25, + from /build/reproducible-path/relion-3.1.3/src/motioncorr_runner_mpi.cpp:20: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -2948,6 +2882,23 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +[ 15%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/numerical_recipes.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/numerical_recipes.cpp.o -MF CMakeFiles/relion_lib.dir/__/numerical_recipes.cpp.o.d -o CMakeFiles/relion_lib.dir/__/numerical_recipes.cpp.o -c /build/reproducible-path/relion-3.1.3/src/numerical_recipes.cpp +[ 15%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/parallel.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/parallel.cpp.o -MF CMakeFiles/relion_lib.dir/__/parallel.cpp.o.d -o CMakeFiles/relion_lib.dir/__/parallel.cpp.o -c /build/reproducible-path/relion-3.1.3/src/parallel.cpp +[ 16%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/particle_subtractor.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/particle_subtractor.cpp.o -MF CMakeFiles/relion_lib.dir/__/particle_subtractor.cpp.o.d -o CMakeFiles/relion_lib.dir/__/particle_subtractor.cpp.o -c /build/reproducible-path/relion-3.1.3/src/particle_subtractor.cpp +In file included from /build/reproducible-path/relion-3.1.3/src/numerical_recipes.h:48, + from /build/reproducible-path/relion-3.1.3/src/numerical_recipes.cpp:49: +In function 'void free_Tvector(T*&, int, int) [with T = double]', + inlined from 'void mnbrak(double*, double*, double*, double*, double*, double*, double (*)(double*, void*), void*, int, double*, double*)' at /build/reproducible-path/relion-3.1.3/src/numerical_recipes.cpp:561:17: +/build/reproducible-path/relion-3.1.3/src/memory.h:74:13: warning: 'void free(void*)' called on pointer 'xt' with nonzero offset 8 [-Wfree-nonheap-object] + 74 | free((char*)(v + nl)); + | ~~~~^~~~~~~~~~~~~~~~~ +/build/reproducible-path/relion-3.1.3/src/numerical_recipes.cpp: In function 'void mnbrak(double*, double*, double*, double*, double*, double*, double (*)(double*, void*), void*, int, double*, double*)': +/build/reproducible-path/relion-3.1.3/src/numerical_recipes.cpp:499:13: note: declared here + 499 | RFLOAT *xt=NULL; + | ^~ In function 'void free_Tvector(T*&, int, int) [with T = double]', inlined from 'double brent(double, double, double, double (*)(double*, void*), void*, double, double*, int, double*, double*)' at /build/reproducible-path/relion-3.1.3/src/numerical_recipes.cpp:594:25: /build/reproducible-path/relion-3.1.3/src/memory.h:74:13: warning: 'void free(void*)' called on pointer 'xt' with nonzero offset 8 [-Wfree-nonheap-object] @@ -2957,8 +2908,6 @@ /build/reproducible-path/relion-3.1.3/src/numerical_recipes.cpp:579:13: note: declared here 579 | RFLOAT *xt=NULL; | ^~ -[ 21%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/symmetries.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/symmetries.cpp.o -MF CMakeFiles/relion_lib.dir/__/symmetries.cpp.o.d -o CMakeFiles/relion_lib.dir/__/symmetries.cpp.o -c /build/reproducible-path/relion-3.1.3/src/symmetries.cpp In function 'void free_Tvector(T*&, int, int) [with T = double]', inlined from 'void linmin(double*, double*, int, double&, double (*)(double*, void*), void*)' at /build/reproducible-path/relion-3.1.3/src/numerical_recipes.cpp:691:17: /build/reproducible-path/relion-3.1.3/src/memory.h:74:13: warning: 'void free(void*)' called on pointer 'xicom' with nonzero offset 8 [-Wfree-nonheap-object] @@ -2977,8 +2926,6 @@ /build/reproducible-path/relion-3.1.3/src/numerical_recipes.cpp:672:13: note: declared here 672 | RFLOAT *pcom=NULL; | ^~~~ -[ 21%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/strings.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/strings.cpp.o -MF CMakeFiles/relion_lib.dir/__/strings.cpp.o.d -o CMakeFiles/relion_lib.dir/__/strings.cpp.o -c /build/reproducible-path/relion-3.1.3/src/strings.cpp In function 'void free_Tvector(T*&, int, int) [with T = double]', inlined from 'void powell(double*, double*, int, double, int&, double&, double (*)(double*, void*), void*, bool)' at /build/reproducible-path/relion-3.1.3/src/numerical_recipes.cpp:767:25: /build/reproducible-path/relion-3.1.3/src/memory.h:74:13: warning: 'void free(void*)' called on pointer 'xit' with nonzero offset 8 [-Wfree-nonheap-object] @@ -3006,11 +2953,12 @@ /build/reproducible-path/relion-3.1.3/src/numerical_recipes.cpp:703:13: note: declared here 703 | RFLOAT *pt, *ptt, *xit; | ^~ -[ 21%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/tabfuncs.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/tabfuncs.cpp.o -MF CMakeFiles/relion_lib.dir/__/tabfuncs.cpp.o.d -o CMakeFiles/relion_lib.dir/__/tabfuncs.cpp.o -c /build/reproducible-path/relion-3.1.3/src/tabfuncs.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/postprocessing.h:24, - from /build/reproducible-path/relion-3.1.3/src/postprocessing.cpp:21: + from /build/reproducible-path/relion-3.1.3/src/projector.h:25, + from /build/reproducible-path/relion-3.1.3/src/ml_model.h:23, + from /build/reproducible-path/relion-3.1.3/src/ml_optimiser.h:35, + from /build/reproducible-path/relion-3.1.3/src/particle_subtractor.h:24, + from /build/reproducible-path/relion-3.1.3/src/particle_subtractor.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -3068,11 +3016,26 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 21%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/tiff_converter.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/tiff_converter.cpp.o -MF CMakeFiles/relion_lib.dir/__/tiff_converter.cpp.o.d -o CMakeFiles/relion_lib.dir/__/tiff_converter.cpp.o -c /build/reproducible-path/relion-3.1.3/src/tiff_converter.cpp +[ 16%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/pipeline_control.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/pipeline_control.cpp.o -MF CMakeFiles/relion_lib.dir/__/pipeline_control.cpp.o.d -o CMakeFiles/relion_lib.dir/__/pipeline_control.cpp.o -c /build/reproducible-path/relion-3.1.3/src/pipeline_control.cpp +In function 'void free_Tvector(T*&, int, int) [with T = double]', + inlined from 'void svbksb(double*, double*, double*, int, int, double*, double*)' at /build/reproducible-path/relion-3.1.3/src/numerical_recipes.cpp:1124:17: +/build/reproducible-path/relion-3.1.3/src/memory.h:74:13: warning: 'void free(void*)' called on pointer 'tmp' with nonzero offset 8 [-Wfree-nonheap-object] + 74 | free((char*)(v + nl)); + | ~~~~^~~~~~~~~~~~~~~~~ +/build/reproducible-path/relion-3.1.3/src/numerical_recipes.cpp: In function 'void svbksb(double*, double*, double*, int, int, double*, double*)': +/build/reproducible-path/relion-3.1.3/src/numerical_recipes.cpp:1103:16: note: declared here + 1103 | RFLOAT s, *tmp; + | ^~~ +[ 17%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/pipeline_jobs.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/pipeline_jobs.cpp.o -MF CMakeFiles/relion_lib.dir/__/pipeline_jobs.cpp.o.d -o CMakeFiles/relion_lib.dir/__/pipeline_jobs.cpp.o -c /build/reproducible-path/relion-3.1.3/src/pipeline_jobs.cpp +[ 17%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/pipeliner.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/pipeliner.cpp.o -MF CMakeFiles/relion_lib.dir/__/pipeliner.cpp.o.d -o CMakeFiles/relion_lib.dir/__/pipeliner.cpp.o -c /build/reproducible-path/relion-3.1.3/src/pipeliner.cpp +[ 17%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/postprocessing.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/postprocessing.cpp.o -MF CMakeFiles/relion_lib.dir/__/postprocessing.cpp.o.d -o CMakeFiles/relion_lib.dir/__/postprocessing.cpp.o -c /build/reproducible-path/relion-3.1.3/src/postprocessing.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/preprocessing.h:29, - from /build/reproducible-path/relion-3.1.3/src/preprocessing.cpp:20: + from /build/reproducible-path/relion-3.1.3/src/postprocessing.h:24, + from /build/reproducible-path/relion-3.1.3/src/postprocessing.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -3130,9 +3093,13 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +[ 18%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/preprocessing.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/preprocessing.cpp.o -MF CMakeFiles/relion_lib.dir/__/preprocessing.cpp.o.d -o CMakeFiles/relion_lib.dir/__/preprocessing.cpp.o -c /build/reproducible-path/relion-3.1.3/src/preprocessing.cpp +[ 18%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/preprocessing_mpi.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/preprocessing_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/preprocessing_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/preprocessing_mpi.cpp.o -c /build/reproducible-path/relion-3.1.3/src/preprocessing_mpi.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/projector.h:25, - from /build/reproducible-path/relion-3.1.3/src/projector.cpp:20: + from /build/reproducible-path/relion-3.1.3/src/preprocessing.h:29, + from /build/reproducible-path/relion-3.1.3/src/preprocessing.cpp:20: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -3190,8 +3157,6 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 22%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/time.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/time.cpp.o -MF CMakeFiles/relion_lib.dir/__/time.cpp.o.d -o CMakeFiles/relion_lib.dir/__/time.cpp.o -c /build/reproducible-path/relion-3.1.3/src/time.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/preprocessing.h:29, from /build/reproducible-path/relion-3.1.3/src/preprocessing_mpi.h:24, @@ -3253,11 +3218,20 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +[ 18%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/projector.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/projector.cpp.o -MF CMakeFiles/relion_lib.dir/__/projector.cpp.o.d -o CMakeFiles/relion_lib.dir/__/projector.cpp.o -c /build/reproducible-path/relion-3.1.3/src/projector.cpp +[ 19%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/reconstructor.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/reconstructor.cpp.o -MF CMakeFiles/relion_lib.dir/__/reconstructor.cpp.o.d -o CMakeFiles/relion_lib.dir/__/reconstructor.cpp.o -c /build/reproducible-path/relion-3.1.3/src/reconstructor.cpp +[ 19%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/reconstructor_mpi.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/reconstructor_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/reconstructor_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/reconstructor_mpi.cpp.o -c /build/reproducible-path/relion-3.1.3/src/reconstructor_mpi.cpp +[ 20%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/renderEER.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/renderEER.cpp.o -MF CMakeFiles/relion_lib.dir/__/renderEER.cpp.o.d -o CMakeFiles/relion_lib.dir/__/renderEER.cpp.o -c /build/reproducible-path/relion-3.1.3/src/renderEER.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/projector.h:25, from /build/reproducible-path/relion-3.1.3/src/backprojector.h:33, from /build/reproducible-path/relion-3.1.3/src/reconstructor.h:23, - from /build/reproducible-path/relion-3.1.3/src/reconstructor.cpp:20: + from /build/reproducible-path/relion-3.1.3/src/reconstructor_mpi.h:25, + from /build/reproducible-path/relion-3.1.3/src/reconstructor_mpi.cpp:20: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -3317,10 +3291,7 @@ | ^~~~~~ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/projector.h:25, - from /build/reproducible-path/relion-3.1.3/src/backprojector.h:33, - from /build/reproducible-path/relion-3.1.3/src/reconstructor.h:23, - from /build/reproducible-path/relion-3.1.3/src/reconstructor_mpi.h:25, - from /build/reproducible-path/relion-3.1.3/src/reconstructor_mpi.cpp:20: + from /build/reproducible-path/relion-3.1.3/src/projector.cpp:20: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -3379,9 +3350,10 @@ 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/jaz/obs_model.h:24, - from /build/reproducible-path/relion-3.1.3/src/scheduler.h:26, - from /build/reproducible-path/relion-3.1.3/src/scheduler.cpp:20: + from /build/reproducible-path/relion-3.1.3/src/projector.h:25, + from /build/reproducible-path/relion-3.1.3/src/backprojector.h:33, + from /build/reproducible-path/relion-3.1.3/src/reconstructor.h:23, + from /build/reproducible-path/relion-3.1.3/src/reconstructor.cpp:20: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -3439,6 +3411,8 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +[ 20%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/scheduler.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/scheduler.cpp.o -MF CMakeFiles/relion_lib.dir/__/scheduler.cpp.o.d -o CMakeFiles/relion_lib.dir/__/scheduler.cpp.o -c /build/reproducible-path/relion-3.1.3/src/scheduler.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/renderEER.cpp:10: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': @@ -3498,21 +3472,83 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -In function 'void free_Tvector(T*&, int, int) [with T = double]', - inlined from 'void svbksb(double*, double*, double*, int, int, double*, double*)' at /build/reproducible-path/relion-3.1.3/src/numerical_recipes.cpp:1124:17: -/build/reproducible-path/relion-3.1.3/src/memory.h:74:13: warning: 'void free(void*)' called on pointer 'tmp' with nonzero offset 8 [-Wfree-nonheap-object] - 74 | free((char*)(v + nl)); - | ~~~~^~~~~~~~~~~~~~~~~ -/build/reproducible-path/relion-3.1.3/src/numerical_recipes.cpp: In function 'void svbksb(double*, double*, double*, int, int, double*, double*)': -/build/reproducible-path/relion-3.1.3/src/numerical_recipes.cpp:1103:16: note: declared here - 1103 | RFLOAT s, *tmp; - | ^~~ -[ 22%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/transformations.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/transformations.cpp.o -MF CMakeFiles/relion_lib.dir/__/transformations.cpp.o.d -o CMakeFiles/relion_lib.dir/__/transformations.cpp.o -c /build/reproducible-path/relion-3.1.3/src/transformations.cpp /build/reproducible-path/relion-3.1.3/src/renderEER.cpp: In member function 'void EERRenderer::readLegacy(FILE*)': /build/reproducible-path/relion-3.1.3/src/renderEER.cpp:191:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 191 | fread(buf, sizeof(char), file_size, fh); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 20%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/strings.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/strings.cpp.o -MF CMakeFiles/relion_lib.dir/__/strings.cpp.o.d -o CMakeFiles/relion_lib.dir/__/strings.cpp.o -c /build/reproducible-path/relion-3.1.3/src/strings.cpp +[ 21%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/symmetries.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/symmetries.cpp.o -MF CMakeFiles/relion_lib.dir/__/symmetries.cpp.o.d -o CMakeFiles/relion_lib.dir/__/symmetries.cpp.o -c /build/reproducible-path/relion-3.1.3/src/symmetries.cpp +[ 21%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/tabfuncs.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/tabfuncs.cpp.o -MF CMakeFiles/relion_lib.dir/__/tabfuncs.cpp.o.d -o CMakeFiles/relion_lib.dir/__/tabfuncs.cpp.o -c /build/reproducible-path/relion-3.1.3/src/tabfuncs.cpp +In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, + from /build/reproducible-path/relion-3.1.3/src/jaz/obs_model.h:24, + from /build/reproducible-path/relion-3.1.3/src/scheduler.h:26, + from /build/reproducible-path/relion-3.1.3/src/scheduler.cpp:20: +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 43 | uint32 width, length; // apparent dimensions in the file + | ^~~~~ +In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, + from /build/reproducible-path/relion-3.1.3/src/image.h:57: +/usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here + 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 43 | uint32 width, length; // apparent dimensions in the file + | ^~~~~~ +/usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here + 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; + | ^~~~~~~~~~~~ +/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; + | ^~~~~~~~~~~~~ +/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; + | ^~~~~~~~~~~~~~ +/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 185 | uint32 cur_width, cur_length; + | ^~~~~~~~~ +/usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here + 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 185 | uint32 cur_width, cur_length; + | ^~~~~~~~~~ +/usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here + 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 186 | uint16 cur_sampleFormat, cur_bitsPerSample; + | ^~~~~~~~~~~~~~~~ +/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 186 | uint16 cur_sampleFormat, cur_bitsPerSample; + | ^~~~~~~~~~~~~~~~~ +/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ +[ 21%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/tiff_converter.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/tiff_converter.cpp.o -MF CMakeFiles/relion_lib.dir/__/tiff_converter.cpp.o.d -o CMakeFiles/relion_lib.dir/__/tiff_converter.cpp.o -c /build/reproducible-path/relion-3.1.3/src/tiff_converter.cpp +[ 22%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/time.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/time.cpp.o -MF CMakeFiles/relion_lib.dir/__/time.cpp.o.d -o CMakeFiles/relion_lib.dir/__/time.cpp.o -c /build/reproducible-path/relion-3.1.3/src/time.cpp +[ 22%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/transformations.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/transformations.cpp.o -MF CMakeFiles/relion_lib.dir/__/transformations.cpp.o.d -o CMakeFiles/relion_lib.dir/__/transformations.cpp.o -c /build/reproducible-path/relion-3.1.3/src/transformations.cpp [ 23%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/Healpix_2.15a/cxxutils.cc.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/Healpix_2.15a/cxxutils.cc.o -MF CMakeFiles/relion_lib.dir/__/Healpix_2.15a/cxxutils.cc.o.d -o CMakeFiles/relion_lib.dir/__/Healpix_2.15a/cxxutils.cc.o -c /build/reproducible-path/relion-3.1.3/src/Healpix_2.15a/cxxutils.cc In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, @@ -3597,6 +3633,10 @@ /build/reproducible-path/relion-3.1.3/src/tiff_converter.cpp:367:23: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | system(("mkdir -p " + fn_out.beforeLastOf("/")).c_str()); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/relion-3.1.3/src/tiff_converter.cpp: In member function 'void TIFFConverter::run()': +/build/reproducible-path/relion-3.1.3/src/tiff_converter.cpp:530:31: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 530 | system(("mkdir -p " + fn_tiff.beforeLastOf("/")).c_str()); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 23%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/Fourier_helper.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/Fourier_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/Fourier_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/Fourier_helper.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/Fourier_helper.cpp [ 24%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/Gaussian_pyramid.cpp.o @@ -3605,25 +3645,11 @@ cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/aberration_fit.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/aberration_fit.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/aberration_fit.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/aberration_fit.cpp [ 25%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/complex_io.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/complex_io.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/complex_io.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/complex_io.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/complex_io.cpp -/build/reproducible-path/relion-3.1.3/src/tiff_converter.cpp: In member function 'void TIFFConverter::run()': -/build/reproducible-path/relion-3.1.3/src/tiff_converter.cpp:530:31: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 530 | system(("mkdir -p " + fn_tiff.beforeLastOf("/")).c_str()); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 25%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/convolution_helper.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/convolution_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/convolution_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/convolution_helper.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/convolution_helper.cpp -[ 25%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf_helper.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf_helper.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/ctf_helper.cpp -[ 26%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/damage_helper.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/damage_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/damage_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/damage_helper.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/damage_helper.cpp -[ 26%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/distribution_helper.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/distribution_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/distribution_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/distribution_helper.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/distribution_helper.cpp -[ 26%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/fftw_helper.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/fftw_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/fftw_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/fftw_helper.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/fftw_helper.cpp -[ 27%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/fsc_helper.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/fsc_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/fsc_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/fsc_helper.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/fsc_helper.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/jaz/aberration_fit.h:24, - from /build/reproducible-path/relion-3.1.3/src/jaz/aberration_fit.cpp:21: + from /build/reproducible-path/relion-3.1.3/src/jaz/Fourier_helper.h:24, + from /build/reproducible-path/relion-3.1.3/src/jaz/Fourier_helper.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -3681,9 +3707,11 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +[ 25%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf_helper.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf_helper.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/ctf_helper.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/jaz/Fourier_helper.h:24, - from /build/reproducible-path/relion-3.1.3/src/jaz/Fourier_helper.cpp:21: + from /build/reproducible-path/relion-3.1.3/src/jaz/complex_io.h:24, + from /build/reproducible-path/relion-3.1.3/src/jaz/complex_io.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -3742,8 +3770,8 @@ 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/jaz/complex_io.h:24, - from /build/reproducible-path/relion-3.1.3/src/jaz/complex_io.cpp:21: + from /build/reproducible-path/relion-3.1.3/src/jaz/aberration_fit.h:24, + from /build/reproducible-path/relion-3.1.3/src/jaz/aberration_fit.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -3801,14 +3829,6 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 27%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/image_log.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/image_log.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/image_log.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/image_log.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/image_log.cpp -[ 28%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/interpolation.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/interpolation.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/interpolation.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/interpolation.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/interpolation.cpp -[ 28%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/jaz_config.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/jaz_config.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/jaz_config.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/jaz_config.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/jaz_config.cpp -[ 28%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/legacy_obs_model.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/legacy_obs_model.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/legacy_obs_model.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/legacy_obs_model.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/legacy_obs_model.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/jaz/convolution_helper.h:24, from /build/reproducible-path/relion-3.1.3/src/jaz/convolution_helper.cpp:21: @@ -3869,11 +3889,13 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +[ 26%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/damage_helper.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/damage_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/damage_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/damage_helper.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/damage_helper.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/jaz/obs_model.h:24, from /build/reproducible-path/relion-3.1.3/src/ctf.h:50, - from /build/reproducible-path/relion-3.1.3/src/jaz/fsc_helper.h:24, - from /build/reproducible-path/relion-3.1.3/src/jaz/damage_helper.cpp:21: + from /build/reproducible-path/relion-3.1.3/src/jaz/ctf_helper.h:24, + from /build/reproducible-path/relion-3.1.3/src/jaz/ctf_helper.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -3931,9 +3953,15 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +[ 26%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/distribution_helper.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/distribution_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/distribution_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/distribution_helper.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/distribution_helper.cpp +[ 26%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/fftw_helper.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/fftw_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/fftw_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/fftw_helper.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/fftw_helper.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/jaz/distribution_helper.h:25, - from /build/reproducible-path/relion-3.1.3/src/jaz/distribution_helper.cpp:21: + from /build/reproducible-path/relion-3.1.3/src/jaz/obs_model.h:24, + from /build/reproducible-path/relion-3.1.3/src/ctf.h:50, + from /build/reproducible-path/relion-3.1.3/src/jaz/fsc_helper.h:24, + from /build/reproducible-path/relion-3.1.3/src/jaz/damage_helper.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -3991,13 +4019,21 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +[ 27%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/fsc_helper.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/fsc_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/fsc_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/fsc_helper.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/fsc_helper.cpp +[ 27%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/image_log.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/image_log.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/image_log.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/image_log.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/image_log.cpp +[ 28%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/interpolation.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/interpolation.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/interpolation.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/interpolation.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/interpolation.cpp +[ 28%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/jaz_config.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/jaz_config.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/jaz_config.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/jaz_config.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/jaz_config.cpp +[ 28%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/legacy_obs_model.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/legacy_obs_model.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/legacy_obs_model.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/legacy_obs_model.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/legacy_obs_model.cpp [ 29%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/local_motion_fit.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/local_motion_fit.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/local_motion_fit.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/local_motion_fit.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/local_motion_fit.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/jaz/obs_model.h:24, - from /build/reproducible-path/relion-3.1.3/src/ctf.h:50, - from /build/reproducible-path/relion-3.1.3/src/jaz/ctf_helper.h:24, - from /build/reproducible-path/relion-3.1.3/src/jaz/ctf_helper.cpp:21: + from /build/reproducible-path/relion-3.1.3/src/jaz/distribution_helper.h:25, + from /build/reproducible-path/relion-3.1.3/src/jaz/distribution_helper.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -4055,15 +4091,9 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 29%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/micrograph_handler.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/micrograph_handler.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/micrograph_handler.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/micrograph_handler.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/micrograph_handler.cpp -[ 29%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/new_ft.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/new_ft.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/new_ft.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/new_ft.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/new_ft.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/jaz/obs_model.h:24, - from /build/reproducible-path/relion-3.1.3/src/ctf.h:50, - from /build/reproducible-path/relion-3.1.3/src/jaz/fsc_helper.h:24, - from /build/reproducible-path/relion-3.1.3/src/jaz/fsc_helper.cpp:21: + from /build/reproducible-path/relion-3.1.3/src/jaz/image_log.h:24, + from /build/reproducible-path/relion-3.1.3/src/jaz/image_log.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -4121,11 +4151,11 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 30%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/noise_helper.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/noise_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/noise_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/noise_helper.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/noise_helper.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/jaz/interpolation.h:24, - from /build/reproducible-path/relion-3.1.3/src/jaz/interpolation.cpp:21: + from /build/reproducible-path/relion-3.1.3/src/jaz/obs_model.h:24, + from /build/reproducible-path/relion-3.1.3/src/ctf.h:50, + from /build/reproducible-path/relion-3.1.3/src/jaz/fsc_helper.h:24, + from /build/reproducible-path/relion-3.1.3/src/jaz/fsc_helper.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -4184,8 +4214,8 @@ 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/jaz/image_log.h:24, - from /build/reproducible-path/relion-3.1.3/src/jaz/image_log.cpp:21: + from /build/reproducible-path/relion-3.1.3/src/jaz/interpolation.h:24, + from /build/reproducible-path/relion-3.1.3/src/jaz/interpolation.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -4243,9 +4273,15 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +[ 29%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/micrograph_handler.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/micrograph_handler.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/micrograph_handler.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/micrograph_handler.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/micrograph_handler.cpp +[ 29%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/new_ft.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/new_ft.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/new_ft.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/new_ft.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/new_ft.cpp +[ 30%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/noise_helper.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/noise_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/noise_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/noise_helper.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/noise_helper.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/jaz/local_motion_fit.h:24, - from /build/reproducible-path/relion-3.1.3/src/jaz/local_motion_fit.cpp:21: + from /build/reproducible-path/relion-3.1.3/src/jaz/legacy_obs_model.h:4, + from /build/reproducible-path/relion-3.1.3/src/jaz/legacy_obs_model.cpp:1: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -4303,9 +4339,11 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +[ 30%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/obs_model.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/obs_model.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/obs_model.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/obs_model.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/obs_model.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/jaz/legacy_obs_model.h:4, - from /build/reproducible-path/relion-3.1.3/src/jaz/legacy_obs_model.cpp:1: + from /build/reproducible-path/relion-3.1.3/src/jaz/local_motion_fit.h:24, + from /build/reproducible-path/relion-3.1.3/src/jaz/local_motion_fit.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -4484,8 +4522,6 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 30%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/obs_model.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/obs_model.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/obs_model.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/obs_model.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/obs_model.cpp [ 31%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/parallel_ft.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/parallel_ft.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/parallel_ft.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/parallel_ft.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/parallel_ft.cpp [ 31%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/reference_map.cpp.o @@ -4496,8 +4532,6 @@ cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/resampling_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/resampling_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/resampling_helper.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/resampling_helper.cpp [ 32%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/slice_helper.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/slice_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/slice_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/slice_helper.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/slice_helper.cpp -[ 32%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/spectral_helper.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/spectral_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/spectral_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/spectral_helper.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/spectral_helper.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/jaz/obs_model.h:24, from /build/reproducible-path/relion-3.1.3/src/jaz/obs_model.cpp:21: @@ -4558,8 +4592,12 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +[ 32%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/spectral_helper.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/spectral_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/spectral_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/spectral_helper.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/spectral_helper.cpp [ 33%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/stack_helper.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/stack_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/stack_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/stack_helper.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/stack_helper.cpp +[ 33%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/structure_tensor.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/structure_tensor.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/structure_tensor.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/structure_tensor.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/structure_tensor.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/jaz/reference_map.h:24, from /build/reproducible-path/relion-3.1.3/src/jaz/reference_map.cpp:21: @@ -4614,14 +4652,12 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 33%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/structure_tensor.cpp.o /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/structure_tensor.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/structure_tensor.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/structure_tensor.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/structure_tensor.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/jaz/obs_model.h:24, from /build/reproducible-path/relion-3.1.3/src/ctf.h:50, @@ -4745,8 +4781,10 @@ 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/jaz/spectral_helper.h:24, - from /build/reproducible-path/relion-3.1.3/src/jaz/spectral_helper.cpp:21: + from /build/reproducible-path/relion-3.1.3/src/jaz/obs_model.h:24, + from /build/reproducible-path/relion-3.1.3/src/ctf.h:50, + from /build/reproducible-path/relion-3.1.3/src/jaz/stack_helper.h:24, + from /build/reproducible-path/relion-3.1.3/src/jaz/stack_helper.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -4804,19 +4842,9 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 34%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/svd_helper.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/svd_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/svd_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/svd_helper.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/svd_helper.cpp -[ 34%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/t_complex.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/t_complex.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/t_complex.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/t_complex.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/t_complex.cpp -[ 34%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/volume_converter.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/volume_converter.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/volume_converter.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/volume_converter.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/volume_converter.cpp -[ 35%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/volume_integration.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/volume_integration.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/volume_integration.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/volume_integration.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/volume_integration.cpp -[ 35%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/vtk_helper.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/vtk_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/vtk_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/vtk_helper.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/vtk_helper.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/jaz/img_proc/filter_helper.h:24, - from /build/reproducible-path/relion-3.1.3/src/jaz/structure_tensor.cpp:22: + from /build/reproducible-path/relion-3.1.3/src/jaz/spectral_helper.h:24, + from /build/reproducible-path/relion-3.1.3/src/jaz/spectral_helper.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -4874,11 +4902,11 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +[ 34%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/svd_helper.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/svd_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/svd_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/svd_helper.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/svd_helper.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/jaz/obs_model.h:24, - from /build/reproducible-path/relion-3.1.3/src/ctf.h:50, - from /build/reproducible-path/relion-3.1.3/src/jaz/stack_helper.h:24, - from /build/reproducible-path/relion-3.1.3/src/jaz/stack_helper.cpp:21: + from /build/reproducible-path/relion-3.1.3/src/jaz/img_proc/filter_helper.h:24, + from /build/reproducible-path/relion-3.1.3/src/jaz/structure_tensor.cpp:22: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -4936,15 +4964,19 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +[ 34%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/t_complex.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/t_complex.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/t_complex.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/t_complex.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/t_complex.cpp +[ 34%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/volume_converter.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/volume_converter.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/volume_converter.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/volume_converter.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/volume_converter.cpp +[ 35%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/volume_integration.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/volume_integration.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/volume_integration.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/volume_integration.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/volume_integration.cpp +[ 35%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/vtk_helper.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/vtk_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/vtk_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/vtk_helper.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/vtk_helper.cpp [ 36%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/gradient_descent.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/gradient_descent.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/optimization/gradient_descent.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/optimization/gradient_descent.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/optimization/gradient_descent.cpp -[ 36%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/lbfgs.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/lbfgs.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/optimization/lbfgs.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/optimization/lbfgs.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/optimization/lbfgs.cpp -[ 36%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/nelder_mead.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/nelder_mead.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/optimization/nelder_mead.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/optimization/nelder_mead.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/optimization/nelder_mead.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/jaz/volume_converter.h:25, - from /build/reproducible-path/relion-3.1.3/src/jaz/volume_converter.cpp:21: + from /build/reproducible-path/relion-3.1.3/src/jaz/volume_integration.h:26, + from /build/reproducible-path/relion-3.1.3/src/jaz/volume_integration.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -5002,9 +5034,11 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +[ 36%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/lbfgs.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/lbfgs.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/optimization/lbfgs.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/optimization/lbfgs.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/optimization/lbfgs.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/jaz/volume_integration.h:26, - from /build/reproducible-path/relion-3.1.3/src/jaz/volume_integration.cpp:21: + from /build/reproducible-path/relion-3.1.3/src/jaz/volume_converter.h:25, + from /build/reproducible-path/relion-3.1.3/src/jaz/volume_converter.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -5122,6 +5156,8 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +[ 36%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/nelder_mead.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/nelder_mead.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/optimization/nelder_mead.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/optimization/nelder_mead.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/optimization/nelder_mead.cpp [ 37%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/optimization.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/optimization.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/optimization/optimization.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/optimization/optimization.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/optimization/optimization.cpp [ 37%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/aberration_estimator.cpp.o @@ -5136,14 +5172,6 @@ cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/defocus_estimator.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/defocus_estimator.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/defocus_estimator.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/ctf/defocus_estimator.cpp [ 39%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/defocus_helper.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/defocus_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/defocus_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/defocus_helper.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/ctf/defocus_helper.cpp -[ 39%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/delocalisation_helper.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/delocalisation_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/delocalisation_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/delocalisation_helper.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/ctf/delocalisation_helper.cpp -[ 40%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/equation2x2.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/equation2x2.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/equation2x2.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/equation2x2.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/ctf/equation2x2.cpp -[ 40%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_estimator.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_estimator.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_estimator.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_estimator.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/ctf/magnification_estimator.cpp -[ 40%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_helper.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_helper.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/ctf/magnification_helper.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/jaz/ctf/aberration_estimator.h:4, from /build/reproducible-path/relion-3.1.3/src/jaz/ctf/aberration_estimator.cpp:1: @@ -5204,8 +5232,8 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 41%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/modular_ctf_optimisation.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/modular_ctf_optimisation.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/modular_ctf_optimisation.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/modular_ctf_optimisation.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/ctf/modular_ctf_optimisation.cpp +[ 39%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/delocalisation_helper.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/delocalisation_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/delocalisation_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/delocalisation_helper.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/ctf/delocalisation_helper.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/jaz/ctf/bfactor_refiner.h:4, from /build/reproducible-path/relion-3.1.3/src/jaz/ctf/bfactor_refiner.cpp:1: @@ -5242,10 +5270,17 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 41%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_estimator.cpp.o /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ +In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, + from /build/reproducible-path/relion-3.1.3/src/jaz/obs_model.h:24, + from /build/reproducible-path/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, + from /build/reproducible-path/relion-3.1.3/src/jaz/ctf/ctf_refiner.cpp:21: +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 43 | uint32 width, length; // apparent dimensions in the file + | ^~~~~ /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ @@ -5267,15 +5302,6 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_estimator.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_estimator.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_estimator.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/ctf/tilt_estimator.cpp -In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/jaz/obs_model.h:24, - from /build/reproducible-path/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, - from /build/reproducible-path/relion-3.1.3/src/jaz/ctf/ctf_refiner.cpp:21: -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] - 43 | uint32 width, length; // apparent dimensions in the file - | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here @@ -5330,8 +5356,10 @@ 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/jaz/ctf/defocus_estimator.h:24, - from /build/reproducible-path/relion-3.1.3/src/jaz/ctf/defocus_estimator.cpp:21: + from /build/reproducible-path/relion-3.1.3/src/jaz/obs_model.h:24, + from /build/reproducible-path/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, + from /build/reproducible-path/relion-3.1.3/src/jaz/ctf/ctf_refiner_mpi.h:26, + from /build/reproducible-path/relion-3.1.3/src/jaz/ctf/ctf_refiner_mpi.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -5389,11 +5417,13 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +[ 40%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/equation2x2.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/equation2x2.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/equation2x2.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/equation2x2.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/ctf/equation2x2.cpp +[ 40%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_estimator.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_estimator.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_estimator.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_estimator.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/ctf/magnification_estimator.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/jaz/obs_model.h:24, - from /build/reproducible-path/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, - from /build/reproducible-path/relion-3.1.3/src/jaz/ctf/ctf_refiner_mpi.h:26, - from /build/reproducible-path/relion-3.1.3/src/jaz/ctf/ctf_refiner_mpi.cpp:21: + from /build/reproducible-path/relion-3.1.3/src/jaz/ctf/defocus_estimator.h:24, + from /build/reproducible-path/relion-3.1.3/src/jaz/ctf/defocus_estimator.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -5513,6 +5543,10 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +[ 40%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_helper.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_helper.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/ctf/magnification_helper.cpp +[ 41%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/modular_ctf_optimisation.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/modular_ctf_optimisation.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/modular_ctf_optimisation.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/modular_ctf_optimisation.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/ctf/modular_ctf_optimisation.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/jaz/obs_model.h:24, from /build/reproducible-path/relion-3.1.3/src/ctf.h:50, @@ -5575,6 +5609,8 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +[ 41%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_estimator.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_estimator.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_estimator.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_estimator.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/ctf/tilt_estimator.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/jaz/ctf/magnification_estimator.h:28, from /build/reproducible-path/relion-3.1.3/src/jaz/ctf/magnification_estimator.cpp:21: @@ -5637,10 +5673,6 @@ | ^~~~~~ [ 42%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_helper.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_helper.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/ctf/tilt_helper.cpp -[ 42%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/alignment_set.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/alignment_set.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/alignment_set.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/alignment_set.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/motion/alignment_set.cpp -[ 42%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/frame_recombiner.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/frame_recombiner.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/frame_recombiner.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/frame_recombiner.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/motion/frame_recombiner.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/jaz/obs_model.h:24, from /build/reproducible-path/relion-3.1.3/src/ctf.h:50, @@ -5703,13 +5735,13 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 43%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/gp_motion_fit.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/gp_motion_fit.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/gp_motion_fit.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/gp_motion_fit.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/motion/gp_motion_fit.cpp -[ 43%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_estimator.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_estimator.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/motion_estimator.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/motion_estimator.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/motion/motion_estimator.cpp +[ 42%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/alignment_set.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/alignment_set.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/alignment_set.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/alignment_set.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/motion/alignment_set.cpp +[ 42%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/frame_recombiner.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/frame_recombiner.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/frame_recombiner.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/frame_recombiner.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/motion/frame_recombiner.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/jaz/ctf/tilt_estimator.h:24, - from /build/reproducible-path/relion-3.1.3/src/jaz/ctf/tilt_estimator.cpp:21: + from /build/reproducible-path/relion-3.1.3/src/jaz/ctf/modular_ctf_optimisation.h:5, + from /build/reproducible-path/relion-3.1.3/src/jaz/ctf/modular_ctf_optimisation.cpp:1: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -5758,27 +5790,29 @@ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ +/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 186 | uint16 cur_sampleFormat, cur_bitsPerSample; + | ^~~~~~~~~~~~~~~~~ +/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ +[ 43%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/gp_motion_fit.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/gp_motion_fit.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/gp_motion_fit.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/gp_motion_fit.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/motion/gp_motion_fit.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/jaz/ctf/modular_ctf_optimisation.h:5, - from /build/reproducible-path/relion-3.1.3/src/jaz/ctf/modular_ctf_optimisation.cpp:1: + from /build/reproducible-path/relion-3.1.3/src/jaz/ctf/tilt_estimator.h:24, + from /build/reproducible-path/relion-3.1.3/src/jaz/ctf/tilt_estimator.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ -/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 186 | uint16 cur_sampleFormat, cur_bitsPerSample; - | ^~~~~~~~~~~~~~~~~ -/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ @@ -5828,10 +5862,8 @@ 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/jaz/obs_model.h:24, - from /build/reproducible-path/relion-3.1.3/src/ctf.h:50, - from /build/reproducible-path/relion-3.1.3/src/jaz/ctf/tilt_helper.h:24, - from /build/reproducible-path/relion-3.1.3/src/jaz/ctf/tilt_helper.cpp:21: + from /build/reproducible-path/relion-3.1.3/src/jaz/motion/frame_recombiner.h:24, + from /build/reproducible-path/relion-3.1.3/src/jaz/motion/frame_recombiner.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -5889,13 +5921,13 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 43%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_helper.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/motion_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/motion_helper.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/motion/motion_helper.cpp -[ 44%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_param_estimator.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_param_estimator.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/motion_param_estimator.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/motion_param_estimator.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/motion/motion_param_estimator.cpp +[ 43%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_estimator.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_estimator.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/motion_estimator.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/motion_estimator.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/motion/motion_estimator.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/jaz/motion/frame_recombiner.h:24, - from /build/reproducible-path/relion-3.1.3/src/jaz/motion/frame_recombiner.cpp:21: + from /build/reproducible-path/relion-3.1.3/src/jaz/obs_model.h:24, + from /build/reproducible-path/relion-3.1.3/src/ctf.h:50, + from /build/reproducible-path/relion-3.1.3/src/jaz/ctf/tilt_helper.h:24, + from /build/reproducible-path/relion-3.1.3/src/jaz/ctf/tilt_helper.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -5954,8 +5986,8 @@ 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/jaz/motion/motion_estimator.h:24, - from /build/reproducible-path/relion-3.1.3/src/jaz/motion/motion_estimator.cpp:21: + from /build/reproducible-path/relion-3.1.3/src/jaz/motion/gp_motion_fit.h:24, + from /build/reproducible-path/relion-3.1.3/src/jaz/motion/gp_motion_fit.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -5989,9 +6021,39 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 185 | uint32 cur_width, cur_length; + | ^~~~~~~~~ +/usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here + 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 185 | uint32 cur_width, cur_length; + | ^~~~~~~~~~ +/usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here + 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 186 | uint16 cur_sampleFormat, cur_bitsPerSample; + | ^~~~~~~~~~~~~~~~ +/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 186 | uint16 cur_sampleFormat, cur_bitsPerSample; + | ^~~~~~~~~~~~~~~~~ +/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ +[ 43%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_helper.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/motion_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/motion_helper.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/motion/motion_helper.cpp +[ 44%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_param_estimator.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_param_estimator.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/motion_param_estimator.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/motion_param_estimator.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/motion/motion_param_estimator.cpp +[ 44%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/motion/motion_refiner.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/jaz/motion/gp_motion_fit.h:24, - from /build/reproducible-path/relion-3.1.3/src/jaz/motion/gp_motion_fit.cpp:21: + from /build/reproducible-path/relion-3.1.3/src/jaz/motion/motion_estimator.h:24, + from /build/reproducible-path/relion-3.1.3/src/jaz/motion/motion_estimator.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -6031,33 +6093,9 @@ /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] - 185 | uint32 cur_width, cur_length; - | ^~~~~~~~~ -/usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here - 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] - 185 | uint32 cur_width, cur_length; - | ^~~~~~~~~~ -/usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here - 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 186 | uint16 cur_sampleFormat, cur_bitsPerSample; - | ^~~~~~~~~~~~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ -/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 186 | uint16 cur_sampleFormat, cur_bitsPerSample; - | ^~~~~~~~~~~~~~~~~ -/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ @@ -6073,10 +6111,6 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 44%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/motion/motion_refiner.cpp -[ 45%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner_mpi.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner_mpi.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/motion/motion_refiner_mpi.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/jaz/obs_model.h:24, from /build/reproducible-path/relion-3.1.3/src/ctf.h:50, @@ -6139,12 +6173,8 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 45%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/three_hyperparameter_fit.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/three_hyperparameter_fit.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/three_hyperparameter_fit.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/three_hyperparameter_fit.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/motion/three_hyperparameter_fit.cpp -[ 45%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/two_hyperparameter_fit.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/two_hyperparameter_fit.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/two_hyperparameter_fit.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/two_hyperparameter_fit.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/motion/two_hyperparameter_fit.cpp -[ 46%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/math/Zernike.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/math/Zernike.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/math/Zernike.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/math/Zernike.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/math/Zernike.cpp +[ 45%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner_mpi.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner_mpi.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/motion/motion_refiner_mpi.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/jaz/motion/alignment_set.h:24, from /build/reproducible-path/relion-3.1.3/src/jaz/motion/motion_param_estimator.h:24, @@ -6206,6 +6236,14 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +[ 45%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/three_hyperparameter_fit.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/three_hyperparameter_fit.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/three_hyperparameter_fit.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/three_hyperparameter_fit.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/motion/three_hyperparameter_fit.cpp +[ 45%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/two_hyperparameter_fit.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/two_hyperparameter_fit.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/two_hyperparameter_fit.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/two_hyperparameter_fit.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/motion/two_hyperparameter_fit.cpp +[ 46%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/math/Zernike.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/math/Zernike.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/math/Zernike.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/math/Zernike.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/math/Zernike.cpp +[ 46%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/img_proc/color_helper.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/img_proc/color_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/img_proc/color_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/img_proc/color_helper.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/img_proc/color_helper.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/jaz/obs_model.h:24, from /build/reproducible-path/relion-3.1.3/src/ctf.h:50, @@ -6268,16 +6306,10 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 46%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/img_proc/color_helper.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/img_proc/color_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/img_proc/color_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/img_proc/color_helper.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/img_proc/color_helper.cpp -[ 46%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/img_proc/filter_helper.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/img_proc/filter_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/img_proc/filter_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/img_proc/filter_helper.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/img_proc/filter_helper.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/jaz/obs_model.h:24, - from /build/reproducible-path/relion-3.1.3/src/ctf.h:50, - from /build/reproducible-path/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, - from /build/reproducible-path/relion-3.1.3/src/jaz/motion/motion_refiner_mpi.h:27, - from /build/reproducible-path/relion-3.1.3/src/jaz/motion/motion_refiner_mpi.cpp:21: + from /build/reproducible-path/relion-3.1.3/src/jaz/motion/alignment_set.h:24, + from /build/reproducible-path/relion-3.1.3/src/jaz/motion/motion_param_estimator.h:24, + from /build/reproducible-path/relion-3.1.3/src/jaz/motion/three_hyperparameter_fit.cpp:22: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -6335,12 +6367,10 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 47%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/img_proc/image_op.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/img_proc/image_op.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/img_proc/image_op.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/img_proc/image_op.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/img_proc/image_op.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/jaz/motion/alignment_set.h:24, from /build/reproducible-path/relion-3.1.3/src/jaz/motion/motion_param_estimator.h:24, - from /build/reproducible-path/relion-3.1.3/src/jaz/motion/three_hyperparameter_fit.cpp:22: + from /build/reproducible-path/relion-3.1.3/src/jaz/motion/two_hyperparameter_fit.cpp:22: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -6398,10 +6428,18 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +[ 46%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/img_proc/filter_helper.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/img_proc/filter_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/img_proc/filter_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/img_proc/filter_helper.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/img_proc/filter_helper.cpp +[ 47%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/img_proc/image_op.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/img_proc/image_op.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/img_proc/image_op.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/img_proc/image_op.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/img_proc/image_op.cpp +[ 47%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/backprojection_helper.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/backprojection_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/tomo/backprojection_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/tomo/backprojection_helper.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/tomo/backprojection_helper.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/jaz/motion/alignment_set.h:24, - from /build/reproducible-path/relion-3.1.3/src/jaz/motion/motion_param_estimator.h:24, - from /build/reproducible-path/relion-3.1.3/src/jaz/motion/two_hyperparameter_fit.cpp:22: + from /build/reproducible-path/relion-3.1.3/src/jaz/obs_model.h:24, + from /build/reproducible-path/relion-3.1.3/src/ctf.h:50, + from /build/reproducible-path/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, + from /build/reproducible-path/relion-3.1.3/src/jaz/motion/motion_refiner_mpi.h:27, + from /build/reproducible-path/relion-3.1.3/src/jaz/motion/motion_refiner_mpi.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -6459,21 +6497,11 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 47%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/backprojection_helper.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/backprojection_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/tomo/backprojection_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/tomo/backprojection_helper.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/tomo/backprojection_helper.cpp [ 48%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/imod_helper.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/imod_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/tomo/imod_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/tomo/imod_helper.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/tomo/imod_helper.cpp -[ 48%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/projection_helper.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/projection_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/tomo/projection_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/tomo/projection_helper.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/tomo/projection_helper.cpp -[ 48%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/tomo_stack.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/tomo_stack.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/tomo/tomo_stack.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/tomo/tomo_stack.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/tomo/tomo_stack.cpp -[ 49%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/io/star_converter.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/io/star_converter.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/io/star_converter.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/io/star_converter.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/io/star_converter.cpp -[ 49%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyev2.c.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyev2.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyev2.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyev2.c.o -c /build/reproducible-path/relion-3.1.3/src/jaz/d3x3/dsyev2.c In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/jaz/img_proc/color_helper.h:5, - from /build/reproducible-path/relion-3.1.3/src/jaz/img_proc/color_helper.cpp:1: + from /build/reproducible-path/relion-3.1.3/src/jaz/tomo/backprojection_helper.h:24, + from /build/reproducible-path/relion-3.1.3/src/jaz/tomo/backprojection_helper.cpp:23: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -6531,11 +6559,9 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 50%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevc3.c.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevc3.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevc3.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevc3.c.o -c /build/reproducible-path/relion-3.1.3/src/jaz/d3x3/dsyevc3.c In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/jaz/img_proc/filter_helper.h:24, - from /build/reproducible-path/relion-3.1.3/src/jaz/img_proc/filter_helper.cpp:21: + from /build/reproducible-path/relion-3.1.3/src/jaz/img_proc/color_helper.h:5, + from /build/reproducible-path/relion-3.1.3/src/jaz/img_proc/color_helper.cpp:1: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -6593,25 +6619,11 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 50%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevd3.c.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevd3.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevd3.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevd3.c.o -c /build/reproducible-path/relion-3.1.3/src/jaz/d3x3/dsyevd3.c -[ 50%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevh3.c.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevh3.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevh3.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevh3.c.o -c /build/reproducible-path/relion-3.1.3/src/jaz/d3x3/dsyevh3.c -[ 51%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevj3.c.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevj3.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevj3.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevj3.c.o -c /build/reproducible-path/relion-3.1.3/src/jaz/d3x3/dsyevj3.c -[ 51%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevq3.c.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevq3.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevq3.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevq3.c.o -c /build/reproducible-path/relion-3.1.3/src/jaz/d3x3/dsyevq3.c -[ 51%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevv3.c.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevv3.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevv3.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevv3.c.o -c /build/reproducible-path/relion-3.1.3/src/jaz/d3x3/dsyevv3.c -[ 52%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsytrd3.c.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsytrd3.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsytrd3.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsytrd3.c.o -c /build/reproducible-path/relion-3.1.3/src/jaz/d3x3/dsytrd3.c -[ 52%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/slvsec3.c.o -[ 53%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/lbfgs/lbfgs.c.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/slvsec3.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/slvsec3.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/slvsec3.c.o -c /build/reproducible-path/relion-3.1.3/src/jaz/d3x3/slvsec3.c -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/lbfgs/lbfgs.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/lbfgs/lbfgs.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/lbfgs/lbfgs.c.o -c /build/reproducible-path/relion-3.1.3/src/jaz/lbfgs/lbfgs.c +[ 48%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/projection_helper.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/projection_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/tomo/projection_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/tomo/projection_helper.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/tomo/projection_helper.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/jaz/tomo/tomo_stack.h:25, - from /build/reproducible-path/relion-3.1.3/src/jaz/tomo/tomo_stack.cpp:21: + from /build/reproducible-path/relion-3.1.3/src/jaz/img_proc/filter_helper.h:24, + from /build/reproducible-path/relion-3.1.3/src/jaz/img_proc/filter_helper.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -6669,9 +6681,33 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +[ 48%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/tomo_stack.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/tomo_stack.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/tomo/tomo_stack.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/tomo/tomo_stack.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/tomo/tomo_stack.cpp +[ 49%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/io/star_converter.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/io/star_converter.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/io/star_converter.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/io/star_converter.cpp.o -c /build/reproducible-path/relion-3.1.3/src/jaz/io/star_converter.cpp +[ 49%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyev2.c.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyev2.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyev2.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyev2.c.o -c /build/reproducible-path/relion-3.1.3/src/jaz/d3x3/dsyev2.c +[ 50%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevc3.c.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevc3.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevc3.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevc3.c.o -c /build/reproducible-path/relion-3.1.3/src/jaz/d3x3/dsyevc3.c +[ 50%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevd3.c.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevd3.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevd3.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevd3.c.o -c /build/reproducible-path/relion-3.1.3/src/jaz/d3x3/dsyevd3.c +[ 50%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevh3.c.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevh3.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevh3.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevh3.c.o -c /build/reproducible-path/relion-3.1.3/src/jaz/d3x3/dsyevh3.c +[ 51%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevj3.c.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevj3.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevj3.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevj3.c.o -c /build/reproducible-path/relion-3.1.3/src/jaz/d3x3/dsyevj3.c +[ 51%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevq3.c.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevq3.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevq3.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevq3.c.o -c /build/reproducible-path/relion-3.1.3/src/jaz/d3x3/dsyevq3.c +[ 51%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevv3.c.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevv3.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevv3.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevv3.c.o -c /build/reproducible-path/relion-3.1.3/src/jaz/d3x3/dsyevv3.c +[ 52%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsytrd3.c.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsytrd3.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsytrd3.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsytrd3.c.o -c /build/reproducible-path/relion-3.1.3/src/jaz/d3x3/dsytrd3.c +[ 52%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/slvsec3.c.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/slvsec3.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/slvsec3.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/slvsec3.c.o -c /build/reproducible-path/relion-3.1.3/src/jaz/d3x3/slvsec3.c +[ 53%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/lbfgs/lbfgs.c.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/lbfgs/lbfgs.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/lbfgs/lbfgs.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/lbfgs/lbfgs.c.o -c /build/reproducible-path/relion-3.1.3/src/jaz/lbfgs/lbfgs.c In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/jaz/tomo/backprojection_helper.h:24, - from /build/reproducible-path/relion-3.1.3/src/jaz/tomo/backprojection_helper.cpp:23: + from /build/reproducible-path/relion-3.1.3/src/jaz/tomo/tomo_stack.h:25, + from /build/reproducible-path/relion-3.1.3/src/jaz/tomo/tomo_stack.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -6801,329 +6837,153 @@ /usr/bin/make -f src/apps/CMakeFiles/autopick.dir/build.make src/apps/CMakeFiles/autopick.dir/depend /usr/bin/make -f src/apps/CMakeFiles/autopick_mpi.dir/build.make src/apps/CMakeFiles/autopick_mpi.dir/depend /usr/bin/make -f src/apps/CMakeFiles/convert_star.dir/build.make src/apps/CMakeFiles/convert_star.dir/depend +/usr/bin/make -f src/apps/CMakeFiles/convert_to_tiff.dir/build.make src/apps/CMakeFiles/convert_to_tiff.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/relion_gui_lib.dir/DependInfo.cmake "--color=" -/usr/bin/make -f src/apps/CMakeFiles/convert_to_tiff.dir/build.make src/apps/CMakeFiles/convert_to_tiff.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/align_symmetry.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/autopick.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/apps/CMakeFiles/convert_to_tiff_mpi.dir/build.make src/apps/CMakeFiles/convert_to_tiff_mpi.dir/depend -/usr/bin/make -f src/apps/CMakeFiles/ctf_mask_test.dir/build.make src/apps/CMakeFiles/ctf_mask_test.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/autopick_mpi.dir/DependInfo.cmake "--color=" +/usr/bin/make -f src/apps/CMakeFiles/ctf_mask_test.dir/build.make src/apps/CMakeFiles/ctf_mask_test.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/ctf_refine.dir/build.make src/apps/CMakeFiles/ctf_refine.dir/depend cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/convert_star.dir/DependInfo.cmake "--color=" +/usr/bin/make -f src/apps/CMakeFiles/ctf_refine.dir/build.make src/apps/CMakeFiles/ctf_refine.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/convert_to_tiff.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/apps/CMakeFiles/ctf_refine_mpi.dir/build.make src/apps/CMakeFiles/ctf_refine_mpi.dir/depend +/usr/bin/make -f src/apps/CMakeFiles/ctf_toolbox.dir/build.make src/apps/CMakeFiles/ctf_toolbox.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/convert_to_tiff_mpi.dir/DependInfo.cmake "--color=" -/usr/bin/make -f src/apps/CMakeFiles/ctf_toolbox.dir/build.make src/apps/CMakeFiles/ctf_toolbox.dir/depend /usr/bin/make -f src/apps/CMakeFiles/demodulate.dir/build.make src/apps/CMakeFiles/demodulate.dir/depend +/usr/bin/make -f src/apps/CMakeFiles/estimate_gain.dir/build.make src/apps/CMakeFiles/estimate_gain.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/ctf_mask_test.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/ctf_refine.dir/DependInfo.cmake "--color=" -/usr/bin/make -f src/apps/CMakeFiles/estimate_gain.dir/build.make src/apps/CMakeFiles/estimate_gain.dir/depend -make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' -cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/ctf_refine_mpi.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/apps/CMakeFiles/external_reconstruct.dir/build.make src/apps/CMakeFiles/external_reconstruct.dir/depend -make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' -cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/ctf_toolbox.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/apps/CMakeFiles/find_tiltpairs.dir/build.make src/apps/CMakeFiles/find_tiltpairs.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' +cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/ctf_refine_mpi.dir/DependInfo.cmake "--color=" +make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/demodulate.dir/DependInfo.cmake "--color=" -/usr/bin/make -f src/apps/CMakeFiles/flex_analyse.dir/build.make src/apps/CMakeFiles/flex_analyse.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/estimate_gain.dir/DependInfo.cmake "--color=" -/usr/bin/make -f src/apps/CMakeFiles/flex_analyse_mpi.dir/build.make src/apps/CMakeFiles/flex_analyse_mpi.dir/depend +make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' +cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/ctf_toolbox.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/external_reconstruct.dir/DependInfo.cmake "--color=" -/usr/bin/make -f src/apps/CMakeFiles/helix_inimodel2d.dir/build.make src/apps/CMakeFiles/helix_inimodel2d.dir/depend +/usr/bin/make -f src/apps/CMakeFiles/flex_analyse.dir/build.make src/apps/CMakeFiles/flex_analyse.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/find_tiltpairs.dir/DependInfo.cmake "--color=" -/usr/bin/make -f src/apps/CMakeFiles/helix_toolbox.dir/build.make src/apps/CMakeFiles/helix_toolbox.dir/depend -make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' -cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/flex_analyse.dir/DependInfo.cmake "--color=" -/usr/bin/make -f src/apps/CMakeFiles/image_handler.dir/build.make src/apps/CMakeFiles/image_handler.dir/depend +/usr/bin/make -f src/apps/CMakeFiles/flex_analyse_mpi.dir/build.make src/apps/CMakeFiles/flex_analyse_mpi.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/flex_analyse_mpi.dir/DependInfo.cmake "--color=" -/usr/bin/make -f src/apps/CMakeFiles/import.dir/build.make src/apps/CMakeFiles/import.dir/depend -make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' -cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/helix_inimodel2d.dir/DependInfo.cmake "--color=" -/usr/bin/make -f src/apps/CMakeFiles/localsym.dir/build.make src/apps/CMakeFiles/localsym.dir/depend -make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' -cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/helix_toolbox.dir/DependInfo.cmake "--color=" -/usr/bin/make -f src/apps/CMakeFiles/localsym_mpi.dir/build.make src/apps/CMakeFiles/localsym_mpi.dir/depend -make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' -cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/image_handler.dir/DependInfo.cmake "--color=" -/usr/bin/make -f src/apps/CMakeFiles/mask_create.dir/build.make src/apps/CMakeFiles/mask_create.dir/depend -make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' -cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/import.dir/DependInfo.cmake "--color=" -/usr/bin/make -f src/apps/CMakeFiles/merge_particles.dir/build.make src/apps/CMakeFiles/merge_particles.dir/depend -make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' -cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/localsym.dir/DependInfo.cmake "--color=" -/usr/bin/make -f src/apps/CMakeFiles/motion_refine.dir/build.make src/apps/CMakeFiles/motion_refine.dir/depend -/usr/bin/make -f src/apps/CMakeFiles/motion_refine_mpi.dir/build.make src/apps/CMakeFiles/motion_refine_mpi.dir/depend -make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' -cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/localsym_mpi.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' -cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/mask_create.dir/DependInfo.cmake "--color=" -/usr/bin/make -f src/apps/CMakeFiles/mrc2vtk.dir/build.make src/apps/CMakeFiles/mrc2vtk.dir/depend -make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' -make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' -cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/merge_particles.dir/DependInfo.cmake "--color=" -cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/motion_refine.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' -cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/motion_refine_mpi.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/particle_FCC.dir/build.make src/apps/CMakeFiles/particle_FCC.dir/depend -cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/mrc2vtk.dir/DependInfo.cmake "--color=" -/usr/bin/make -f src/apps/CMakeFiles/particle_reposition.dir/build.make src/apps/CMakeFiles/particle_reposition.dir/depend -/usr/bin/make -f src/apps/CMakeFiles/particle_select.dir/build.make src/apps/CMakeFiles/particle_select.dir/depend -/usr/bin/make -f src/apps/CMakeFiles/particle_subtract.dir/build.make src/apps/CMakeFiles/particle_subtract.dir/depend -/usr/bin/make -f src/apps/CMakeFiles/particle_subtract_mpi.dir/build.make src/apps/CMakeFiles/particle_subtract_mpi.dir/depend -make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' -cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/particle_FCC.dir/DependInfo.cmake "--color=" -/usr/bin/make -f src/apps/CMakeFiles/particle_symmetry_expand.dir/build.make src/apps/CMakeFiles/particle_symmetry_expand.dir/depend -make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' -cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/particle_reposition.dir/DependInfo.cmake "--color=" -/usr/bin/make -f src/apps/CMakeFiles/pipeliner.dir/build.make src/apps/CMakeFiles/pipeliner.dir/depend -make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/plot_delocalisation.dir/build.make src/apps/CMakeFiles/plot_delocalisation.dir/depend -cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/particle_select.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' -cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/particle_subtract.dir/DependInfo.cmake "--color=" -/usr/bin/make -f src/apps/CMakeFiles/postprocess.dir/build.make src/apps/CMakeFiles/postprocess.dir/depend -make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' -cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/particle_subtract_mpi.dir/DependInfo.cmake "--color=" -/usr/bin/make -f src/apps/CMakeFiles/postprocess_mpi.dir/build.make src/apps/CMakeFiles/postprocess_mpi.dir/depend -make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' -cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/particle_symmetry_expand.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' -cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/pipeliner.dir/DependInfo.cmake "--color=" -/usr/bin/make -f src/apps/CMakeFiles/prepare_subtomo.dir/build.make src/apps/CMakeFiles/prepare_subtomo.dir/depend -make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' -cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/plot_delocalisation.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' -cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/postprocess.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' -cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/postprocess_mpi.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' +/usr/bin/make -f src/apps/CMakeFiles/helix_inimodel2d.dir/build.make src/apps/CMakeFiles/helix_inimodel2d.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' -cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/prepare_subtomo.dir/DependInfo.cmake "--color=" -/usr/bin/make -f src/apps/CMakeFiles/relion_gui_lib.dir/build.make src/apps/CMakeFiles/relion_gui_lib.dir/build -make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' +cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/flex_analyse.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/align_symmetry.dir/build.make src/apps/CMakeFiles/align_symmetry.dir/build make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/autopick.dir/build.make src/apps/CMakeFiles/autopick.dir/build make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' /usr/bin/make -f src/apps/CMakeFiles/autopick_mpi.dir/build.make src/apps/CMakeFiles/autopick_mpi.dir/build -make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/convert_star.dir/build.make src/apps/CMakeFiles/convert_star.dir/build -make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' -make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/convert_to_tiff.dir/build.make src/apps/CMakeFiles/convert_to_tiff.dir/build make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/convert_to_tiff_mpi.dir/build.make src/apps/CMakeFiles/convert_to_tiff_mpi.dir/build +cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/helix_inimodel2d.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' +/usr/bin/make -f src/apps/CMakeFiles/relion_gui_lib.dir/build.make src/apps/CMakeFiles/relion_gui_lib.dir/build make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/ctf_mask_test.dir/build.make src/apps/CMakeFiles/ctf_mask_test.dir/build -/usr/bin/make -f src/apps/CMakeFiles/ctf_refine.dir/build.make src/apps/CMakeFiles/ctf_refine.dir/build make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/ctf_refine_mpi.dir/build.make src/apps/CMakeFiles/ctf_refine_mpi.dir/build make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/ctf_toolbox.dir/build.make src/apps/CMakeFiles/ctf_toolbox.dir/build -/usr/bin/make -f src/apps/CMakeFiles/demodulate.dir/build.make src/apps/CMakeFiles/demodulate.dir/build -make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' -make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/estimate_gain.dir/build.make src/apps/CMakeFiles/estimate_gain.dir/build -make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/external_reconstruct.dir/build.make src/apps/CMakeFiles/external_reconstruct.dir/build make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/find_tiltpairs.dir/build.make src/apps/CMakeFiles/find_tiltpairs.dir/build +/usr/bin/make -f src/apps/CMakeFiles/align_symmetry.dir/build.make src/apps/CMakeFiles/align_symmetry.dir/build make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/flex_analyse.dir/build.make src/apps/CMakeFiles/flex_analyse.dir/build make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/flex_analyse_mpi.dir/build.make src/apps/CMakeFiles/flex_analyse_mpi.dir/build +/usr/bin/make -f src/apps/CMakeFiles/autopick.dir/build.make src/apps/CMakeFiles/autopick.dir/build make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/helix_inimodel2d.dir/build.make src/apps/CMakeFiles/helix_inimodel2d.dir/build -/usr/bin/make -f src/apps/CMakeFiles/helix_toolbox.dir/build.make src/apps/CMakeFiles/helix_toolbox.dir/build -make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' -make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' -make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' -make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' +/usr/bin/make -f src/apps/CMakeFiles/convert_star.dir/build.make src/apps/CMakeFiles/convert_star.dir/build make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' +/usr/bin/make -f src/apps/CMakeFiles/convert_to_tiff.dir/build.make src/apps/CMakeFiles/convert_to_tiff.dir/build make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/image_handler.dir/build.make src/apps/CMakeFiles/image_handler.dir/build -/usr/bin/make -f src/apps/CMakeFiles/import.dir/build.make src/apps/CMakeFiles/import.dir/build -make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/motion_refine.dir/build.make src/apps/CMakeFiles/motion_refine.dir/build -make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/mask_create.dir/build.make src/apps/CMakeFiles/mask_create.dir/build -make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/localsym.dir/build.make src/apps/CMakeFiles/localsym.dir/build +/usr/bin/make -f src/apps/CMakeFiles/convert_to_tiff_mpi.dir/build.make src/apps/CMakeFiles/convert_to_tiff_mpi.dir/build make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/merge_particles.dir/build.make src/apps/CMakeFiles/merge_particles.dir/build +[ 53%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/gui_jobwindow.cpp.o make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' +/usr/bin/make -f src/apps/CMakeFiles/ctf_mask_test.dir/build.make src/apps/CMakeFiles/ctf_mask_test.dir/build +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_gui_lib.dir/__/gui_jobwindow.cpp.o -MF CMakeFiles/relion_gui_lib.dir/__/gui_jobwindow.cpp.o.d -o CMakeFiles/relion_gui_lib.dir/__/gui_jobwindow.cpp.o -c /build/reproducible-path/relion-3.1.3/src/gui_jobwindow.cpp +/usr/bin/make -f src/apps/CMakeFiles/ctf_refine.dir/build.make src/apps/CMakeFiles/ctf_refine.dir/build make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' +/usr/bin/make -f src/apps/CMakeFiles/ctf_refine_mpi.dir/build.make src/apps/CMakeFiles/ctf_refine_mpi.dir/build make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/localsym_mpi.dir/build.make src/apps/CMakeFiles/localsym_mpi.dir/build -make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/motion_refine_mpi.dir/build.make src/apps/CMakeFiles/motion_refine_mpi.dir/build make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/mrc2vtk.dir/build.make src/apps/CMakeFiles/mrc2vtk.dir/build -make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' -make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' +/usr/bin/make -f src/apps/CMakeFiles/ctf_toolbox.dir/build.make src/apps/CMakeFiles/ctf_toolbox.dir/build make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' -[ 54%] Building CXX object src/apps/CMakeFiles/autopick.dir/autopick.cpp.o -make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' +[ 54%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/gui_entries.cpp.o +[ 54%] Building CXX object src/apps/CMakeFiles/autopick_mpi.dir/autopick_mpi.cpp.o +/usr/bin/make -f src/apps/CMakeFiles/demodulate.dir/build.make src/apps/CMakeFiles/demodulate.dir/build make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_gui_lib.dir/__/gui_entries.cpp.o -MF CMakeFiles/relion_gui_lib.dir/__/gui_entries.cpp.o.d -o CMakeFiles/relion_gui_lib.dir/__/gui_entries.cpp.o -c /build/reproducible-path/relion-3.1.3/src/gui_entries.cpp +[ 54%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/displayer.cpp.o make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/particle_FCC.dir/build.make src/apps/CMakeFiles/particle_FCC.dir/build -make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/particle_reposition.dir/build.make src/apps/CMakeFiles/particle_reposition.dir/build -/usr/bin/make -f src/apps/CMakeFiles/particle_subtract_mpi.dir/build.make src/apps/CMakeFiles/particle_subtract_mpi.dir/build -/usr/bin/make -f src/apps/CMakeFiles/particle_symmetry_expand.dir/build.make src/apps/CMakeFiles/particle_symmetry_expand.dir/build -make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/autopick_mpi.dir/autopick_mpi.cpp.o -MF CMakeFiles/autopick_mpi.dir/autopick_mpi.cpp.o.d -o CMakeFiles/autopick_mpi.dir/autopick_mpi.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/autopick_mpi.cpp +[ 55%] Building CXX object src/apps/CMakeFiles/autopick.dir/autopick.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_gui_lib.dir/__/displayer.cpp.o -MF CMakeFiles/relion_gui_lib.dir/__/displayer.cpp.o.d -o CMakeFiles/relion_gui_lib.dir/__/displayer.cpp.o -c /build/reproducible-path/relion-3.1.3/src/displayer.cpp +[ 55%] Building CXX object src/apps/CMakeFiles/align_symmetry.dir/align_symmetry.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/autopick.dir/autopick.cpp.o -MF CMakeFiles/autopick.dir/autopick.cpp.o.d -o CMakeFiles/autopick.dir/autopick.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/autopick.cpp -make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/particle_subtract.dir/build.make src/apps/CMakeFiles/particle_subtract.dir/build -/usr/bin/make -f src/apps/CMakeFiles/plot_delocalisation.dir/build.make src/apps/CMakeFiles/plot_delocalisation.dir/build -make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' -[ 54%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/displayer.cpp.o -/usr/bin/make -f src/apps/CMakeFiles/postprocess.dir/build.make src/apps/CMakeFiles/postprocess.dir/build -make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/align_symmetry.dir/align_symmetry.cpp.o -MF CMakeFiles/align_symmetry.dir/align_symmetry.cpp.o.d -o CMakeFiles/align_symmetry.dir/align_symmetry.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/align_symmetry.cpp [ 55%] Building CXX object src/apps/CMakeFiles/convert_star.dir/convert_star.cpp.o -make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -[ 55%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/gui_entries.cpp.o -[ 55%] Building CXX object src/apps/CMakeFiles/autopick_mpi.dir/autopick_mpi.cpp.o -make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' -make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' [ 55%] Building CXX object src/apps/CMakeFiles/convert_to_tiff.dir/convert_to_tiff.cpp.o -[ 55%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/gui_jobwindow.cpp.o -make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/particle_select.dir/build.make src/apps/CMakeFiles/particle_select.dir/build -/usr/bin/make -f src/apps/CMakeFiles/pipeliner.dir/build.make src/apps/CMakeFiles/pipeliner.dir/build -make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' -make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/postprocess_mpi.dir/build.make src/apps/CMakeFiles/postprocess_mpi.dir/build -[ 55%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/gui_mainwindow.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/autopick_mpi.dir/autopick_mpi.cpp.o -MF CMakeFiles/autopick_mpi.dir/autopick_mpi.cpp.o.d -o CMakeFiles/autopick_mpi.dir/autopick_mpi.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/autopick_mpi.cpp +/usr/bin/make -f src/apps/CMakeFiles/estimate_gain.dir/build.make src/apps/CMakeFiles/estimate_gain.dir/build +/usr/bin/make -f src/apps/CMakeFiles/external_reconstruct.dir/build.make src/apps/CMakeFiles/external_reconstruct.dir/build cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/convert_star.dir/convert_star.cpp.o -MF CMakeFiles/convert_star.dir/convert_star.cpp.o.d -o CMakeFiles/convert_star.dir/convert_star.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/convert_star.cpp -[ 56%] Building CXX object src/apps/CMakeFiles/convert_to_tiff_mpi.dir/convert_to_tiff_mpi.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_gui_lib.dir/__/displayer.cpp.o -MF CMakeFiles/relion_gui_lib.dir/__/displayer.cpp.o.d -o CMakeFiles/relion_gui_lib.dir/__/displayer.cpp.o -c /build/reproducible-path/relion-3.1.3/src/displayer.cpp -[ 56%] Building CXX object src/apps/CMakeFiles/ctf_mask_test.dir/ctf_mask_test.cpp.o +/usr/bin/make -f src/apps/CMakeFiles/find_tiltpairs.dir/build.make src/apps/CMakeFiles/find_tiltpairs.dir/build make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_gui_lib.dir/__/gui_entries.cpp.o -MF CMakeFiles/relion_gui_lib.dir/__/gui_entries.cpp.o.d -o CMakeFiles/relion_gui_lib.dir/__/gui_entries.cpp.o -c /build/reproducible-path/relion-3.1.3/src/gui_entries.cpp -[ 56%] Building CXX object src/apps/CMakeFiles/find_tiltpairs.dir/find_tiltpairs.cpp.o -[ 56%] Building CXX object src/apps/CMakeFiles/ctf_refine.dir/ctf_refine.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_gui_lib.dir/__/gui_jobwindow.cpp.o -MF CMakeFiles/relion_gui_lib.dir/__/gui_jobwindow.cpp.o.d -o CMakeFiles/relion_gui_lib.dir/__/gui_jobwindow.cpp.o -c /build/reproducible-path/relion-3.1.3/src/gui_jobwindow.cpp make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_gui_lib.dir/__/gui_mainwindow.cpp.o -MF CMakeFiles/relion_gui_lib.dir/__/gui_mainwindow.cpp.o.d -o CMakeFiles/relion_gui_lib.dir/__/gui_mainwindow.cpp.o -c /build/reproducible-path/relion-3.1.3/src/gui_mainwindow.cpp -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/convert_to_tiff_mpi.dir/convert_to_tiff_mpi.cpp.o -MF CMakeFiles/convert_to_tiff_mpi.dir/convert_to_tiff_mpi.cpp.o.d -o CMakeFiles/convert_to_tiff_mpi.dir/convert_to_tiff_mpi.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/convert_to_tiff_mpi.cpp -[ 56%] Building CXX object src/apps/CMakeFiles/demodulate.dir/demodulate.cpp.o -make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -[ 56%] Building CXX object src/apps/CMakeFiles/ctf_refine_mpi.dir/ctf_refine_mpi.cpp.o -[ 57%] Building CXX object src/apps/CMakeFiles/ctf_toolbox.dir/ctf_toolbox.cpp.o -[ 57%] Building CXX object src/apps/CMakeFiles/align_symmetry.dir/align_symmetry.cpp.o -/usr/bin/make -f src/apps/CMakeFiles/prepare_subtomo.dir/build.make src/apps/CMakeFiles/prepare_subtomo.dir/build -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/ctf_mask_test.dir/ctf_mask_test.cpp.o -MF CMakeFiles/ctf_mask_test.dir/ctf_mask_test.cpp.o.d -o CMakeFiles/ctf_mask_test.dir/ctf_mask_test.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/ctf_mask_test.cpp +/usr/bin/make -f src/apps/CMakeFiles/flex_analyse.dir/build.make src/apps/CMakeFiles/flex_analyse.dir/build cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/convert_to_tiff.dir/convert_to_tiff.cpp.o -MF CMakeFiles/convert_to_tiff.dir/convert_to_tiff.cpp.o.d -o CMakeFiles/convert_to_tiff.dir/convert_to_tiff.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/convert_to_tiff.cpp -[ 57%] Building CXX object src/apps/CMakeFiles/estimate_gain.dir/estimate_gain.cpp.o -[ 58%] Building CXX object src/apps/CMakeFiles/external_reconstruct.dir/external_reconstruct.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/demodulate.dir/demodulate.cpp.o -MF CMakeFiles/demodulate.dir/demodulate.cpp.o.d -o CMakeFiles/demodulate.dir/demodulate.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/demodulate.cpp -[ 58%] Building CXX object src/apps/CMakeFiles/flex_analyse.dir/flex_analyse.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/align_symmetry.dir/align_symmetry.cpp.o -MF CMakeFiles/align_symmetry.dir/align_symmetry.cpp.o.d -o CMakeFiles/align_symmetry.dir/align_symmetry.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/align_symmetry.cpp make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/estimate_gain.dir/estimate_gain.cpp.o -MF CMakeFiles/estimate_gain.dir/estimate_gain.cpp.o.d -o CMakeFiles/estimate_gain.dir/estimate_gain.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/estimate_gain.cpp +/usr/bin/make -f src/apps/CMakeFiles/flex_analyse_mpi.dir/build.make src/apps/CMakeFiles/flex_analyse_mpi.dir/build +make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' +[ 55%] Building CXX object src/apps/CMakeFiles/ctf_refine_mpi.dir/ctf_refine_mpi.cpp.o +[ 55%] Building CXX object src/apps/CMakeFiles/ctf_mask_test.dir/ctf_mask_test.cpp.o +[ 56%] Building CXX object src/apps/CMakeFiles/ctf_toolbox.dir/ctf_toolbox.cpp.o +[ 56%] Building CXX object src/apps/CMakeFiles/ctf_refine.dir/ctf_refine.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/ctf_refine_mpi.dir/ctf_refine_mpi.cpp.o -MF CMakeFiles/ctf_refine_mpi.dir/ctf_refine_mpi.cpp.o.d -o CMakeFiles/ctf_refine_mpi.dir/ctf_refine_mpi.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/ctf_refine_mpi.cpp +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/ctf_mask_test.dir/ctf_mask_test.cpp.o -MF CMakeFiles/ctf_mask_test.dir/ctf_mask_test.cpp.o.d -o CMakeFiles/ctf_mask_test.dir/ctf_mask_test.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/ctf_mask_test.cpp cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/ctf_toolbox.dir/ctf_toolbox.cpp.o -MF CMakeFiles/ctf_toolbox.dir/ctf_toolbox.cpp.o.d -o CMakeFiles/ctf_toolbox.dir/ctf_toolbox.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/ctf_toolbox.cpp -[ 59%] Building CXX object src/apps/CMakeFiles/helix_toolbox.dir/helix_toolbox.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/ctf_refine.dir/ctf_refine.cpp.o -MF CMakeFiles/ctf_refine.dir/ctf_refine.cpp.o.d -o CMakeFiles/ctf_refine.dir/ctf_refine.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/ctf_refine.cpp +make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' +[ 56%] Building CXX object src/apps/CMakeFiles/find_tiltpairs.dir/find_tiltpairs.cpp.o +/usr/bin/make -f src/apps/CMakeFiles/helix_inimodel2d.dir/build.make src/apps/CMakeFiles/helix_inimodel2d.dir/build +[ 56%] Building CXX object src/apps/CMakeFiles/demodulate.dir/demodulate.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/demodulate.dir/demodulate.cpp.o -MF CMakeFiles/demodulate.dir/demodulate.cpp.o.d -o CMakeFiles/demodulate.dir/demodulate.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/demodulate.cpp +make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/find_tiltpairs.dir/find_tiltpairs.cpp.o -MF CMakeFiles/find_tiltpairs.dir/find_tiltpairs.cpp.o.d -o CMakeFiles/find_tiltpairs.dir/find_tiltpairs.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/find_tiltpairs.cpp +[ 57%] Building CXX object src/apps/CMakeFiles/external_reconstruct.dir/external_reconstruct.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/external_reconstruct.dir/external_reconstruct.cpp.o -MF CMakeFiles/external_reconstruct.dir/external_reconstruct.cpp.o.d -o CMakeFiles/external_reconstruct.dir/external_reconstruct.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/external_reconstruct.cpp +[ 58%] Building CXX object src/apps/CMakeFiles/flex_analyse.dir/flex_analyse.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/flex_analyse.dir/flex_analyse.cpp.o -MF CMakeFiles/flex_analyse.dir/flex_analyse.cpp.o.d -o CMakeFiles/flex_analyse.dir/flex_analyse.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/flex_analyse.cpp +[ 58%] Building CXX object src/apps/CMakeFiles/convert_to_tiff_mpi.dir/convert_to_tiff_mpi.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/convert_to_tiff_mpi.dir/convert_to_tiff_mpi.cpp.o -MF CMakeFiles/convert_to_tiff_mpi.dir/convert_to_tiff_mpi.cpp.o.d -o CMakeFiles/convert_to_tiff_mpi.dir/convert_to_tiff_mpi.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/convert_to_tiff_mpi.cpp +[ 59%] Building CXX object src/apps/CMakeFiles/helix_inimodel2d.dir/helix_inimodel2d.cpp.o [ 59%] Building CXX object src/apps/CMakeFiles/flex_analyse_mpi.dir/flex_analyse_mpi.cpp.o -[ 59%] Building CXX object src/apps/CMakeFiles/mask_create.dir/mask_create.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/find_tiltpairs.dir/find_tiltpairs.cpp.o -MF CMakeFiles/find_tiltpairs.dir/find_tiltpairs.cpp.o.d -o CMakeFiles/find_tiltpairs.dir/find_tiltpairs.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/find_tiltpairs.cpp -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/helix_toolbox.dir/helix_toolbox.cpp.o -MF CMakeFiles/helix_toolbox.dir/helix_toolbox.cpp.o.d -o CMakeFiles/helix_toolbox.dir/helix_toolbox.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/helix_toolbox.cpp -[ 60%] Building CXX object src/apps/CMakeFiles/helix_inimodel2d.dir/helix_inimodel2d.cpp.o -[ 60%] Building CXX object src/apps/CMakeFiles/image_handler.dir/image_handler.cpp.o -[ 60%] Building CXX object src/apps/CMakeFiles/import.dir/import.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/mask_create.dir/mask_create.cpp.o -MF CMakeFiles/mask_create.dir/mask_create.cpp.o.d -o CMakeFiles/mask_create.dir/mask_create.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/mask_create.cpp cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/helix_inimodel2d.dir/helix_inimodel2d.cpp.o -MF CMakeFiles/helix_inimodel2d.dir/helix_inimodel2d.cpp.o.d -o CMakeFiles/helix_inimodel2d.dir/helix_inimodel2d.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/helix_inimodel2d.cpp -[ 62%] Building CXX object src/apps/CMakeFiles/localsym.dir/localsym.cpp.o -[ 62%] Building CXX object src/apps/CMakeFiles/motion_refine.dir/motion_refine.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/image_handler.dir/image_handler.cpp.o -MF CMakeFiles/image_handler.dir/image_handler.cpp.o.d -o CMakeFiles/image_handler.dir/image_handler.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/image_handler.cpp -[ 63%] Building CXX object src/apps/CMakeFiles/merge_particles.dir/merge_particles.cpp.o -[ 63%] Building CXX object src/apps/CMakeFiles/motion_refine_mpi.dir/motion_refine_mpi.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ 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-ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/import.dir/import.cpp.o -MF CMakeFiles/import.dir/import.cpp.o.d -o CMakeFiles/import.dir/import.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/import.cpp -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 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CMakeFiles/merge_particles.dir/merge_particles.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/merge_particles.cpp -[ 63%] Building CXX object src/apps/CMakeFiles/mrc2vtk.dir/mrc2vtk.cpp.o +[ 59%] Building CXX object src/apps/CMakeFiles/estimate_gain.dir/estimate_gain.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/flex_analyse_mpi.dir/flex_analyse_mpi.cpp.o -MF CMakeFiles/flex_analyse_mpi.dir/flex_analyse_mpi.cpp.o.d -o CMakeFiles/flex_analyse_mpi.dir/flex_analyse_mpi.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/flex_analyse_mpi.cpp -[ 64%] Building CXX object src/apps/CMakeFiles/localsym_mpi.dir/localsym_mpi.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/motion_refine_mpi.dir/motion_refine_mpi.cpp.o -MF CMakeFiles/motion_refine_mpi.dir/motion_refine_mpi.cpp.o.d -o CMakeFiles/motion_refine_mpi.dir/motion_refine_mpi.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/motion_refine_mpi.cpp -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/localsym_mpi.dir/localsym_mpi.cpp.o -MF CMakeFiles/localsym_mpi.dir/localsym_mpi.cpp.o.d -o CMakeFiles/localsym_mpi.dir/localsym_mpi.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/localsym_mpi.cpp -[ 65%] Building CXX object src/apps/CMakeFiles/particle_reposition.dir/particle_reposition.cpp.o -[ 66%] Building CXX object src/apps/CMakeFiles/particle_FCC.dir/particle_FCC.cpp.o -[ 66%] Building CXX object src/apps/CMakeFiles/particle_subtract.dir/particle_subtract.cpp.o -[ 66%] Building CXX object src/apps/CMakeFiles/particle_subtract_mpi.dir/particle_subtract_mpi.cpp.o -[ 67%] Building CXX object src/apps/CMakeFiles/particle_symmetry_expand.dir/particle_symmetry_expand.cpp.o -[ 67%] Building CXX object src/apps/CMakeFiles/plot_delocalisation.dir/plot_delocalisation.cpp.o -[ 67%] Building CXX object src/apps/CMakeFiles/postprocess.dir/postprocess.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk 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/build/reproducible-path/relion-3.1.3/src/apps/mrc2vtk.cpp -[ 68%] Building CXX object src/apps/CMakeFiles/postprocess_mpi.dir/postprocess_mpi.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/plot_delocalisation.dir/plot_delocalisation.cpp.o -MF CMakeFiles/plot_delocalisation.dir/plot_delocalisation.cpp.o.d -o CMakeFiles/plot_delocalisation.dir/plot_delocalisation.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/plot_delocalisation.cpp -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/particle_select.dir/particle_select.cpp.o -MF CMakeFiles/particle_select.dir/particle_select.cpp.o.d -o CMakeFiles/particle_select.dir/particle_select.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/particle_select.cpp -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/postprocess.dir/postprocess.cpp.o -MF CMakeFiles/postprocess.dir/postprocess.cpp.o.d -o CMakeFiles/postprocess.dir/postprocess.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/postprocess.cpp -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/particle_symmetry_expand.dir/particle_symmetry_expand.cpp.o -MF CMakeFiles/particle_symmetry_expand.dir/particle_symmetry_expand.cpp.o.d -o CMakeFiles/particle_symmetry_expand.dir/particle_symmetry_expand.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/particle_symmetry_expand.cpp -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/pipeliner.dir/pipeliner.cpp.o -MF CMakeFiles/pipeliner.dir/pipeliner.cpp.o.d -o CMakeFiles/pipeliner.dir/pipeliner.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/pipeliner.cpp -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/postprocess_mpi.dir/postprocess_mpi.cpp.o -MF CMakeFiles/postprocess_mpi.dir/postprocess_mpi.cpp.o.d -o CMakeFiles/postprocess_mpi.dir/postprocess_mpi.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/postprocess_mpi.cpp -[ 68%] Building CXX object src/apps/CMakeFiles/prepare_subtomo.dir/prepare_subtomo.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/prepare_subtomo.dir/prepare_subtomo.cpp.o -MF CMakeFiles/prepare_subtomo.dir/prepare_subtomo.cpp.o.d -o CMakeFiles/prepare_subtomo.dir/prepare_subtomo.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/prepare_subtomo.cpp -In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/jaz/obs_model.h:24, - from /build/reproducible-path/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, - from /build/reproducible-path/relion-3.1.3/src/apps/ctf_refine.cpp:21: -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] - 43 | uint32 width, length; // apparent dimensions in the file - | ^~~~~ +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/estimate_gain.dir/estimate_gain.cpp.o -MF CMakeFiles/estimate_gain.dir/estimate_gain.cpp.o.d -o CMakeFiles/estimate_gain.dir/estimate_gain.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/estimate_gain.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/apps/ctf_toolbox.cpp:21: + from /build/reproducible-path/relion-3.1.3/src/autopicker.h:10, + from /build/reproducible-path/relion-3.1.3/src/autopicker_mpi.h:12, + from /build/reproducible-path/relion-3.1.3/src/apps/autopick_mpi.cpp:20: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -7148,35 +7008,6 @@ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ -In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, - from /build/reproducible-path/relion-3.1.3/src/image.h:57: -/usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here - 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; - | ^~~~~~~~~~~~~~ -/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations] - 43 | uint32 width, length; // apparent dimensions in the file - | ^~~~~~ -/usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here - 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; - | ^~~~~~~~~~~~ -/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; - | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ @@ -7210,33 +7041,11 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] - 185 | uint32 cur_width, cur_length; - | ^~~~~~~~~ -/usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here - 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] - 185 | uint32 cur_width, cur_length; - | ^~~~~~~~~~ -/usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here - 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 186 | uint16 cur_sampleFormat, cur_bitsPerSample; - | ^~~~~~~~~~~~~~~~ -/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 186 | uint16 cur_sampleFormat, cur_bitsPerSample; - | ^~~~~~~~~~~~~~~~~ -/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/tiff_converter.h:24, - from /build/reproducible-path/relion-3.1.3/src/apps/convert_to_tiff.cpp:21: + from /build/reproducible-path/relion-3.1.3/src/jaz/obs_model.h:24, + from /build/reproducible-path/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, + from /build/reproducible-path/relion-3.1.3/src/jaz/ctf/ctf_refiner_mpi.h:26, + from /build/reproducible-path/relion-3.1.3/src/apps/ctf_refine_mpi.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -7295,8 +7104,8 @@ 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/jaz/io/star_converter.h:5, - from /build/reproducible-path/relion-3.1.3/src/apps/convert_star.cpp:24: + from /build/reproducible-path/relion-3.1.3/src/autopicker.h:10, + from /build/reproducible-path/relion-3.1.3/src/apps/autopick.cpp:20: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -7355,7 +7164,8 @@ 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/apps/image_handler.cpp:21: + from /build/reproducible-path/relion-3.1.3/src/tiff_converter.h:24, + from /build/reproducible-path/relion-3.1.3/src/apps/convert_to_tiff_mpi.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -7389,8 +7199,33 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 185 | uint32 cur_width, cur_length; + | ^~~~~~~~~ +/usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here + 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 185 | uint32 cur_width, cur_length; + | ^~~~~~~~~~ +/usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here + 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 186 | uint16 cur_sampleFormat, cur_bitsPerSample; + | ^~~~~~~~~~~~~~~~ +/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 186 | uint16 cur_sampleFormat, cur_bitsPerSample; + | ^~~~~~~~~~~~~~~~~ +/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/apps/estimate_gain.cpp:27: + from /build/reproducible-path/relion-3.1.3/src/tiff_converter.h:24, + from /build/reproducible-path/relion-3.1.3/src/apps/convert_to_tiff.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -7449,8 +7284,8 @@ 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/jaz/obs_model.h:24, - from /build/reproducible-path/relion-3.1.3/src/apps/import.cpp:22: + from /build/reproducible-path/relion-3.1.3/src/jaz/vtk_helper.h:24, + from /build/reproducible-path/relion-3.1.3/src/apps/demodulate.cpp:1: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -7472,84 +7307,49 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/projector.h:25, - from /build/reproducible-path/relion-3.1.3/src/apps/align_symmetry.cpp:21: -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] - 43 | uint32 width, length; // apparent dimensions in the file - | ^~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] - 185 | uint32 cur_width, cur_length; - | ^~~~~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ -/usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here - 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; - | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; - | ^~~~~~~~~~ + | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ -In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, - from /build/reproducible-path/relion-3.1.3/src/image.h:57: +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 185 | uint32 cur_width, cur_length; + | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations] - 43 | uint32 width, length; // apparent dimensions in the file - | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -/usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here - 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; - | ^~~~~~~~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; - | ^~~~~~~~~~~~~ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/apps/external_reconstruct.cpp:24: + from /build/reproducible-path/relion-3.1.3/src/apps/../helix_inimodel2d.h:29, + from /build/reproducible-path/relion-3.1.3/src/apps/helix_inimodel2d.cpp:22: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ -/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; - | ^~~~~~~~~~~~~~ -/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here @@ -7597,30 +7397,6 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] - 185 | uint32 cur_width, cur_length; - | ^~~~~~~~~ -/usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here - 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] - 185 | uint32 cur_width, cur_length; - | ^~~~~~~~~~ -/usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here - 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 186 | uint16 cur_sampleFormat, cur_bitsPerSample; - | ^~~~~~~~~~~~~~~~~ -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 186 | uint16 cur_sampleFormat, cur_bitsPerSample; - | ^~~~~~~~~~~~~~~~ -/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ @@ -7628,17 +7404,12 @@ 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/jaz/obs_model.h:24, - from /build/reproducible-path/relion-3.1.3/src/ctf.h:50, - from /build/reproducible-path/relion-3.1.3/src/jaz/stack_helper.h:24, - from /build/reproducible-path/relion-3.1.3/src/apps/particle_select.cpp:1: + from /build/reproducible-path/relion-3.1.3/src/projector.h:25, + from /build/reproducible-path/relion-3.1.3/src/apps/align_symmetry.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] - 185 | uint32 cur_width, cur_length; - | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here @@ -7650,12 +7421,6 @@ /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ -/usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here - 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] - 185 | uint32 cur_width, cur_length; - | ^~~~~~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ @@ -7674,24 +7439,8 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -/usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here - 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 186 | uint16 cur_sampleFormat, cur_bitsPerSample; - | ^~~~~~~~~~~~~~~~ -/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 186 | uint16 cur_sampleFormat, cur_bitsPerSample; - | ^~~~~~~~~~~~~~~~~ -/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/jaz/io/star_converter.h:5, - from /build/reproducible-path/relion-3.1.3/src/apps/merge_particles.cpp:2: + from /build/reproducible-path/relion-3.1.3/src/apps/estimate_gain.cpp:27: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -7749,9 +7498,34 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 185 | uint32 cur_width, cur_length; + | ^~~~~~~~~ +/usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here + 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 185 | uint32 cur_width, cur_length; + | ^~~~~~~~~~ +/usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here + 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 186 | uint16 cur_sampleFormat, cur_bitsPerSample; + | ^~~~~~~~~~~~~~~~ +/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 186 | uint16 cur_sampleFormat, cur_bitsPerSample; + | ^~~~~~~~~~~~~~~~~ +/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/apps/../helix_inimodel2d.h:29, - from /build/reproducible-path/relion-3.1.3/src/apps/helix_inimodel2d.cpp:22: + from /build/reproducible-path/relion-3.1.3/src/exp_model.h:24, + from /build/reproducible-path/relion-3.1.3/src/apps/../flex_analyser.h:24, + from /build/reproducible-path/relion-3.1.3/src/apps/flex_analyse.cpp:22: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -7810,8 +7584,8 @@ 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/autopicker.h:10, - from /build/reproducible-path/relion-3.1.3/src/apps/autopick.cpp:20: + from /build/reproducible-path/relion-3.1.3/src/displayer.h:40, + from /build/reproducible-path/relion-3.1.3/src/displayer.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -7827,12 +7601,6 @@ /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ -In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/apps/mrc2vtk.cpp:1: -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] - 43 | uint32 width, length; // apparent dimensions in the file - | ^~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ @@ -7851,6 +7619,36 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 185 | uint32 cur_width, cur_length; + | ^~~~~~~~~ +/usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here + 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 185 | uint32 cur_width, cur_length; + | ^~~~~~~~~~ +/usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here + 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 186 | uint16 cur_sampleFormat, cur_bitsPerSample; + | ^~~~~~~~~~~~~~~~ +/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 186 | uint16 cur_sampleFormat, cur_bitsPerSample; + | ^~~~~~~~~~~~~~~~~ +/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ +In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, + from /build/reproducible-path/relion-3.1.3/src/apps/external_reconstruct.cpp:24: +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 43 | uint32 width, length; // apparent dimensions in the file + | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here @@ -7905,8 +7703,8 @@ 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/postprocessing.h:24, - from /build/reproducible-path/relion-3.1.3/src/apps/postprocess.cpp:20: + from /build/reproducible-path/relion-3.1.3/src/jaz/io/star_converter.h:5, + from /build/reproducible-path/relion-3.1.3/src/apps/convert_star.cpp:24: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -7934,48 +7732,24 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] - 185 | uint32 cur_width, cur_length; - | ^~~~~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ -/usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here - 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; - | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] - 185 | uint32 cur_width, cur_length; - | ^~~~~~~~~~ -/usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here - 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; - | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 186 | uint16 cur_sampleFormat, cur_bitsPerSample; - | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ -/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 186 | uint16 cur_sampleFormat, cur_bitsPerSample; - | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ -/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ @@ -7989,14 +7763,9 @@ 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/helix.h:30, - from /build/reproducible-path/relion-3.1.3/src/apps/helix_toolbox.cpp:22: -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] - 43 | uint32 width, length; // apparent dimensions in the file - | ^~~~~ -In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/apps/mask_create.cpp:21: + from /build/reproducible-path/relion-3.1.3/src/jaz/obs_model.h:24, + from /build/reproducible-path/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, + from /build/reproducible-path/relion-3.1.3/src/apps/ctf_refine.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -8024,17 +7793,23 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, - from /build/reproducible-path/relion-3.1.3/src/image.h:57: -/usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here - 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; - | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, + from /build/reproducible-path/relion-3.1.3/src/apps/ctf_toolbox.cpp:21: +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 43 | uint32 width, length; // apparent dimensions in the file + | ^~~~~ +In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, + from /build/reproducible-path/relion-3.1.3/src/image.h:57: +/usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here + 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; + | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ @@ -8074,30 +7849,6 @@ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] - 185 | uint32 cur_width, cur_length; - | ^~~~~~~~~ -/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 186 | uint16 cur_sampleFormat, cur_bitsPerSample; - | ^~~~~~~~~~~~~~~~~ -/usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here - 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] - 185 | uint32 cur_width, cur_length; - | ^~~~~~~~~~ -/usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here - 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 186 | uint16 cur_sampleFormat, cur_bitsPerSample; - | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ @@ -8131,11 +7882,16 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +[ 59%] Linking CXX executable ../../bin/relion_convert_to_tiff +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/convert_to_tiff.dir/link.txt --verbose=1 +[ 59%] Linking CXX executable ../../bin/relion_convert_to_tiff_mpi +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/convert_to_tiff_mpi.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/convert_to_tiff.dir/convert_to_tiff.cpp.o -o ../../bin/relion_convert_to_tiff ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/convert_to_tiff_mpi.dir/convert_to_tiff_mpi.cpp.o -o ../../bin/relion_convert_to_tiff_mpi ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/jaz/obs_model.h:24, - from /build/reproducible-path/relion-3.1.3/src/ctf.h:50, - from /build/reproducible-path/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, - from /build/reproducible-path/relion-3.1.3/src/apps/motion_refine.cpp:21: + from /build/reproducible-path/relion-3.1.3/src/exp_model.h:24, + from /build/reproducible-path/relion-3.1.3/src/apps/../flex_analyser.h:24, + from /build/reproducible-path/relion-3.1.3/src/apps/flex_analyse_mpi.cpp:22: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -8169,10 +7925,34 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 185 | uint32 cur_width, cur_length; + | ^~~~~~~~~ +/usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here + 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 185 | uint32 cur_width, cur_length; + | ^~~~~~~~~~ +/usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here + 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 186 | uint16 cur_sampleFormat, cur_bitsPerSample; + | ^~~~~~~~~~~~~~~~ +/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 186 | uint16 cur_sampleFormat, cur_bitsPerSample; + | ^~~~~~~~~~~~~~~~~ +/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ +[ 59%] Linking CXX executable ../../bin/relion_helix_inimodel2d +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/helix_inimodel2d.dir/link.txt --verbose=1 In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/exp_model.h:24, - from /build/reproducible-path/relion-3.1.3/src/apps/../flex_analyser.h:24, - from /build/reproducible-path/relion-3.1.3/src/apps/flex_analyse_mpi.cpp:22: + from /build/reproducible-path/relion-3.1.3/src/apps/ctf_mask_test.cpp:7: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -8218,15 +7998,6 @@ /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ -In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/projector.h:25, - from /build/reproducible-path/relion-3.1.3/src/ml_model.h:23, - from /build/reproducible-path/relion-3.1.3/src/ml_optimiser.h:35, - from /build/reproducible-path/relion-3.1.3/src/apps/particle_reposition.cpp:22: -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] - 43 | uint32 width, length; // apparent dimensions in the file - | ^~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ @@ -8239,6 +8010,120 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/helix_inimodel2d.dir/helix_inimodel2d.cpp.o -o ../../bin/relion_helix_inimodel2d ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +[ 60%] Linking CXX executable ../../bin/relion_autopick_mpi +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/autopick_mpi.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/autopick_mpi.dir/autopick_mpi.cpp.o -o ../../bin/relion_autopick_mpi ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' +[ 60%] Linking CXX executable ../../bin/relion_autopick +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/autopick.dir/link.txt --verbose=1 +[ 60%] Built target convert_to_tiff +/usr/bin/make -f src/apps/CMakeFiles/helix_toolbox.dir/build.make src/apps/CMakeFiles/helix_toolbox.dir/depend +make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' +cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/helix_toolbox.dir/DependInfo.cmake "--color=" +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/autopick.dir/autopick.cpp.o -o ../../bin/relion_autopick ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' +/usr/bin/make -f src/apps/CMakeFiles/helix_toolbox.dir/build.make src/apps/CMakeFiles/helix_toolbox.dir/build +make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' +[ 61%] Building CXX object src/apps/CMakeFiles/helix_toolbox.dir/helix_toolbox.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/helix_toolbox.dir/helix_toolbox.cpp.o -MF CMakeFiles/helix_toolbox.dir/helix_toolbox.cpp.o.d -o CMakeFiles/helix_toolbox.dir/helix_toolbox.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/helix_toolbox.cpp +make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' +[ 61%] Built target convert_to_tiff_mpi +/usr/bin/make -f src/apps/CMakeFiles/image_handler.dir/build.make src/apps/CMakeFiles/image_handler.dir/depend +make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' +cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/image_handler.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' +/usr/bin/make -f src/apps/CMakeFiles/image_handler.dir/build.make src/apps/CMakeFiles/image_handler.dir/build +make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' +[ 61%] Building CXX object src/apps/CMakeFiles/image_handler.dir/image_handler.cpp.o +make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/image_handler.dir/image_handler.cpp.o -MF CMakeFiles/image_handler.dir/image_handler.cpp.o.d -o CMakeFiles/image_handler.dir/image_handler.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/image_handler.cpp +[ 61%] Built target helix_inimodel2d +/usr/bin/make -f src/apps/CMakeFiles/import.dir/build.make src/apps/CMakeFiles/import.dir/depend +make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' +cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/import.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' +/usr/bin/make -f src/apps/CMakeFiles/import.dir/build.make src/apps/CMakeFiles/import.dir/build +make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' +[ 61%] Building CXX object src/apps/CMakeFiles/import.dir/import.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/import.dir/import.cpp.o -MF CMakeFiles/import.dir/import.cpp.o.d -o CMakeFiles/import.dir/import.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/import.cpp +make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' +[ 61%] Built target autopick_mpi +/usr/bin/make -f src/apps/CMakeFiles/localsym.dir/build.make src/apps/CMakeFiles/localsym.dir/depend +make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' +cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/localsym.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' +/usr/bin/make -f src/apps/CMakeFiles/localsym.dir/build.make src/apps/CMakeFiles/localsym.dir/build +make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' +[ 61%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/gui_mainwindow.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_gui_lib.dir/__/gui_mainwindow.cpp.o -MF CMakeFiles/relion_gui_lib.dir/__/gui_mainwindow.cpp.o.d -o CMakeFiles/relion_gui_lib.dir/__/gui_mainwindow.cpp.o -c /build/reproducible-path/relion-3.1.3/src/gui_mainwindow.cpp +[ 62%] Building CXX object src/apps/CMakeFiles/localsym.dir/localsym.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/localsym.dir/localsym.cpp.o -MF CMakeFiles/localsym.dir/localsym.cpp.o.d -o CMakeFiles/localsym.dir/localsym.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/localsym.cpp +make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' +[ 63%] Linking CXX executable ../../bin/relion_convert_star +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/convert_star.dir/link.txt --verbose=1 +[ 63%] Built target autopick +/usr/bin/make -f src/apps/CMakeFiles/localsym_mpi.dir/build.make src/apps/CMakeFiles/localsym_mpi.dir/depend +make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' +cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/localsym_mpi.dir/DependInfo.cmake "--color=" +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/convert_star.dir/convert_star.cpp.o -o ../../bin/relion_convert_star ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' +/usr/bin/make -f src/apps/CMakeFiles/localsym_mpi.dir/build.make src/apps/CMakeFiles/localsym_mpi.dir/build +make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' +[ 63%] Linking CXX executable ../../bin/relion_ctf_refine_mpi +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/ctf_refine_mpi.dir/link.txt --verbose=1 +[ 64%] Building CXX object src/apps/CMakeFiles/localsym_mpi.dir/localsym_mpi.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/localsym_mpi.dir/localsym_mpi.cpp.o -MF CMakeFiles/localsym_mpi.dir/localsym_mpi.cpp.o.d -o CMakeFiles/localsym_mpi.dir/localsym_mpi.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/localsym_mpi.cpp +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ctf_refine_mpi.dir/ctf_refine_mpi.cpp.o -o ../../bin/relion_ctf_refine_mpi ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +[ 65%] Linking CXX executable ../../bin/relion_ctf_refine +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/ctf_refine.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ctf_refine.dir/ctf_refine.cpp.o -o ../../bin/relion_ctf_refine ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +In file included from /build/reproducible-path/relion-3.1.3/src/numerical_recipes.h:48, + from /build/reproducible-path/relion-3.1.3/src/funcs.h:59, + from /build/reproducible-path/relion-3.1.3/src/args.h:56, + from /build/reproducible-path/relion-3.1.3/src/apps/find_tiltpairs.cpp:20: +In function 'void free_Tvector(T*&, int, int) [with T = int]', + inlined from 'void gaussj(T*, int, T*, int) [with T = double]' at /build/reproducible-path/relion-3.1.3/src/numerical_recipes.h:262:17: +/build/reproducible-path/relion-3.1.3/src/memory.h:74:13: warning: 'void free(void*)' called on pointer 'ipiv' with nonzero offset 4 [-Wfree-nonheap-object] + 74 | free((char*)(v + nl)); + | ~~~~^~~~~~~~~~~~~~~~~ +/build/reproducible-path/relion-3.1.3/src/numerical_recipes.h: In function 'void gaussj(T*, int, T*, int) [with T = double]': +/build/reproducible-path/relion-3.1.3/src/numerical_recipes.h:198:26: note: declared here + 198 | int *indxc, *indxr, *ipiv; + | ^~~~ +In function 'void free_Tvector(T*&, int, int) [with T = int]', + inlined from 'void gaussj(T*, int, T*, int) [with T = double]' at /build/reproducible-path/relion-3.1.3/src/numerical_recipes.h:262:17: +/build/reproducible-path/relion-3.1.3/src/memory.h:74:13: warning: 'void free(void*)' called on pointer 'ipiv' with nonzero offset 4 [-Wfree-nonheap-object] + 74 | free((char*)(v + nl)); + | ~~~~^~~~~~~~~~~~~~~~~ +/build/reproducible-path/relion-3.1.3/src/numerical_recipes.h: In function 'void gaussj(T*, int, T*, int) [with T = double]': +/build/reproducible-path/relion-3.1.3/src/numerical_recipes.h:198:26: note: declared here + 198 | int *indxc, *indxr, *ipiv; + | ^~~~ +In function 'void free_Tvector(T*&, int, int) [with T = int]', + inlined from 'void gaussj(T*, int, T*, int) [with T = double]' at /build/reproducible-path/relion-3.1.3/src/numerical_recipes.h:263:17: +/build/reproducible-path/relion-3.1.3/src/memory.h:74:13: warning: 'void free(void*)' called on pointer 'indxr' with nonzero offset 4 [-Wfree-nonheap-object] + 74 | free((char*)(v + nl)); + | ~~~~^~~~~~~~~~~~~~~~~ +/build/reproducible-path/relion-3.1.3/src/numerical_recipes.h: In function 'void gaussj(T*, int, T*, int) [with T = double]': +/build/reproducible-path/relion-3.1.3/src/numerical_recipes.h:198:18: note: declared here + 198 | int *indxc, *indxr, *ipiv; + | ^~~~~ +In function 'void free_Tvector(T*&, int, int) [with T = int]', + inlined from 'void gaussj(T*, int, T*, int) [with T = double]' at /build/reproducible-path/relion-3.1.3/src/numerical_recipes.h:264:17: +/build/reproducible-path/relion-3.1.3/src/memory.h:74:13: warning: 'void free(void*)' called on pointer 'indxc' with nonzero offset 4 [-Wfree-nonheap-object] + 74 | free((char*)(v + nl)); + | ~~~~^~~~~~~~~~~~~~~~~ +/build/reproducible-path/relion-3.1.3/src/numerical_recipes.h: In function 'void gaussj(T*, int, T*, int) [with T = double]': +/build/reproducible-path/relion-3.1.3/src/numerical_recipes.h:198:10: note: declared here + 198 | int *indxc, *indxr, *ipiv; + | ^~~~~ +In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, + from /build/reproducible-path/relion-3.1.3/src/apps/image_handler.cpp:21: +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 43 | uint32 width, length; // apparent dimensions in the file + | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here @@ -8268,9 +8153,33 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 185 | uint32 cur_width, cur_length; + | ^~~~~~~~~ +/usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here + 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 185 | uint32 cur_width, cur_length; + | ^~~~~~~~~~ +/usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here + 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 186 | uint16 cur_sampleFormat, cur_bitsPerSample; + | ^~~~~~~~~~~~~~~~ +/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 186 | uint16 cur_sampleFormat, cur_bitsPerSample; + | ^~~~~~~~~~~~~~~~~ +/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/jaz/obs_model.h:24, - from /build/reproducible-path/relion-3.1.3/src/apps/particle_symmetry_expand.cpp:26: + from /build/reproducible-path/relion-3.1.3/src/helix.h:30, + from /build/reproducible-path/relion-3.1.3/src/apps/helix_toolbox.cpp:22: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -8328,36 +8237,32 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] - 185 | uint32 cur_width, cur_length; - | ^~~~~~~~~ -/usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here - 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] - 185 | uint32 cur_width, cur_length; - | ^~~~~~~~~~ -/usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here - 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 186 | uint16 cur_sampleFormat, cur_bitsPerSample; - | ^~~~~~~~~~~~~~~~ -/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 186 | uint16 cur_sampleFormat, cur_bitsPerSample; - | ^~~~~~~~~~~~~~~~~ -/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ +make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' +make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' +[ 65%] Built target convert_star +/usr/bin/make -f src/apps/CMakeFiles/mask_create.dir/build.make src/apps/CMakeFiles/mask_create.dir/depend +make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' +cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/mask_create.dir/DependInfo.cmake "--color=" +[ 65%] Built target ctf_refine +/usr/bin/make -f src/apps/CMakeFiles/merge_particles.dir/build.make src/apps/CMakeFiles/merge_particles.dir/depend +make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' +cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/merge_particles.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' +/usr/bin/make -f src/apps/CMakeFiles/mask_create.dir/build.make src/apps/CMakeFiles/mask_create.dir/build +make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' +make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' +/usr/bin/make -f src/apps/CMakeFiles/merge_particles.dir/build.make src/apps/CMakeFiles/merge_particles.dir/build +[ 65%] Linking CXX executable ../../bin/relion_flex_analyse_mpi +make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/flex_analyse_mpi.dir/link.txt --verbose=1 +[ 65%] Building CXX object src/apps/CMakeFiles/mask_create.dir/mask_create.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/mask_create.dir/mask_create.cpp.o -MF CMakeFiles/mask_create.dir/mask_create.cpp.o.d -o CMakeFiles/mask_create.dir/mask_create.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/mask_create.cpp +[ 66%] Building CXX object src/apps/CMakeFiles/merge_particles.dir/merge_particles.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/merge_particles.dir/merge_particles.cpp.o -MF CMakeFiles/merge_particles.dir/merge_particles.cpp.o.d -o CMakeFiles/merge_particles.dir/merge_particles.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/merge_particles.cpp +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/flex_analyse_mpi.dir/flex_analyse_mpi.cpp.o -o ../../bin/relion_flex_analyse_mpi ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/projector.h:25, - from /build/reproducible-path/relion-3.1.3/src/ml_model.h:23, - from /build/reproducible-path/relion-3.1.3/src/ml_optimiser.h:35, - from /build/reproducible-path/relion-3.1.3/src/apps/../particle_subtractor.h:24, - from /build/reproducible-path/relion-3.1.3/src/apps/particle_subtract.cpp:22: + from /build/reproducible-path/relion-3.1.3/src/local_symmetry.h:30, + from /build/reproducible-path/relion-3.1.3/src/apps/localsym.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -8391,9 +8296,35 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 185 | uint32 cur_width, cur_length; + | ^~~~~~~~~ +/usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here + 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 185 | uint32 cur_width, cur_length; + | ^~~~~~~~~~ +/usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here + 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 186 | uint16 cur_sampleFormat, cur_bitsPerSample; + | ^~~~~~~~~~~~~~~~ +/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 186 | uint16 cur_sampleFormat, cur_bitsPerSample; + | ^~~~~~~~~~~~~~~~~ +/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/local_symmetry.h:30, - from /build/reproducible-path/relion-3.1.3/src/apps/localsym.cpp:21: + from /build/reproducible-path/relion-3.1.3/src/jaz/obs_model.h:24, + from /build/reproducible-path/relion-3.1.3/src/scheduler.h:26, + from /build/reproducible-path/relion-3.1.3/src/gui_mainwindow.h:28, + from /build/reproducible-path/relion-3.1.3/src/gui_mainwindow.cpp:22: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -8451,43 +8382,48 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] - 185 | uint32 cur_width, cur_length; - | ^~~~~~~~~ +make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' +[ 66%] Built target ctf_refine_mpi +In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, + from /build/reproducible-path/relion-3.1.3/src/jaz/obs_model.h:24, + from /build/reproducible-path/relion-3.1.3/src/apps/import.cpp:22: +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 43 | uint32 width, length; // apparent dimensions in the file + | ^~~~~ +In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, + from /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] - 185 | uint32 cur_width, cur_length; - | ^~~~~~~~~~ +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 43 | uint32 width, length; // apparent dimensions in the file + | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 186 | uint16 cur_sampleFormat, cur_bitsPerSample; - | ^~~~~~~~~~~~~~~~ +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; + | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 186 | uint16 cur_sampleFormat, cur_bitsPerSample; - | ^~~~~~~~~~~~~~~~~ +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; + | ^~~~~~~~~~~~~ +/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; + | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +/usr/bin/make -f src/apps/CMakeFiles/motion_refine.dir/build.make src/apps/CMakeFiles/motion_refine.dir/depend /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ -In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/projector.h:25, - from /build/reproducible-path/relion-3.1.3/src/ml_model.h:23, - from /build/reproducible-path/relion-3.1.3/src/ml_optimiser.h:35, - from /build/reproducible-path/relion-3.1.3/src/apps/../particle_subtractor.h:24, - from /build/reproducible-path/relion-3.1.3/src/apps/particle_subtract_mpi.cpp:22: -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] - 43 | uint32 width, length; // apparent dimensions in the file - | ^~~~~ /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ @@ -8500,58 +8436,41 @@ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ -In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, - from /build/reproducible-path/relion-3.1.3/src/image.h:57: -/usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here - 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; - | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations] - 43 | uint32 width, length; // apparent dimensions in the file - | ^~~~~~ +/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ +make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' +cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/motion_refine.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' +/usr/bin/make -f src/apps/CMakeFiles/motion_refine.dir/build.make src/apps/CMakeFiles/motion_refine.dir/build +make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' +[ 67%] Building CXX object src/apps/CMakeFiles/motion_refine.dir/motion_refine.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/motion_refine.dir/motion_refine.cpp.o -MF CMakeFiles/motion_refine.dir/motion_refine.cpp.o.d -o CMakeFiles/motion_refine.dir/motion_refine.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/motion_refine.cpp +[ 68%] Linking CXX executable ../../bin/relion_flex_analyse +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/flex_analyse.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/flex_analyse.dir/flex_analyse.cpp.o -o ../../bin/relion_flex_analyse ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/apps/plot_delocalisation.cpp:7: + from /build/reproducible-path/relion-3.1.3/src/local_symmetry.h:30, + from /build/reproducible-path/relion-3.1.3/src/local_symmetry_mpi.h:5, + from /build/reproducible-path/relion-3.1.3/src/apps/localsym_mpi.cpp:1: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ -/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here - 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; - | ^~~~~~~~~~~~ -/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; - | ^~~~~~~~~~~~~ -/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; - | ^~~~~~~~~~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ -/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ @@ -8597,34 +8516,12 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] - 185 | uint32 cur_width, cur_length; - | ^~~~~~~~~ -/usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here - 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] - 185 | uint32 cur_width, cur_length; - | ^~~~~~~~~~ -/usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here - 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 186 | uint16 cur_sampleFormat, cur_bitsPerSample; - | ^~~~~~~~~~~~~~~~ -/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 186 | uint16 cur_sampleFormat, cur_bitsPerSample; - | ^~~~~~~~~~~~~~~~~ -/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ +[ 68%] Linking CXX executable ../../bin/relion_localsym +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/localsym.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/localsym.dir/localsym.cpp.o -o ../../bin/relion_localsym ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/autopicker.h:10, - from /build/reproducible-path/relion-3.1.3/src/autopicker_mpi.h:12, - from /build/reproducible-path/relion-3.1.3/src/apps/autopick_mpi.cpp:20: + from /build/reproducible-path/relion-3.1.3/src/jaz/io/star_converter.h:5, + from /build/reproducible-path/relion-3.1.3/src/apps/merge_particles.cpp:2: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -8658,10 +8555,32 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 185 | uint32 cur_width, cur_length; + | ^~~~~~~~~ +/usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here + 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 185 | uint32 cur_width, cur_length; + | ^~~~~~~~~~ +/usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here + 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 186 | uint16 cur_sampleFormat, cur_bitsPerSample; + | ^~~~~~~~~~~~~~~~ +/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 186 | uint16 cur_sampleFormat, cur_bitsPerSample; + | ^~~~~~~~~~~~~~~~~ +/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/exp_model.h:24, - from /build/reproducible-path/relion-3.1.3/src/apps/../flex_analyser.h:24, - from /build/reproducible-path/relion-3.1.3/src/apps/flex_analyse.cpp:22: + from /build/reproducible-path/relion-3.1.3/src/apps/mask_create.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -8719,8 +8638,24 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +[ 68%] Linking CXX executable ../../bin/relion_localsym_mpi +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/localsym_mpi.dir/link.txt --verbose=1 +make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/localsym_mpi.dir/localsym_mpi.cpp.o -o ../../bin/relion_localsym_mpi ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +[ 68%] Built target flex_analyse_mpi +/usr/bin/make -f src/apps/CMakeFiles/motion_refine_mpi.dir/build.make src/apps/CMakeFiles/motion_refine_mpi.dir/depend +make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' +cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/motion_refine_mpi.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' +/usr/bin/make -f src/apps/CMakeFiles/motion_refine_mpi.dir/build.make src/apps/CMakeFiles/motion_refine_mpi.dir/build +make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' +[ 68%] Building CXX object src/apps/CMakeFiles/motion_refine_mpi.dir/motion_refine_mpi.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/motion_refine_mpi.dir/motion_refine_mpi.cpp.o -MF CMakeFiles/motion_refine_mpi.dir/motion_refine_mpi.cpp.o.d -o CMakeFiles/motion_refine_mpi.dir/motion_refine_mpi.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/motion_refine_mpi.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/apps/particle_FCC.cpp:7: + from /build/reproducible-path/relion-3.1.3/src/jaz/obs_model.h:24, + from /build/reproducible-path/relion-3.1.3/src/ctf.h:50, + from /build/reproducible-path/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, + from /build/reproducible-path/relion-3.1.3/src/apps/motion_refine.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -8778,35 +8713,68 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] - 185 | uint32 cur_width, cur_length; - | ^~~~~~~~~ -/usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here - 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] - 185 | uint32 cur_width, cur_length; - | ^~~~~~~~~~ -/usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here - 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 186 | uint16 cur_sampleFormat, cur_bitsPerSample; - | ^~~~~~~~~~~~~~~~ -/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 186 | uint16 cur_sampleFormat, cur_bitsPerSample; - | ^~~~~~~~~~~~~~~~~ -/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ +[ 69%] Linking CXX executable ../../bin/relion_find_tiltpairs +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/find_tiltpairs.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/find_tiltpairs.dir/find_tiltpairs.cpp.o -o ../../bin/relion_find_tiltpairs ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +[ 69%] Linking CXX executable ../../bin/relion_merge_particles +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/merge_particles.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/merge_particles.dir/merge_particles.cpp.o -o ../../bin/relion_merge_particles ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' +[ 69%] Built target localsym_mpi +make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' +make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' +/usr/bin/make -f src/apps/CMakeFiles/mrc2vtk.dir/build.make src/apps/CMakeFiles/mrc2vtk.dir/depend +[ 69%] Built target flex_analyse +make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' +cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/mrc2vtk.dir/DependInfo.cmake "--color=" +/usr/bin/make -f src/apps/CMakeFiles/particle_FCC.dir/build.make src/apps/CMakeFiles/particle_FCC.dir/depend +make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' +cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/particle_FCC.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' +/usr/bin/make -f src/apps/CMakeFiles/mrc2vtk.dir/build.make src/apps/CMakeFiles/mrc2vtk.dir/build +[ 69%] Built target localsym +make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' +/usr/bin/make -f src/apps/CMakeFiles/particle_reposition.dir/build.make src/apps/CMakeFiles/particle_reposition.dir/depend +make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' +cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/particle_reposition.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' +/usr/bin/make -f src/apps/CMakeFiles/particle_FCC.dir/build.make src/apps/CMakeFiles/particle_FCC.dir/build +[ 69%] Building CXX object src/apps/CMakeFiles/mrc2vtk.dir/mrc2vtk.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/mrc2vtk.dir/mrc2vtk.cpp.o -MF CMakeFiles/mrc2vtk.dir/mrc2vtk.cpp.o.d -o CMakeFiles/mrc2vtk.dir/mrc2vtk.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/mrc2vtk.cpp +make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' +[ 70%] Building CXX object src/apps/CMakeFiles/particle_FCC.dir/particle_FCC.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/particle_FCC.dir/particle_FCC.cpp.o -MF CMakeFiles/particle_FCC.dir/particle_FCC.cpp.o.d -o CMakeFiles/particle_FCC.dir/particle_FCC.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/particle_FCC.cpp +make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' +/usr/bin/make -f src/apps/CMakeFiles/particle_reposition.dir/build.make src/apps/CMakeFiles/particle_reposition.dir/build +make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' +[ 71%] Building CXX object src/apps/CMakeFiles/particle_reposition.dir/particle_reposition.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/particle_reposition.dir/particle_reposition.cpp.o -MF CMakeFiles/particle_reposition.dir/particle_reposition.cpp.o.d -o CMakeFiles/particle_reposition.dir/particle_reposition.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/particle_reposition.cpp +make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' +[ 71%] Built target find_tiltpairs +/usr/bin/make -f src/apps/CMakeFiles/particle_select.dir/build.make src/apps/CMakeFiles/particle_select.dir/depend +make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' +cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/particle_select.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' +/usr/bin/make -f src/apps/CMakeFiles/particle_select.dir/build.make src/apps/CMakeFiles/particle_select.dir/build +make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' +[ 71%] Building CXX object src/apps/CMakeFiles/particle_select.dir/particle_select.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/particle_select.dir/particle_select.cpp.o -MF CMakeFiles/particle_select.dir/particle_select.cpp.o.d -o CMakeFiles/particle_select.dir/particle_select.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/particle_select.cpp +make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' +[ 71%] Built target merge_particles +/usr/bin/make -f src/apps/CMakeFiles/particle_subtract.dir/build.make src/apps/CMakeFiles/particle_subtract.dir/depend +make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' +cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/particle_subtract.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' +/usr/bin/make -f src/apps/CMakeFiles/particle_subtract.dir/build.make src/apps/CMakeFiles/particle_subtract.dir/build +make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' +[ 71%] Building CXX object src/apps/CMakeFiles/particle_subtract.dir/particle_subtract.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/particle_subtract.dir/particle_subtract.cpp.o -MF CMakeFiles/particle_subtract.dir/particle_subtract.cpp.o.d -o CMakeFiles/particle_subtract.dir/particle_subtract.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/particle_subtract.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/jaz/obs_model.h:24, - from /build/reproducible-path/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, - from /build/reproducible-path/relion-3.1.3/src/jaz/ctf/ctf_refiner_mpi.h:26, - from /build/reproducible-path/relion-3.1.3/src/apps/ctf_refine_mpi.cpp:21: + from /build/reproducible-path/relion-3.1.3/src/ctf.h:50, + from /build/reproducible-path/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, + from /build/reproducible-path/relion-3.1.3/src/jaz/motion/motion_refiner_mpi.h:27, + from /build/reproducible-path/relion-3.1.3/src/apps/motion_refine_mpi.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -8865,8 +8833,10 @@ 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/tiff_converter.h:24, - from /build/reproducible-path/relion-3.1.3/src/apps/convert_to_tiff_mpi.cpp:21: + from /build/reproducible-path/relion-3.1.3/src/projector.h:25, + from /build/reproducible-path/relion-3.1.3/src/ml_model.h:23, + from /build/reproducible-path/relion-3.1.3/src/ml_optimiser.h:35, + from /build/reproducible-path/relion-3.1.3/src/apps/particle_reposition.cpp:22: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -8925,7 +8895,7 @@ 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/apps/ctf_mask_test.cpp:7: + from /build/reproducible-path/relion-3.1.3/src/apps/mrc2vtk.cpp:1: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -8959,9 +8929,32 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 185 | uint32 cur_width, cur_length; + | ^~~~~~~~~ +/usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here + 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 185 | uint32 cur_width, cur_length; + | ^~~~~~~~~~ +/usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here + 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 186 | uint16 cur_sampleFormat, cur_bitsPerSample; + | ^~~~~~~~~~~~~~~~ +/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 186 | uint16 cur_sampleFormat, cur_bitsPerSample; + | ^~~~~~~~~~~~~~~~~ +/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/displayer.h:40, - from /build/reproducible-path/relion-3.1.3/src/displayer.cpp:21: + from /build/reproducible-path/relion-3.1.3/src/apps/particle_FCC.cpp:7: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -9019,6 +9012,45 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, + from /build/reproducible-path/relion-3.1.3/src/projector.h:25, + from /build/reproducible-path/relion-3.1.3/src/ml_model.h:23, + from /build/reproducible-path/relion-3.1.3/src/ml_optimiser.h:35, + from /build/reproducible-path/relion-3.1.3/src/apps/../particle_subtractor.h:24, + from /build/reproducible-path/relion-3.1.3/src/apps/particle_subtract.cpp:22: +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 43 | uint32 width, length; // apparent dimensions in the file + | ^~~~~ +In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, + from /build/reproducible-path/relion-3.1.3/src/image.h:57: +/usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here + 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 43 | uint32 width, length; // apparent dimensions in the file + | ^~~~~~ +/usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here + 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; + | ^~~~~~~~~~~~ +/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; + | ^~~~~~~~~~~~~ +/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; + | ^~~~~~~~~~~~~~ +/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ @@ -9043,10 +9075,17 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +[ 71%] Linking CXX executable ../../bin/relion_estimate_gain +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/estimate_gain.dir/link.txt --verbose=1 +[ 72%] Linking CXX executable ../../bin/relion_demodulate +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/demodulate.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/estimate_gain.dir/estimate_gain.cpp.o -o ../../bin/relion_estimate_gain ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/demodulate.dir/demodulate.cpp.o -o ../../bin/relion_demodulate ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/local_symmetry.h:30, - from /build/reproducible-path/relion-3.1.3/src/local_symmetry_mpi.h:5, - from /build/reproducible-path/relion-3.1.3/src/apps/localsym_mpi.cpp:1: + from /build/reproducible-path/relion-3.1.3/src/jaz/obs_model.h:24, + from /build/reproducible-path/relion-3.1.3/src/ctf.h:50, + from /build/reproducible-path/relion-3.1.3/src/jaz/stack_helper.h:24, + from /build/reproducible-path/relion-3.1.3/src/apps/particle_select.cpp:1: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -9104,9 +9143,88 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +[ 73%] Linking CXX executable ../../bin/relion_ctf_mask_test +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/ctf_mask_test.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ctf_mask_test.dir/ctf_mask_test.cpp.o -o ../../bin/relion_ctf_mask_test ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +[ 73%] Linking CXX executable ../../bin/relion_motion_refine +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/motion_refine.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/motion_refine.dir/motion_refine.cpp.o -o ../../bin/relion_motion_refine ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' +[ 73%] Built target demodulate +/usr/bin/make -f src/apps/CMakeFiles/particle_subtract_mpi.dir/build.make src/apps/CMakeFiles/particle_subtract_mpi.dir/depend +make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' +cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/particle_subtract_mpi.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' +make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' +/usr/bin/make -f src/apps/CMakeFiles/particle_subtract_mpi.dir/build.make src/apps/CMakeFiles/particle_subtract_mpi.dir/build +make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' +[ 73%] Built target estimate_gain +[ 73%] Building CXX object src/apps/CMakeFiles/particle_subtract_mpi.dir/particle_subtract_mpi.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/particle_subtract_mpi.dir/particle_subtract_mpi.cpp.o -MF CMakeFiles/particle_subtract_mpi.dir/particle_subtract_mpi.cpp.o.d -o CMakeFiles/particle_subtract_mpi.dir/particle_subtract_mpi.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/particle_subtract_mpi.cpp +/usr/bin/make -f src/apps/CMakeFiles/particle_symmetry_expand.dir/build.make src/apps/CMakeFiles/particle_symmetry_expand.dir/depend +make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' +cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/particle_symmetry_expand.dir/DependInfo.cmake "--color=" +[ 73%] Linking CXX executable ../../bin/relion_import +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/import.dir/link.txt --verbose=1 +make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' +/usr/bin/make -f src/apps/CMakeFiles/particle_symmetry_expand.dir/build.make src/apps/CMakeFiles/particle_symmetry_expand.dir/build +make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/import.dir/import.cpp.o -o ../../bin/relion_import ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +[ 74%] Building CXX object src/apps/CMakeFiles/particle_symmetry_expand.dir/particle_symmetry_expand.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/particle_symmetry_expand.dir/particle_symmetry_expand.cpp.o -MF CMakeFiles/particle_symmetry_expand.dir/particle_symmetry_expand.cpp.o.d -o CMakeFiles/particle_symmetry_expand.dir/particle_symmetry_expand.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/particle_symmetry_expand.cpp +make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' +[ 74%] Built target ctf_mask_test +/usr/bin/make -f src/apps/CMakeFiles/pipeliner.dir/build.make src/apps/CMakeFiles/pipeliner.dir/depend +make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' +cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/pipeliner.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' +/usr/bin/make -f src/apps/CMakeFiles/pipeliner.dir/build.make src/apps/CMakeFiles/pipeliner.dir/build +make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' +make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' +[ 74%] Building CXX object src/apps/CMakeFiles/pipeliner.dir/pipeliner.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/pipeliner.dir/pipeliner.cpp.o -MF CMakeFiles/pipeliner.dir/pipeliner.cpp.o.d -o CMakeFiles/pipeliner.dir/pipeliner.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/pipeliner.cpp +[ 74%] Built target import +/usr/bin/make -f src/apps/CMakeFiles/plot_delocalisation.dir/build.make src/apps/CMakeFiles/plot_delocalisation.dir/depend +make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' +cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/plot_delocalisation.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' +/usr/bin/make -f src/apps/CMakeFiles/plot_delocalisation.dir/build.make src/apps/CMakeFiles/plot_delocalisation.dir/build +make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' +[ 74%] Building CXX object src/apps/CMakeFiles/plot_delocalisation.dir/plot_delocalisation.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/plot_delocalisation.dir/plot_delocalisation.cpp.o -MF CMakeFiles/plot_delocalisation.dir/plot_delocalisation.cpp.o.d -o CMakeFiles/plot_delocalisation.dir/plot_delocalisation.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/plot_delocalisation.cpp +[ 74%] Linking CXX executable ../../bin/relion_external_reconstruct +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/external_reconstruct.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/external_reconstruct.dir/external_reconstruct.cpp.o -o ../../bin/relion_external_reconstruct ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' +[ 75%] Linking CXX executable ../../bin/relion_motion_refine_mpi +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/motion_refine_mpi.dir/link.txt --verbose=1 +[ 75%] Built target motion_refine +/usr/bin/make -f src/apps/CMakeFiles/postprocess.dir/build.make src/apps/CMakeFiles/postprocess.dir/depend +make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' +cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/postprocess.dir/DependInfo.cmake "--color=" +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/motion_refine_mpi.dir/motion_refine_mpi.cpp.o -o ../../bin/relion_motion_refine_mpi ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' +/usr/bin/make -f src/apps/CMakeFiles/postprocess.dir/build.make src/apps/CMakeFiles/postprocess.dir/build +make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' +[ 75%] Building CXX object src/apps/CMakeFiles/postprocess.dir/postprocess.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/postprocess.dir/postprocess.cpp.o -MF CMakeFiles/postprocess.dir/postprocess.cpp.o.d -o CMakeFiles/postprocess.dir/postprocess.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/postprocess.cpp +[ 75%] Linking CXX executable ../../bin/relion_particle_FCC +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/particle_FCC.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/particle_FCC.dir/particle_FCC.cpp.o -o ../../bin/relion_particle_FCC ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' +[ 75%] Built target external_reconstruct +/usr/bin/make -f src/apps/CMakeFiles/postprocess_mpi.dir/build.make src/apps/CMakeFiles/postprocess_mpi.dir/depend +make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' +cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/postprocess_mpi.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' +/usr/bin/make -f src/apps/CMakeFiles/postprocess_mpi.dir/build.make src/apps/CMakeFiles/postprocess_mpi.dir/build +make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/postprocessing.h:24, - from /build/reproducible-path/relion-3.1.3/src/apps/postprocess_mpi.cpp:20: + from /build/reproducible-path/relion-3.1.3/src/projector.h:25, + from /build/reproducible-path/relion-3.1.3/src/ml_model.h:23, + from /build/reproducible-path/relion-3.1.3/src/ml_optimiser.h:35, + from /build/reproducible-path/relion-3.1.3/src/apps/../particle_subtractor.h:24, + from /build/reproducible-path/relion-3.1.3/src/apps/particle_subtract_mpi.cpp:22: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -9164,9 +9282,14 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +[ 75%] Linking CXX executable ../../bin/relion_ctf_toolbox +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/ctf_toolbox.dir/link.txt --verbose=1 +[ 76%] Building CXX object src/apps/CMakeFiles/postprocess_mpi.dir/postprocess_mpi.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/postprocess_mpi.dir/postprocess_mpi.cpp.o -MF CMakeFiles/postprocess_mpi.dir/postprocess_mpi.cpp.o.d -o CMakeFiles/postprocess_mpi.dir/postprocess_mpi.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/postprocess_mpi.cpp +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ctf_toolbox.dir/ctf_toolbox.cpp.o -o ../../bin/relion_ctf_toolbox ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/jaz/vtk_helper.h:24, - from /build/reproducible-path/relion-3.1.3/src/apps/demodulate.cpp:1: + from /build/reproducible-path/relion-3.1.3/src/jaz/obs_model.h:24, + from /build/reproducible-path/relion-3.1.3/src/apps/particle_symmetry_expand.cpp:26: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -9225,10 +9348,8 @@ 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/jaz/obs_model.h:24, - from /build/reproducible-path/relion-3.1.3/src/scheduler.h:26, - from /build/reproducible-path/relion-3.1.3/src/gui_mainwindow.h:28, - from /build/reproducible-path/relion-3.1.3/src/gui_mainwindow.cpp:22: + from /build/reproducible-path/relion-3.1.3/src/postprocessing.h:24, + from /build/reproducible-path/relion-3.1.3/src/apps/postprocess.cpp:20: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -9286,9 +9407,10 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +[ 77%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/manualpicker.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_gui_lib.dir/__/manualpicker.cpp.o -MF CMakeFiles/relion_gui_lib.dir/__/manualpicker.cpp.o.d -o CMakeFiles/relion_gui_lib.dir/__/manualpicker.cpp.o -c /build/reproducible-path/relion-3.1.3/src/manualpicker.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/helix.h:30, - from /build/reproducible-path/relion-3.1.3/src/apps/prepare_subtomo.cpp:22: + from /build/reproducible-path/relion-3.1.3/src/apps/plot_delocalisation.cpp:7: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -9346,12 +9468,38 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +[ 78%] Linking CXX executable ../../bin/relion_particle_select +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/particle_select.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/particle_select.dir/particle_select.cpp.o -o ../../bin/relion_particle_select ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +[ 78%] Linking CXX executable ../../bin/relion_align_symmetry +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/align_symmetry.dir/link.txt --verbose=1 +make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/align_symmetry.dir/align_symmetry.cpp.o -o ../../bin/relion_align_symmetry ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +[ 78%] Built target ctf_toolbox +/usr/bin/make -f src/apps/CMakeFiles/prepare_subtomo.dir/build.make src/apps/CMakeFiles/prepare_subtomo.dir/depend +[ 78%] Linking CXX executable ../../bin/relion_mrc2vtk +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/mrc2vtk.dir/link.txt --verbose=1 +make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' +cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/prepare_subtomo.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/mrc2vtk.dir/mrc2vtk.cpp.o -o ../../bin/relion_mrc2vtk ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' +/usr/bin/make -f src/apps/CMakeFiles/prepare_subtomo.dir/build.make src/apps/CMakeFiles/prepare_subtomo.dir/build +make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' +[ 78%] Built target particle_FCC +/usr/bin/make -f src/apps/CMakeFiles/preprocess.dir/build.make src/apps/CMakeFiles/preprocess.dir/depend +make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' +cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/preprocess.dir/DependInfo.cmake "--color=" +[ 78%] Building CXX object src/apps/CMakeFiles/prepare_subtomo.dir/prepare_subtomo.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/prepare_subtomo.dir/prepare_subtomo.cpp.o -MF CMakeFiles/prepare_subtomo.dir/prepare_subtomo.cpp.o.d -o CMakeFiles/prepare_subtomo.dir/prepare_subtomo.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/prepare_subtomo.cpp +make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' +/usr/bin/make -f src/apps/CMakeFiles/preprocess.dir/build.make src/apps/CMakeFiles/preprocess.dir/build +make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' +[ 78%] Building CXX object src/apps/CMakeFiles/preprocess.dir/preprocess.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/preprocess.dir/preprocess.cpp.o -MF CMakeFiles/preprocess.dir/preprocess.cpp.o.d -o CMakeFiles/preprocess.dir/preprocess.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/preprocess.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/jaz/obs_model.h:24, - from /build/reproducible-path/relion-3.1.3/src/ctf.h:50, - from /build/reproducible-path/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, - from /build/reproducible-path/relion-3.1.3/src/jaz/motion/motion_refiner_mpi.h:27, - from /build/reproducible-path/relion-3.1.3/src/apps/motion_refine_mpi.cpp:21: + from /build/reproducible-path/relion-3.1.3/src/postprocessing.h:24, + from /build/reproducible-path/relion-3.1.3/src/apps/postprocess_mpi.cpp:20: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -9409,169 +9557,65 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 68%] Linking CXX executable ../../bin/relion_convert_to_tiff -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/convert_to_tiff.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/convert_to_tiff.dir/convert_to_tiff.cpp.o -o ../../bin/relion_convert_to_tiff ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -[ 68%] Linking CXX executable ../../bin/relion_localsym -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/localsym.dir/link.txt --verbose=1 -[ 68%] Linking CXX executable ../../bin/relion_helix_inimodel2d -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/helix_inimodel2d.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/localsym.dir/localsym.cpp.o -o ../../bin/relion_localsym ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -[ 68%] Linking CXX executable ../../bin/relion_localsym_mpi -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/localsym_mpi.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/helix_inimodel2d.dir/helix_inimodel2d.cpp.o -o ../../bin/relion_helix_inimodel2d ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -[ 68%] Linking CXX executable ../../bin/relion_convert_to_tiff_mpi -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/convert_to_tiff_mpi.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/localsym_mpi.dir/localsym_mpi.cpp.o -o ../../bin/relion_localsym_mpi ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/convert_to_tiff_mpi.dir/convert_to_tiff_mpi.cpp.o -o ../../bin/relion_convert_to_tiff_mpi ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -[ 68%] Built target convert_to_tiff -/usr/bin/make -f src/apps/CMakeFiles/preprocess.dir/build.make src/apps/CMakeFiles/preprocess.dir/depend -make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' -cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/preprocess.dir/DependInfo.cmake "--color=" -[ 68%] Linking CXX executable ../../bin/relion_postprocess -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/postprocess.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/postprocess.dir/postprocess.cpp.o -o ../../bin/relion_postprocess ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/preprocess.dir/build.make src/apps/CMakeFiles/preprocess.dir/build -make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' -[ 69%] Linking CXX executable ../../bin/relion_convert_star -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/convert_star.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/convert_star.dir/convert_star.cpp.o -o ../../bin/relion_convert_star ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -[ 69%] Building CXX object src/apps/CMakeFiles/preprocess.dir/preprocess.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/preprocess.dir/preprocess.cpp.o -MF CMakeFiles/preprocess.dir/preprocess.cpp.o.d -o CMakeFiles/preprocess.dir/preprocess.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/preprocess.cpp -make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -[ 69%] Built target helix_inimodel2d +[ 78%] Built target motion_refine_mpi /usr/bin/make -f src/apps/CMakeFiles/preprocess_mpi.dir/build.make src/apps/CMakeFiles/preprocess_mpi.dir/depend +[ 78%] Linking CXX executable ../../bin/relion_mask_create +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/mask_create.dir/link.txt --verbose=1 make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/preprocess_mpi.dir/DependInfo.cmake "--color=" -[ 69%] Linking CXX executable ../../bin/relion_autopick -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/autopick.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/mask_create.dir/mask_create.cpp.o -o ../../bin/relion_mask_create ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -[ 69%] Built target convert_to_tiff_mpi -/usr/bin/make -f src/apps/CMakeFiles/project.dir/build.make src/apps/CMakeFiles/project.dir/depend +/usr/bin/make -f src/apps/CMakeFiles/preprocess_mpi.dir/build.make src/apps/CMakeFiles/preprocess_mpi.dir/build +make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' +[ 78%] Building CXX object src/apps/CMakeFiles/preprocess_mpi.dir/preprocess_mpi.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/preprocess_mpi.dir/preprocess_mpi.cpp.o -MF CMakeFiles/preprocess_mpi.dir/preprocess_mpi.cpp.o.d -o CMakeFiles/preprocess_mpi.dir/preprocess_mpi.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/preprocess_mpi.cpp +[ 78%] Built target particle_select +/usr/bin/make -f src/apps/CMakeFiles/project.dir/build.make src/apps/CMakeFiles/project.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/project.dir/DependInfo.cmake "--color=" -/usr/bin/make -f src/apps/CMakeFiles/preprocess_mpi.dir/build.make src/apps/CMakeFiles/preprocess_mpi.dir/build -make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/autopick.dir/autopick.cpp.o -o ../../bin/relion_autopick ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -[ 69%] Linking CXX executable ../../bin/relion_postprocess_mpi -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/postprocess_mpi.dir/link.txt --verbose=1 -[ 70%] Linking CXX executable ../../bin/relion_autopick_mpi -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/autopick_mpi.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' /usr/bin/make -f src/apps/CMakeFiles/project.dir/build.make src/apps/CMakeFiles/project.dir/build make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' -[ 70%] Building CXX object src/apps/CMakeFiles/preprocess_mpi.dir/preprocess_mpi.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/preprocess_mpi.dir/preprocess_mpi.cpp.o -MF CMakeFiles/preprocess_mpi.dir/preprocess_mpi.cpp.o.d -o CMakeFiles/preprocess_mpi.dir/preprocess_mpi.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/preprocess_mpi.cpp -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/postprocess_mpi.dir/postprocess_mpi.cpp.o -o ../../bin/relion_postprocess_mpi ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/autopick_mpi.dir/autopick_mpi.cpp.o -o ../../bin/relion_autopick_mpi ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -[ 71%] Building CXX object src/apps/CMakeFiles/project.dir/project.cpp.o +[ 79%] Building CXX object src/apps/CMakeFiles/project.dir/project.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/project.dir/project.cpp.o -MF CMakeFiles/project.dir/project.cpp.o.d -o CMakeFiles/project.dir/project.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/project.cpp make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -[ 71%] Linking CXX executable ../../bin/relion_merge_particles -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/merge_particles.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/merge_particles.dir/merge_particles.cpp.o -o ../../bin/relion_merge_particles ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -[ 71%] Built target localsym +[ 79%] Built target mrc2vtk /usr/bin/make -f src/apps/CMakeFiles/reconstruct.dir/build.make src/apps/CMakeFiles/reconstruct.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/reconstruct.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' /usr/bin/make -f src/apps/CMakeFiles/reconstruct.dir/build.make src/apps/CMakeFiles/reconstruct.dir/build make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' -[ 71%] Built target localsym_mpi +[ 79%] Building CXX object src/apps/CMakeFiles/reconstruct.dir/reconstruct.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/reconstruct.dir/reconstruct.cpp.o -MF CMakeFiles/reconstruct.dir/reconstruct.cpp.o.d -o CMakeFiles/reconstruct.dir/reconstruct.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/reconstruct.cpp +make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' +[ 79%] Built target align_symmetry /usr/bin/make -f src/apps/CMakeFiles/reconstruct_mpi.dir/build.make src/apps/CMakeFiles/reconstruct_mpi.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/reconstruct_mpi.dir/DependInfo.cmake "--color=" -[ 71%] Building CXX object src/apps/CMakeFiles/reconstruct.dir/reconstruct.cpp.o make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' /usr/bin/make -f src/apps/CMakeFiles/reconstruct_mpi.dir/build.make src/apps/CMakeFiles/reconstruct_mpi.dir/build make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/reconstruct.dir/reconstruct.cpp.o -MF CMakeFiles/reconstruct.dir/reconstruct.cpp.o.d -o CMakeFiles/reconstruct.dir/reconstruct.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/reconstruct.cpp -[ 71%] Building CXX object src/apps/CMakeFiles/reconstruct_mpi.dir/reconstruct_mpi.cpp.o +[ 79%] Linking CXX executable ../../bin/relion_postprocess +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/postprocess.dir/link.txt --verbose=1 +[ 79%] Building CXX object src/apps/CMakeFiles/reconstruct_mpi.dir/reconstruct_mpi.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/reconstruct_mpi.dir/reconstruct_mpi.cpp.o -MF CMakeFiles/reconstruct_mpi.dir/reconstruct_mpi.cpp.o.d -o CMakeFiles/reconstruct_mpi.dir/reconstruct_mpi.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/reconstruct_mpi.cpp -[ 72%] Linking CXX executable ../../bin/relion_ctf_refine -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/ctf_refine.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ctf_refine.dir/ctf_refine.cpp.o -o ../../bin/relion_ctf_refine ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -[ 72%] Built target postprocess +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/postprocess.dir/postprocess.cpp.o -o ../../bin/relion_postprocess ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +[ 79%] Built target mask_create /usr/bin/make -f src/apps/CMakeFiles/refine.dir/build.make src/apps/CMakeFiles/refine.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/refine.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' /usr/bin/make -f src/apps/CMakeFiles/refine.dir/build.make src/apps/CMakeFiles/refine.dir/build make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' -[ 72%] Building CXX object src/apps/CMakeFiles/refine.dir/refine.cpp.o +[ 79%] Building CXX object src/apps/CMakeFiles/refine.dir/refine.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/refine.dir/refine.cpp.o -MF CMakeFiles/refine.dir/refine.cpp.o.d -o CMakeFiles/refine.dir/refine.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/refine.cpp -[ 72%] Linking CXX executable ../../bin/relion_ctf_refine_mpi -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/ctf_refine_mpi.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ctf_refine_mpi.dir/ctf_refine_mpi.cpp.o -o ../../bin/relion_ctf_refine_mpi ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -[ 72%] Built target convert_star -/usr/bin/make -f src/apps/CMakeFiles/refine_mpi.dir/build.make src/apps/CMakeFiles/refine_mpi.dir/depend -make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' -cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/refine_mpi.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/refine_mpi.dir/build.make src/apps/CMakeFiles/refine_mpi.dir/build -make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' -make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -[ 73%] Building CXX object src/apps/CMakeFiles/refine_mpi.dir/refine_mpi.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/refine_mpi.dir/refine_mpi.cpp.o -MF CMakeFiles/refine_mpi.dir/refine_mpi.cpp.o.d -o CMakeFiles/refine_mpi.dir/refine_mpi.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/refine_mpi.cpp -[ 74%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/manualpicker.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_gui_lib.dir/__/manualpicker.cpp.o -MF CMakeFiles/relion_gui_lib.dir/__/manualpicker.cpp.o.d -o CMakeFiles/relion_gui_lib.dir/__/manualpicker.cpp.o -c /build/reproducible-path/relion-3.1.3/src/manualpicker.cpp -[ 74%] Built target postprocess_mpi -/usr/bin/make -f src/apps/CMakeFiles/reposition.dir/build.make src/apps/CMakeFiles/reposition.dir/depend -make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' -cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/reposition.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/reposition.dir/build.make src/apps/CMakeFiles/reposition.dir/build -make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' -[ 74%] Built target merge_particles -/usr/bin/make -f src/apps/CMakeFiles/run_ctffind.dir/build.make src/apps/CMakeFiles/run_ctffind.dir/depend -make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' -cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/run_ctffind.dir/DependInfo.cmake "--color=" -[ 74%] Building CXX object src/apps/CMakeFiles/reposition.dir/reposition.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/reposition.dir/reposition.cpp.o -MF CMakeFiles/reposition.dir/reposition.cpp.o.d -o CMakeFiles/reposition.dir/reposition.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/reposition.cpp -make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/run_ctffind.dir/build.make src/apps/CMakeFiles/run_ctffind.dir/build -make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' -[ 74%] Building CXX object src/apps/CMakeFiles/run_ctffind.dir/run_ctffind.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/run_ctffind.dir/run_ctffind.cpp.o -MF CMakeFiles/run_ctffind.dir/run_ctffind.cpp.o.d -o CMakeFiles/run_ctffind.dir/run_ctffind.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/run_ctffind.cpp -make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -[ 74%] Built target autopick -/usr/bin/make -f src/apps/CMakeFiles/run_ctffind_mpi.dir/build.make src/apps/CMakeFiles/run_ctffind_mpi.dir/depend -make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' -cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/run_ctffind_mpi.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/run_ctffind_mpi.dir/build.make src/apps/CMakeFiles/run_ctffind_mpi.dir/build -make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' -[ 75%] Building CXX object src/apps/CMakeFiles/run_ctffind_mpi.dir/run_ctffind_mpi.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/run_ctffind_mpi.dir/run_ctffind_mpi.cpp.o -MF CMakeFiles/run_ctffind_mpi.dir/run_ctffind_mpi.cpp.o.d -o CMakeFiles/run_ctffind_mpi.dir/run_ctffind_mpi.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/run_ctffind_mpi.cpp -[ 75%] Linking CXX executable ../../bin/relion_particle_FCC -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/particle_FCC.dir/link.txt --verbose=1 -make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -[ 76%] Linking CXX executable ../../bin/relion_particle_select -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/particle_select.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/particle_FCC.dir/particle_FCC.cpp.o -o ../../bin/relion_particle_FCC ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/particle_select.dir/particle_select.cpp.o -o ../../bin/relion_particle_select ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -[ 76%] Built target autopick_mpi -/usr/bin/make -f src/apps/CMakeFiles/run_motioncorr.dir/build.make src/apps/CMakeFiles/run_motioncorr.dir/depend -make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' -cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/run_motioncorr.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/run_motioncorr.dir/build.make src/apps/CMakeFiles/run_motioncorr.dir/build -make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' -[ 77%] Building CXX object src/apps/CMakeFiles/run_motioncorr.dir/run_motioncorr.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/run_motioncorr.dir/run_motioncorr.cpp.o -MF CMakeFiles/run_motioncorr.dir/run_motioncorr.cpp.o.d -o CMakeFiles/run_motioncorr.dir/run_motioncorr.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/run_motioncorr.cpp -[ 77%] Linking CXX executable ../../bin/relion_motion_refine -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/motion_refine.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/motion_refine.dir/motion_refine.cpp.o -o ../../bin/relion_motion_refine ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/preprocessing.h:29, - from /build/reproducible-path/relion-3.1.3/src/apps/preprocess.cpp:20: + from /build/reproducible-path/relion-3.1.3/src/helix.h:30, + from /build/reproducible-path/relion-3.1.3/src/apps/prepare_subtomo.cpp:22: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -9605,46 +9649,6 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -In file included from /build/reproducible-path/relion-3.1.3/src/numerical_recipes.h:48, - from /build/reproducible-path/relion-3.1.3/src/funcs.h:59, - from /build/reproducible-path/relion-3.1.3/src/args.h:56, - from /build/reproducible-path/relion-3.1.3/src/apps/find_tiltpairs.cpp:20: -In function 'void free_Tvector(T*&, int, int) [with T = int]', - inlined from 'void gaussj(T*, int, T*, int) [with T = double]' at /build/reproducible-path/relion-3.1.3/src/numerical_recipes.h:262:17: -/build/reproducible-path/relion-3.1.3/src/memory.h:74:13: warning: 'void free(void*)' called on pointer 'ipiv' with nonzero offset 4 [-Wfree-nonheap-object] - 74 | free((char*)(v + nl)); - | ~~~~^~~~~~~~~~~~~~~~~ -/build/reproducible-path/relion-3.1.3/src/numerical_recipes.h: In function 'void gaussj(T*, int, T*, int) [with T = double]': -/build/reproducible-path/relion-3.1.3/src/numerical_recipes.h:198:26: note: declared here - 198 | int *indxc, *indxr, *ipiv; - | ^~~~ -In function 'void free_Tvector(T*&, int, int) [with T = int]', - inlined from 'void gaussj(T*, int, T*, int) [with T = double]' at /build/reproducible-path/relion-3.1.3/src/numerical_recipes.h:262:17: -/build/reproducible-path/relion-3.1.3/src/memory.h:74:13: warning: 'void free(void*)' called on pointer 'ipiv' with nonzero offset 4 [-Wfree-nonheap-object] - 74 | free((char*)(v + nl)); - | ~~~~^~~~~~~~~~~~~~~~~ -/build/reproducible-path/relion-3.1.3/src/numerical_recipes.h: In function 'void gaussj(T*, int, T*, int) [with T = double]': -/build/reproducible-path/relion-3.1.3/src/numerical_recipes.h:198:26: note: declared here - 198 | int *indxc, *indxr, *ipiv; - | ^~~~ -In function 'void free_Tvector(T*&, int, int) [with T = int]', - inlined from 'void gaussj(T*, int, T*, int) [with T = double]' at /build/reproducible-path/relion-3.1.3/src/numerical_recipes.h:263:17: -/build/reproducible-path/relion-3.1.3/src/memory.h:74:13: warning: 'void free(void*)' called on pointer 'indxr' with nonzero offset 4 [-Wfree-nonheap-object] - 74 | free((char*)(v + nl)); - | ~~~~^~~~~~~~~~~~~~~~~ -/build/reproducible-path/relion-3.1.3/src/numerical_recipes.h: In function 'void gaussj(T*, int, T*, int) [with T = double]': -/build/reproducible-path/relion-3.1.3/src/numerical_recipes.h:198:18: note: declared here - 198 | int *indxc, *indxr, *ipiv; - | ^~~~~ -In function 'void free_Tvector(T*&, int, int) [with T = int]', - inlined from 'void gaussj(T*, int, T*, int) [with T = double]' at /build/reproducible-path/relion-3.1.3/src/numerical_recipes.h:264:17: -/build/reproducible-path/relion-3.1.3/src/memory.h:74:13: warning: 'void free(void*)' called on pointer 'indxc' with nonzero offset 4 [-Wfree-nonheap-object] - 74 | free((char*)(v + nl)); - | ~~~~^~~~~~~~~~~~~~~~~ -/build/reproducible-path/relion-3.1.3/src/numerical_recipes.h: In function 'void gaussj(T*, int, T*, int) [with T = double]': -/build/reproducible-path/relion-3.1.3/src/numerical_recipes.h:198:10: note: declared here - 198 | int *indxc, *indxr, *ipiv; - | ^~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ @@ -9669,23 +9673,10 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -[ 77%] Built target ctf_refine -/usr/bin/make -f src/apps/CMakeFiles/run_motioncorr_mpi.dir/build.make src/apps/CMakeFiles/run_motioncorr_mpi.dir/depend -make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' -cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/run_motioncorr_mpi.dir/DependInfo.cmake "--color=" -[ 78%] Linking CXX executable ../../bin/relion_plot_delocalisation -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/plot_delocalisation.dir/link.txt --verbose=1 -make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/run_motioncorr_mpi.dir/build.make src/apps/CMakeFiles/run_motioncorr_mpi.dir/build -make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/plot_delocalisation.dir/plot_delocalisation.cpp.o -o ../../bin/relion_plot_delocalisation ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -[ 78%] Building CXX object src/apps/CMakeFiles/run_motioncorr_mpi.dir/run_motioncorr_mpi.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/run_motioncorr_mpi.dir/run_motioncorr_mpi.cpp.o -MF CMakeFiles/run_motioncorr_mpi.dir/run_motioncorr_mpi.cpp.o.d -o CMakeFiles/run_motioncorr_mpi.dir/run_motioncorr_mpi.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/run_motioncorr_mpi.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/preprocessing.h:29, - from /build/reproducible-path/relion-3.1.3/src/preprocessing_mpi.h:24, - from /build/reproducible-path/relion-3.1.3/src/apps/preprocess_mpi.cpp:20: + from /build/reproducible-path/relion-3.1.3/src/jaz/obs_model.h:24, + from /build/reproducible-path/relion-3.1.3/src/manualpicker.h:43, + from /build/reproducible-path/relion-3.1.3/src/manualpicker.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -9743,16 +9734,12 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 78%] Linking CXX executable ../../bin/relion_particle_symmetry_expand -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/particle_symmetry_expand.dir/link.txt --verbose=1 -make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -[ 79%] Linking CXX executable ../../bin/relion_pipeliner -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/pipeliner.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/particle_symmetry_expand.dir/particle_symmetry_expand.cpp.o -o ../../bin/relion_particle_symmetry_expand ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' +[ 79%] Linking CXX executable ../../bin/relion_postprocess_mpi +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/postprocess_mpi.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/postprocess_mpi.dir/postprocess_mpi.cpp.o -o ../../bin/relion_postprocess_mpi ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/projector.h:25, - from /build/reproducible-path/relion-3.1.3/src/apps/project.cpp:21: + from /build/reproducible-path/relion-3.1.3/src/preprocessing.h:29, + from /build/reproducible-path/relion-3.1.3/src/apps/preprocess.cpp:20: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -9810,16 +9797,23 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/pipeliner.dir/pipeliner.cpp.o -o ../../bin/relion_pipeliner ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -[ 79%] Built target ctf_refine_mpi -/usr/bin/make -f src/apps/CMakeFiles/scheduler.dir/build.make src/apps/CMakeFiles/scheduler.dir/depend +make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' +[ 79%] Built target postprocess +/usr/bin/make -f src/apps/CMakeFiles/refine_mpi.dir/build.make src/apps/CMakeFiles/refine_mpi.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' -cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/scheduler.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/refine_mpi.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' +/usr/bin/make -f src/apps/CMakeFiles/refine_mpi.dir/build.make src/apps/CMakeFiles/refine_mpi.dir/build +make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' +[ 80%] Linking CXX executable ../../bin/relion_particle_subtract +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/particle_subtract.dir/link.txt --verbose=1 +[ 81%] Building CXX object src/apps/CMakeFiles/refine_mpi.dir/refine_mpi.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/refine_mpi.dir/refine_mpi.cpp.o -MF CMakeFiles/refine_mpi.dir/refine_mpi.cpp.o.d -o CMakeFiles/refine_mpi.dir/refine_mpi.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/refine_mpi.cpp +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/particle_subtract.dir/particle_subtract.cpp.o -o ../../bin/relion_particle_subtract ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/projector.h:25, - from /build/reproducible-path/relion-3.1.3/src/backprojector.h:33, - from /build/reproducible-path/relion-3.1.3/src/reconstructor.h:23, - from /build/reproducible-path/relion-3.1.3/src/apps/reconstruct.cpp:21: + from /build/reproducible-path/relion-3.1.3/src/preprocessing.h:29, + from /build/reproducible-path/relion-3.1.3/src/preprocessing_mpi.h:24, + from /build/reproducible-path/relion-3.1.3/src/apps/preprocess_mpi.cpp:20: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -9838,7 +9832,6 @@ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ -[ 79%] Built target particle_select /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ @@ -9854,7 +9847,6 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -/usr/bin/make -f src/apps/CMakeFiles/stack_create.dir/build.make src/apps/CMakeFiles/stack_create.dir/depend /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ @@ -9879,20 +9871,9 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' -cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/stack_create.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/scheduler.dir/build.make src/apps/CMakeFiles/scheduler.dir/build -make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' -make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/stack_create.dir/build.make src/apps/CMakeFiles/stack_create.dir/build -make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/projector.h:25, - from /build/reproducible-path/relion-3.1.3/src/backprojector.h:33, - from /build/reproducible-path/relion-3.1.3/src/reconstructor.h:23, - from /build/reproducible-path/relion-3.1.3/src/reconstructor_mpi.h:25, - from /build/reproducible-path/relion-3.1.3/src/apps/reconstruct_mpi.cpp:21: + from /build/reproducible-path/relion-3.1.3/src/apps/project.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -9926,7 +9907,6 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 79%] Building CXX object src/apps/CMakeFiles/scheduler.dir/scheduler.cpp.o /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ @@ -9951,24 +9931,19 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/scheduler.dir/scheduler.cpp.o -MF CMakeFiles/scheduler.dir/scheduler.cpp.o.d -o CMakeFiles/scheduler.dir/scheduler.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/scheduler.cpp +[ 81%] Linking CXX executable ../../bin/relion_particle_symmetry_expand +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/particle_symmetry_expand.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/particle_symmetry_expand.dir/particle_symmetry_expand.cpp.o -o ../../bin/relion_particle_symmetry_expand ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -[ 80%] Building CXX object src/apps/CMakeFiles/stack_create.dir/stack_create.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/stack_create.dir/stack_create.cpp.o -MF CMakeFiles/stack_create.dir/stack_create.cpp.o.d -o CMakeFiles/stack_create.dir/stack_create.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/stack_create.cpp -[ 80%] Built target particle_FCC -/usr/bin/make -f src/apps/CMakeFiles/star_handler.dir/build.make src/apps/CMakeFiles/star_handler.dir/depend +[ 81%] Built target postprocess_mpi +/usr/bin/make -f src/apps/CMakeFiles/reposition.dir/build.make src/apps/CMakeFiles/reposition.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' -cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/star_handler.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/reposition.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/star_handler.dir/build.make src/apps/CMakeFiles/star_handler.dir/build +/usr/bin/make -f src/apps/CMakeFiles/reposition.dir/build.make src/apps/CMakeFiles/reposition.dir/build make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' -[ 80%] Linking CXX executable ../../bin/relion_flex_analyse_mpi -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/flex_analyse_mpi.dir/link.txt --verbose=1 -[ 81%] Linking CXX executable ../../bin/relion_flex_analyse -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/flex_analyse.dir/link.txt --verbose=1 -[ 82%] Building CXX object src/apps/CMakeFiles/star_handler.dir/star_handler.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/star_handler.dir/star_handler.cpp.o -MF CMakeFiles/star_handler.dir/star_handler.cpp.o.d -o CMakeFiles/star_handler.dir/star_handler.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/star_handler.cpp -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/flex_analyse_mpi.dir/flex_analyse_mpi.cpp.o -o ../../bin/relion_flex_analyse_mpi ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +[ 81%] Building CXX object src/apps/CMakeFiles/reposition.dir/reposition.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/reposition.dir/reposition.cpp.o -MF CMakeFiles/reposition.dir/reposition.cpp.o.d -o CMakeFiles/reposition.dir/reposition.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/reposition.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/projector.h:25, from /build/reproducible-path/relion-3.1.3/src/ml_model.h:23, @@ -10007,7 +9982,6 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/flex_analyse.dir/flex_analyse.cpp.o -o ../../bin/relion_flex_analyse ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ @@ -10032,11 +10006,21 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 83%] Linking CXX executable ../../bin/relion_motion_refine_mpi -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/motion_refine_mpi.dir/link.txt --verbose=1 +make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' +[ 81%] Built target particle_symmetry_expand +/usr/bin/make -f src/apps/CMakeFiles/run_ctffind.dir/build.make src/apps/CMakeFiles/run_ctffind.dir/depend +make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' +cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/run_ctffind.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' +/usr/bin/make -f src/apps/CMakeFiles/run_ctffind.dir/build.make src/apps/CMakeFiles/run_ctffind.dir/build +make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' +[ 81%] Building CXX object src/apps/CMakeFiles/run_ctffind.dir/run_ctffind.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/run_ctffind.dir/run_ctffind.cpp.o -MF CMakeFiles/run_ctffind.dir/run_ctffind.cpp.o.d -o CMakeFiles/run_ctffind.dir/run_ctffind.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/run_ctffind.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/ctffind_runner.h:31, - from /build/reproducible-path/relion-3.1.3/src/apps/run_ctffind.cpp:20: + from /build/reproducible-path/relion-3.1.3/src/projector.h:25, + from /build/reproducible-path/relion-3.1.3/src/backprojector.h:33, + from /build/reproducible-path/relion-3.1.3/src/reconstructor.h:23, + from /build/reproducible-path/relion-3.1.3/src/apps/reconstruct.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -10094,11 +10078,26 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/motion_refine_mpi.dir/motion_refine_mpi.cpp.o -o ../../bin/relion_motion_refine_mpi ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +[ 82%] Linking CXX executable ../../bin/relion_pipeliner +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/pipeliner.dir/link.txt --verbose=1 +[ 83%] Linking CXX executable ../../bin/relion_preprocess +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/preprocess.dir/link.txt --verbose=1 +[ 84%] Linking CXX executable ../../bin/relion_plot_delocalisation +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/plot_delocalisation.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/pipeliner.dir/pipeliner.cpp.o -o ../../bin/relion_pipeliner ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/preprocess.dir/preprocess.cpp.o -o ../../bin/relion_preprocess ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/plot_delocalisation.dir/plot_delocalisation.cpp.o -o ../../bin/relion_plot_delocalisation ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' +[ 84%] Built target particle_subtract +/usr/bin/make -f src/apps/CMakeFiles/run_ctffind_mpi.dir/build.make src/apps/CMakeFiles/run_ctffind_mpi.dir/depend +make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' +cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/run_ctffind_mpi.dir/DependInfo.cmake "--color=" In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/jaz/obs_model.h:24, - from /build/reproducible-path/relion-3.1.3/src/manualpicker.h:43, - from /build/reproducible-path/relion-3.1.3/src/manualpicker.cpp:21: + from /build/reproducible-path/relion-3.1.3/src/projector.h:25, + from /build/reproducible-path/relion-3.1.3/src/backprojector.h:33, + from /build/reproducible-path/relion-3.1.3/src/reconstructor.h:23, + from /build/reproducible-path/relion-3.1.3/src/reconstructor_mpi.h:25, + from /build/reproducible-path/relion-3.1.3/src/apps/reconstruct_mpi.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -10132,9 +10131,54 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 185 | uint32 cur_width, cur_length; + | ^~~~~~~~~ +/usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here + 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 185 | uint32 cur_width, cur_length; + | ^~~~~~~~~~ +/usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here + 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 186 | uint16 cur_sampleFormat, cur_bitsPerSample; + | ^~~~~~~~~~~~~~~~ +/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 186 | uint16 cur_sampleFormat, cur_bitsPerSample; + | ^~~~~~~~~~~~~~~~~ +/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ +make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' +/usr/bin/make -f src/apps/CMakeFiles/run_ctffind_mpi.dir/build.make src/apps/CMakeFiles/run_ctffind_mpi.dir/build +make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' +[ 85%] Building CXX object src/apps/CMakeFiles/run_ctffind_mpi.dir/run_ctffind_mpi.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/run_ctffind_mpi.dir/run_ctffind_mpi.cpp.o -MF CMakeFiles/run_ctffind_mpi.dir/run_ctffind_mpi.cpp.o.d -o CMakeFiles/run_ctffind_mpi.dir/run_ctffind_mpi.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/run_ctffind_mpi.cpp +[ 85%] Linking CXX executable ../../bin/relion_preprocess_mpi +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/preprocess_mpi.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/preprocess_mpi.dir/preprocess_mpi.cpp.o -o ../../bin/relion_preprocess_mpi ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' +[ 85%] Built target pipeliner +/usr/bin/make -f src/apps/CMakeFiles/run_motioncorr.dir/build.make src/apps/CMakeFiles/run_motioncorr.dir/depend +make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' +cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/run_motioncorr.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' +/usr/bin/make -f src/apps/CMakeFiles/run_motioncorr.dir/build.make src/apps/CMakeFiles/run_motioncorr.dir/build +make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' +[ 86%] Building CXX object src/apps/CMakeFiles/run_motioncorr.dir/run_motioncorr.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/run_motioncorr.dir/run_motioncorr.cpp.o -MF CMakeFiles/run_motioncorr.dir/run_motioncorr.cpp.o.d -o CMakeFiles/run_motioncorr.dir/run_motioncorr.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/run_motioncorr.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/jaz/obs_model.h:24, - from /build/reproducible-path/relion-3.1.3/src/apps/reposition.cpp:1: + from /build/reproducible-path/relion-3.1.3/src/projector.h:25, + from /build/reproducible-path/relion-3.1.3/src/ml_model.h:23, + from /build/reproducible-path/relion-3.1.3/src/ml_optimiser.h:35, + from /build/reproducible-path/relion-3.1.3/src/ml_optimiser_mpi.h:24, + from /build/reproducible-path/relion-3.1.3/src/apps/refine_mpi.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -10147,9 +10191,6 @@ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] - 185 | uint32 cur_width, cur_length; - | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ @@ -10162,9 +10203,6 @@ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ -/usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here - 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; - | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ @@ -10174,24 +10212,6 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] - 185 | uint32 cur_width, cur_length; - | ^~~~~~~~~~ -/usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here - 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 186 | uint16 cur_sampleFormat, cur_bitsPerSample; - | ^~~~~~~~~~~~~~~~ -/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 186 | uint16 cur_sampleFormat, cur_bitsPerSample; - | ^~~~~~~~~~~~~~~~~ -/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ @@ -10216,12 +10236,17 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' +[ 86%] Built target plot_delocalisation +/usr/bin/make -f src/apps/CMakeFiles/run_motioncorr_mpi.dir/build.make src/apps/CMakeFiles/run_motioncorr_mpi.dir/depend +make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' +cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/run_motioncorr_mpi.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' +make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' +/usr/bin/make -f src/apps/CMakeFiles/run_motioncorr_mpi.dir/build.make src/apps/CMakeFiles/run_motioncorr_mpi.dir/build In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/projector.h:25, - from /build/reproducible-path/relion-3.1.3/src/ml_model.h:23, - from /build/reproducible-path/relion-3.1.3/src/ml_optimiser.h:35, - from /build/reproducible-path/relion-3.1.3/src/ml_optimiser_mpi.h:24, - from /build/reproducible-path/relion-3.1.3/src/apps/refine_mpi.cpp:21: + from /build/reproducible-path/relion-3.1.3/src/jaz/obs_model.h:24, + from /build/reproducible-path/relion-3.1.3/src/apps/reposition.cpp:1: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -10255,7 +10280,8 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' +make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' +[ 86%] Built target preprocess /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ @@ -10280,21 +10306,17 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 83%] Built target plot_delocalisation -/usr/bin/make -f src/apps/CMakeFiles/tiltpair_plot.dir/build.make src/apps/CMakeFiles/tiltpair_plot.dir/depend +/usr/bin/make -f src/apps/CMakeFiles/scheduler.dir/build.make src/apps/CMakeFiles/scheduler.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' -cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/tiltpair_plot.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/scheduler.dir/DependInfo.cmake "--color=" +[ 86%] Building CXX object src/apps/CMakeFiles/run_motioncorr_mpi.dir/run_motioncorr_mpi.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/run_motioncorr_mpi.dir/run_motioncorr_mpi.cpp.o -MF CMakeFiles/run_motioncorr_mpi.dir/run_motioncorr_mpi.cpp.o.d -o CMakeFiles/run_motioncorr_mpi.dir/run_motioncorr_mpi.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/run_motioncorr_mpi.cpp make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/tiltpair_plot.dir/build.make src/apps/CMakeFiles/tiltpair_plot.dir/build +/usr/bin/make -f src/apps/CMakeFiles/scheduler.dir/build.make src/apps/CMakeFiles/scheduler.dir/build make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' -[ 83%] Building CXX object src/apps/CMakeFiles/tiltpair_plot.dir/tiltpair_plot.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/tiltpair_plot.dir/tiltpair_plot.cpp.o -MF CMakeFiles/tiltpair_plot.dir/tiltpair_plot.cpp.o.d -o CMakeFiles/tiltpair_plot.dir/tiltpair_plot.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/tiltpair_plot.cpp -make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/ctffind_runner.h:31, - from /build/reproducible-path/relion-3.1.3/src/ctffind_runner_mpi.h:25, - from /build/reproducible-path/relion-3.1.3/src/apps/run_ctffind_mpi.cpp:20: + from /build/reproducible-path/relion-3.1.3/src/apps/run_ctffind.cpp:20: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -10352,20 +10374,22 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 83%] Built target pipeliner -[ 83%] Built target particle_symmetry_expand -[ 83%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/cxxutils.cc.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/cxxutils.cc.o -MF CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/cxxutils.cc.o.d -o CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/cxxutils.cc.o -c /build/reproducible-path/relion-3.1.3/src/Healpix_2.15a/cxxutils.cc -[ 84%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/healpix_base.cc.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/healpix_base.cc.o -MF CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/healpix_base.cc.o.d -o CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/healpix_base.cc.o -c /build/reproducible-path/relion-3.1.3/src/Healpix_2.15a/healpix_base.cc +[ 86%] Building CXX object src/apps/CMakeFiles/scheduler.dir/scheduler.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/scheduler.dir/scheduler.cpp.o -MF CMakeFiles/scheduler.dir/scheduler.cpp.o.d -o CMakeFiles/scheduler.dir/scheduler.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/scheduler.cpp make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -[ 84%] Built target motion_refine -/usr/bin/make -f src/apps/CMakeFiles/tomo_test.dir/build.make src/apps/CMakeFiles/tomo_test.dir/depend +[ 86%] Built target preprocess_mpi +/usr/bin/make -f src/apps/CMakeFiles/stack_create.dir/build.make src/apps/CMakeFiles/stack_create.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' -cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/tomo_test.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/stack_create.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' +/usr/bin/make -f src/apps/CMakeFiles/stack_create.dir/build.make src/apps/CMakeFiles/stack_create.dir/build +make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' +[ 87%] Building CXX object src/apps/CMakeFiles/stack_create.dir/stack_create.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/stack_create.dir/stack_create.cpp.o -MF CMakeFiles/stack_create.dir/stack_create.cpp.o.d -o CMakeFiles/stack_create.dir/stack_create.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/stack_create.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/motioncorr_runner.h:32, - from /build/reproducible-path/relion-3.1.3/src/apps/run_motioncorr.cpp:20: + from /build/reproducible-path/relion-3.1.3/src/ctffind_runner.h:31, + from /build/reproducible-path/relion-3.1.3/src/ctffind_runner_mpi.h:25, + from /build/reproducible-path/relion-3.1.3/src/apps/run_ctffind_mpi.cpp:20: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -10423,28 +10447,9 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/tomo_test.dir/build.make src/apps/CMakeFiles/tomo_test.dir/build -make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' -[ 84%] Building CXX object src/apps/CMakeFiles/tomo_test.dir/tomo_test.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/tomo_test.dir/tomo_test.cpp.o -MF CMakeFiles/tomo_test.dir/tomo_test.cpp.o.d -o CMakeFiles/tomo_test.dir/tomo_test.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/tomo_test.cpp -[ 84%] Linking CXX executable ../../bin/relion_mrc2vtk -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/mrc2vtk.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/mrc2vtk.dir/mrc2vtk.cpp.o -o ../../bin/relion_mrc2vtk ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -[ 85%] Linking CXX executable ../../bin/relion_preprocess -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/preprocess.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/preprocess.dir/preprocess.cpp.o -o ../../bin/relion_preprocess ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -[ 85%] Linking CXX executable ../../bin/relion_preprocess_mpi -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/preprocess_mpi.dir/link.txt --verbose=1 -[ 85%] Built target flex_analyse_mpi -make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/preprocess_mpi.dir/preprocess_mpi.cpp.o -o ../../bin/relion_preprocess_mpi ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -[ 85%] Built target flex_analyse In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/motioncorr_runner.h:32, - from /build/reproducible-path/relion-3.1.3/src/motioncorr_runner_mpi.h:25, - from /build/reproducible-path/relion-3.1.3/src/apps/run_motioncorr_mpi.cpp:20: + from /build/reproducible-path/relion-3.1.3/src/apps/run_motioncorr.cpp:20: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -10502,6 +10507,7 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +[ 87%] Linking CXX executable ../../bin/relion_run_ctffind In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/jaz/obs_model.h:24, from /build/reproducible-path/relion-3.1.3/src/scheduler.h:26, @@ -10539,6 +10545,7 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/run_ctffind.dir/link.txt --verbose=1 /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ @@ -10563,8 +10570,46 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/run_ctffind.dir/run_ctffind.cpp.o -o ../../bin/relion_run_ctffind ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/apps/star_handler.cpp:21: + from /build/reproducible-path/relion-3.1.3/src/apps/stack_create.cpp:21: +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 43 | uint32 width, length; // apparent dimensions in the file + | ^~~~~ +In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, + from /build/reproducible-path/relion-3.1.3/src/image.h:57: +/usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here + 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 43 | uint32 width, length; // apparent dimensions in the file + | ^~~~~~ +/usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here + 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; + | ^~~~~~~~~~~~ +/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; + | ^~~~~~~~~~~~~ +/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; + | ^~~~~~~~~~~~~~ +/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ +In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, + from /build/reproducible-path/relion-3.1.3/src/motioncorr_runner.h:32, + from /build/reproducible-path/relion-3.1.3/src/motioncorr_runner_mpi.h:25, + from /build/reproducible-path/relion-3.1.3/src/apps/run_motioncorr_mpi.cpp:20: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -10622,8 +10667,83 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 185 | uint32 cur_width, cur_length; + | ^~~~~~~~~ +/usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here + 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 185 | uint32 cur_width, cur_length; + | ^~~~~~~~~~ +/usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here + 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 186 | uint16 cur_sampleFormat, cur_bitsPerSample; + | ^~~~~~~~~~~~~~~~ +/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 186 | uint16 cur_sampleFormat, cur_bitsPerSample; + | ^~~~~~~~~~~~~~~~~ +/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ +[ 87%] Linking CXX executable ../../bin/relion_particle_subtract_mpi +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/particle_subtract_mpi.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/particle_subtract_mpi.dir/particle_subtract_mpi.cpp.o -o ../../bin/relion_particle_subtract_mpi ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' +[ 87%] Built target run_ctffind +/usr/bin/make -f src/apps/CMakeFiles/star_handler.dir/build.make src/apps/CMakeFiles/star_handler.dir/depend +make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' +cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/star_handler.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' +/usr/bin/make -f src/apps/CMakeFiles/star_handler.dir/build.make src/apps/CMakeFiles/star_handler.dir/build +make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' +[ 88%] Building CXX object src/apps/CMakeFiles/star_handler.dir/star_handler.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/star_handler.dir/star_handler.cpp.o -MF CMakeFiles/star_handler.dir/star_handler.cpp.o.d -o CMakeFiles/star_handler.dir/star_handler.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/star_handler.cpp +[ 88%] Linking CXX executable ../../bin/relion_run_motioncorr +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/run_motioncorr.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/run_motioncorr.dir/run_motioncorr.cpp.o -o ../../bin/relion_run_motioncorr ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +[ 89%] Linking CXX executable ../../bin/relion_reconstruct_mpi +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/reconstruct_mpi.dir/link.txt --verbose=1 +[ 89%] Linking CXX executable ../../bin/relion_run_ctffind_mpi +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/run_ctffind_mpi.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/reconstruct_mpi.dir/reconstruct_mpi.cpp.o -o ../../bin/relion_reconstruct_mpi ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/run_ctffind_mpi.dir/run_ctffind_mpi.cpp.o -o ../../bin/relion_run_ctffind_mpi ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +[ 90%] Linking CXX executable ../../bin/relion_reconstruct +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/reconstruct.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/reconstruct.dir/reconstruct.cpp.o -o ../../bin/relion_reconstruct ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' +[ 91%] Linking CXX executable ../../bin/relion_run_motioncorr_mpi +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/run_motioncorr_mpi.dir/link.txt --verbose=1 +[ 91%] Built target particle_subtract_mpi +/usr/bin/make -f src/apps/CMakeFiles/tiltpair_plot.dir/build.make src/apps/CMakeFiles/tiltpair_plot.dir/depend +make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' +cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/tiltpair_plot.dir/DependInfo.cmake "--color=" +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/run_motioncorr_mpi.dir/run_motioncorr_mpi.cpp.o -o ../../bin/relion_run_motioncorr_mpi ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' +/usr/bin/make -f src/apps/CMakeFiles/tiltpair_plot.dir/build.make src/apps/CMakeFiles/tiltpair_plot.dir/build +make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' +[ 91%] Building CXX object src/apps/CMakeFiles/tiltpair_plot.dir/tiltpair_plot.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/tiltpair_plot.dir/tiltpair_plot.cpp.o -MF CMakeFiles/tiltpair_plot.dir/tiltpair_plot.cpp.o.d -o CMakeFiles/tiltpair_plot.dir/tiltpair_plot.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/tiltpair_plot.cpp +make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' +[ 91%] Built target run_motioncorr +/usr/bin/make -f src/apps/CMakeFiles/tomo_test.dir/build.make src/apps/CMakeFiles/tomo_test.dir/depend +make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' +cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/tomo_test.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' +/usr/bin/make -f src/apps/CMakeFiles/tomo_test.dir/build.make src/apps/CMakeFiles/tomo_test.dir/build +make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' +[ 91%] Building CXX object src/apps/CMakeFiles/tomo_test.dir/tomo_test.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/tomo_test.dir/tomo_test.cpp.o -MF CMakeFiles/tomo_test.dir/tomo_test.cpp.o.d -o CMakeFiles/tomo_test.dir/tomo_test.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/tomo_test.cpp +[ 91%] Linking CXX executable ../../bin/relion_helix_toolbox +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/helix_toolbox.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/helix_toolbox.dir/helix_toolbox.cpp.o -o ../../bin/relion_helix_toolbox ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, - from /build/reproducible-path/relion-3.1.3/src/apps/stack_create.cpp:21: + from /build/reproducible-path/relion-3.1.3/src/apps/star_handler.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -10681,18 +10801,18 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 85%] Linking CXX executable ../../bin/relion_run_ctffind -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/run_ctffind.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/run_ctffind.dir/run_ctffind.cpp.o -o ../../bin/relion_run_ctffind ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -[ 85%] Built target mrc2vtk make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -[ 85%] Built target motion_refine_mpi -[ 85%] Linking CXX executable ../../bin/relion_run_ctffind_mpi -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/run_ctffind_mpi.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/run_ctffind_mpi.dir/run_ctffind_mpi.cpp.o -o ../../bin/relion_run_ctffind_mpi ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -[ 85%] Built target preprocess +[ 91%] Built target run_motioncorr_mpi +[ 91%] Built target reconstruct +[ 91%] Built target run_ctffind_mpi +[ 91%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/cxxutils.cc.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/cxxutils.cc.o -MF CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/cxxutils.cc.o.d -o CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/cxxutils.cc.o -c /build/reproducible-path/relion-3.1.3/src/Healpix_2.15a/cxxutils.cc +[ 92%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/healpix_base.cc.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/healpix_base.cc.o -MF CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/healpix_base.cc.o.d -o CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/healpix_base.cc.o -c /build/reproducible-path/relion-3.1.3/src/Healpix_2.15a/healpix_base.cc +make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' +[ 92%] Built target reconstruct_mpi In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/apps/tiltpair_plot.cpp:25: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': @@ -10752,16 +10872,14 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 86%] Linking CXX executable ../../bin/relion_find_tiltpairs -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/find_tiltpairs.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -[ 86%] Built target run_ctffind -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/find_tiltpairs.dir/find_tiltpairs.cpp.o -o ../../bin/relion_find_tiltpairs ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -[ 86%] Built target preprocess_mpi -[ 86%] Linking CXX executable ../../bin/relion_run_motioncorr -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/run_motioncorr.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/run_motioncorr.dir/run_motioncorr.cpp.o -o ../../bin/relion_run_motioncorr ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +[ 92%] Built target helix_toolbox +[ 92%] Linking CXX executable ../../bin/relion_refine_mpi +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/refine_mpi.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/refine_mpi.dir/refine_mpi.cpp.o -o ../../bin/relion_refine_mpi ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +[ 92%] Linking CXX executable ../../bin/relion_refine +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/refine.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/refine.dir/refine.cpp.o -o ../../bin/relion_refine ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/jaz/tomo/tomo_stack.h:25, from /build/reproducible-path/relion-3.1.3/src/apps/tomo_test.cpp:2: @@ -10822,173 +10940,79 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 87%] Linking CXX executable ../../bin/relion_particle_subtract -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/particle_subtract.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/particle_subtract.dir/particle_subtract.cpp.o -o ../../bin/relion_particle_subtract ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -[ 87%] Linking CXX executable ../../bin/relion_import -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/import.dir/link.txt --verbose=1 -[ 87%] Built target find_tiltpairs -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/import.dir/import.cpp.o -o ../../bin/relion_import ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -[ 87%] Built target run_ctffind_mpi -[ 88%] Linking CXX executable ../../bin/relion_reconstruct_mpi -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/reconstruct_mpi.dir/link.txt --verbose=1 -[ 89%] Linking CXX executable ../../bin/relion_run_motioncorr_mpi -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/reconstruct_mpi.dir/reconstruct_mpi.cpp.o -o ../../bin/relion_reconstruct_mpi ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/run_motioncorr_mpi.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/run_motioncorr_mpi.dir/run_motioncorr_mpi.cpp.o -o ../../bin/relion_run_motioncorr_mpi ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -[ 90%] Linking CXX executable ../../bin/relion_reconstruct -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/reconstruct.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/reconstruct.dir/reconstruct.cpp.o -o ../../bin/relion_reconstruct ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -[ 90%] Built target run_motioncorr -[ 90%] Linking CXX executable ../../bin/relion_particle_subtract_mpi -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/particle_subtract_mpi.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/particle_subtract_mpi.dir/particle_subtract_mpi.cpp.o -o ../../bin/relion_particle_subtract_mpi ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -[ 90%] Built target import -make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -[ 90%] Built target run_motioncorr_mpi make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -[ 91%] Linking CXX executable ../../bin/relion_ctf_mask_test -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/ctf_mask_test.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ctf_mask_test.dir/ctf_mask_test.cpp.o -o ../../bin/relion_ctf_mask_test ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -[ 91%] Built target reconstruct -[ 91%] Built target particle_subtract -make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -[ 91%] Built target reconstruct_mpi -make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -[ 91%] Built target particle_subtract_mpi -[ 91%] Built target ctf_mask_test -[ 91%] Linking CXX executable ../../bin/relion_refine -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/refine.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/refine.dir/refine.cpp.o -o ../../bin/relion_refine ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -[ 91%] Linking CXX executable ../../bin/relion_mask_create -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/mask_create.dir/link.txt --verbose=1 -[ 92%] Linking CXX executable ../../bin/relion_tomo_test -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/tomo_test.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/mask_create.dir/mask_create.cpp.o -o ../../bin/relion_mask_create ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/tomo_test.dir/tomo_test.cpp.o -o ../../bin/relion_tomo_test ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +[ 92%] Built target refine_mpi [ 93%] Linking CXX executable ../../bin/relion_reposition cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/reposition.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/reposition.dir/reposition.cpp.o -o ../../bin/relion_reposition ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -[ 93%] Linking CXX executable ../../bin/relion_ctf_toolbox -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/ctf_toolbox.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ctf_toolbox.dir/ctf_toolbox.cpp.o -o ../../bin/relion_ctf_toolbox ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -[ 94%] Linking CXX executable ../../bin/relion_tiltpair_plot -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiltpair_plot.dir/link.txt --verbose=1 -[ 94%] Built target mask_create -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/tiltpair_plot.dir/tiltpair_plot.cpp.o -o ../../bin/relion_tiltpair_plot ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -[ 94%] Built target tomo_test -make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' +[ 93%] Built target refine +[ 94%] Linking CXX executable ../../bin/relion_image_handler +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/image_handler.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/image_handler.dir/image_handler.cpp.o -o ../../bin/relion_image_handler ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -[ 94%] Built target ctf_toolbox -[ 94%] Linking CXX executable ../../bin/relion_external_reconstruct -[ 94%] Linking CXX executable ../../bin/relion_refine_mpi [ 94%] Built target reposition -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/external_reconstruct.dir/link.txt --verbose=1 -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/refine_mpi.dir/link.txt --verbose=1 +make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 94%] Linking CXX executable ../../bin/relion_scheduler -[ 94%] Linking CXX executable ../../bin/relion_estimate_gain cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/scheduler.dir/link.txt --verbose=1 -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/estimate_gain.dir/link.txt --verbose=1 -make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -[ 94%] Built target refine -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/refine_mpi.dir/refine_mpi.cpp.o -o ../../bin/relion_refine_mpi ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/external_reconstruct.dir/external_reconstruct.cpp.o -o ../../bin/relion_external_reconstruct ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/scheduler.dir/scheduler.cpp.o -o ../../bin/relion_scheduler ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/estimate_gain.dir/estimate_gain.cpp.o -o ../../bin/relion_estimate_gain ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -[ 94%] Built target tiltpair_plot -[ 95%] Linking CXX executable ../../bin/relion_demodulate -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/demodulate.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/demodulate.dir/demodulate.cpp.o -o ../../bin/relion_demodulate ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -[ 95%] Built target estimate_gain -make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -[ 95%] Built target external_reconstruct -[ 95%] Linking CXX executable ../../bin/relion_align_symmetry -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/align_symmetry.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/align_symmetry.dir/align_symmetry.cpp.o -o ../../bin/relion_align_symmetry ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -[ 95%] Built target demodulate +[ 94%] Built target image_handler +[ 95%] Linking CXX executable ../../bin/relion_tiltpair_plot +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiltpair_plot.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/tiltpair_plot.dir/tiltpair_plot.cpp.o -o ../../bin/relion_tiltpair_plot ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 95%] Built target scheduler make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -[ 95%] Built target refine_mpi -make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -[ 95%] Built target align_symmetry +[ 95%] Built target tiltpair_plot [ 95%] Linking CXX executable ../../bin/relion_particle_reposition cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/particle_reposition.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/particle_reposition.dir/particle_reposition.cpp.o -o ../../bin/relion_particle_reposition ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +[ 96%] Linking CXX executable ../../bin/relion_tomo_test +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/tomo_test.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/tomo_test.dir/tomo_test.cpp.o -o ../../bin/relion_tomo_test ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -[ 95%] Built target particle_reposition -[ 95%] Linking CXX executable ../../bin/relion_stack_create -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/stack_create.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/stack_create.dir/stack_create.cpp.o -o ../../bin/relion_stack_create ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -[ 95%] Linking CXX executable ../../bin/relion_helix_toolbox -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/helix_toolbox.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/helix_toolbox.dir/helix_toolbox.cpp.o -o ../../bin/relion_helix_toolbox ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -[ 95%] Built target stack_create -make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -[ 95%] Built target helix_toolbox -[ 96%] Linking CXX executable ../../bin/relion_image_handler -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/image_handler.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/image_handler.dir/image_handler.cpp.o -o ../../bin/relion_image_handler ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -[ 96%] Linking CXX executable ../../bin/relion_project -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/project.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/project.dir/project.cpp.o -o ../../bin/relion_project ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -[ 96%] Built target image_handler -make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -[ 96%] Built target project +[ 96%] Built target tomo_test [ 96%] Linking CXX static library ../../lib/librelion_gui_lib.a cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -P CMakeFiles/relion_gui_lib.dir/cmake_clean_target.cmake cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/relion_gui_lib.dir/link.txt --verbose=1 /usr/bin/ar qc ../../lib/librelion_gui_lib.a CMakeFiles/relion_gui_lib.dir/__/displayer.cpp.o CMakeFiles/relion_gui_lib.dir/__/gui_entries.cpp.o CMakeFiles/relion_gui_lib.dir/__/gui_jobwindow.cpp.o CMakeFiles/relion_gui_lib.dir/__/gui_mainwindow.cpp.o CMakeFiles/relion_gui_lib.dir/__/manualpicker.cpp.o CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/cxxutils.cc.o CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/healpix_base.cc.o -[ 97%] Linking CXX executable ../../bin/relion_prepare_subtomo -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/prepare_subtomo.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/prepare_subtomo.dir/prepare_subtomo.cpp.o -o ../../bin/relion_prepare_subtomo ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -/usr/bin/ranlib ../../lib/librelion_gui_lib.a -[ 97%] Linking CXX executable ../../bin/relion_star_handler -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/star_handler.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/star_handler.dir/star_handler.cpp.o -o ../../bin/relion_star_handler ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -[ 97%] Built target prepare_subtomo make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -[ 97%] Built target star_handler +[ 96%] Built target particle_reposition +/usr/bin/ranlib ../../lib/librelion_gui_lib.a make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -[ 97%] Built target relion_gui_lib +[ 96%] Built target relion_gui_lib /usr/bin/make -f src/apps/CMakeFiles/display.dir/build.make src/apps/CMakeFiles/display.dir/depend -/usr/bin/make -f src/apps/CMakeFiles/relion.dir/build.make src/apps/CMakeFiles/relion.dir/depend -/usr/bin/make -f src/apps/CMakeFiles/manualpick.dir/build.make src/apps/CMakeFiles/manualpick.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/display.dir/DependInfo.cmake "--color=" +/usr/bin/make -f src/apps/CMakeFiles/relion.dir/build.make src/apps/CMakeFiles/relion.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/relion.dir/DependInfo.cmake "--color=" +/usr/bin/make -f src/apps/CMakeFiles/manualpick.dir/build.make src/apps/CMakeFiles/manualpick.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/manualpick.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/relion.dir/build.make src/apps/CMakeFiles/relion.dir/build -make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' /usr/bin/make -f src/apps/CMakeFiles/display.dir/build.make src/apps/CMakeFiles/display.dir/build -/usr/bin/make -f src/apps/CMakeFiles/manualpick.dir/build.make src/apps/CMakeFiles/manualpick.dir/build +make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' +/usr/bin/make -f src/apps/CMakeFiles/relion.dir/build.make src/apps/CMakeFiles/relion.dir/build make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' +make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' +/usr/bin/make -f src/apps/CMakeFiles/manualpick.dir/build.make src/apps/CMakeFiles/manualpick.dir/build make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' -[ 97%] Building CXX object src/apps/CMakeFiles/relion.dir/maingui.cpp.o -[ 97%] Building CXX object src/apps/CMakeFiles/display.dir/display.cpp.o -[ 97%] Building CXX object src/apps/CMakeFiles/manualpick.dir/manualpick.cpp.o -cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion.dir/maingui.cpp.o -MF CMakeFiles/relion.dir/maingui.cpp.o.d -o CMakeFiles/relion.dir/maingui.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/maingui.cpp +[ 96%] Building CXX object src/apps/CMakeFiles/display.dir/display.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/display.dir/display.cpp.o -MF CMakeFiles/display.dir/display.cpp.o.d -o CMakeFiles/display.dir/display.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/display.cpp +[ 96%] Building CXX object src/apps/CMakeFiles/relion.dir/maingui.cpp.o +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion.dir/maingui.cpp.o -MF CMakeFiles/relion.dir/maingui.cpp.o.d -o CMakeFiles/relion.dir/maingui.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/maingui.cpp +[ 96%] Building CXX object src/apps/CMakeFiles/manualpick.dir/manualpick.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/manualpick.dir/manualpick.cpp.o -MF CMakeFiles/manualpick.dir/manualpick.cpp.o.d -o CMakeFiles/manualpick.dir/manualpick.cpp.o -c /build/reproducible-path/relion-3.1.3/src/apps/manualpick.cpp +[ 96%] Linking CXX executable ../../bin/relion_project +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/project.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/project.dir/project.cpp.o -o ../../bin/relion_project ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +[ 96%] Linking CXX executable ../../bin/relion_stack_create +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/stack_create.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/stack_create.dir/stack_create.cpp.o -o ../../bin/relion_stack_create ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' +[ 96%] Built target project In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/apps/display.cpp:25: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': @@ -11048,6 +11072,8 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' +[ 96%] Built target stack_create In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/apps/manualpick.cpp:25: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': @@ -11169,21 +11195,31 @@ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 98%] Linking CXX executable ../../bin/relion_display +[ 97%] Linking CXX executable ../../bin/relion_display cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/display.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/display.dir/display.cpp.o -o ../../bin/relion_display ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gui_lib.a /usr/lib/x86_64-linux-gnu/libfltk_images.so /usr/lib/x86_64-linux-gnu/libfltk_forms.so /usr/lib/x86_64-linux-gnu/libfltk.so -lX11 -lm -ltiff ../../lib/librelion_lib.a -lfftw3f -lfftw3 -ltiff -[ 99%] Linking CXX executable ../../bin/relion_manualpick +make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' +[ 97%] Built target display +[ 98%] Linking CXX executable ../../bin/relion_manualpick cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/manualpick.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/manualpick.dir/manualpick.cpp.o -o ../../bin/relion_manualpick ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gui_lib.a /usr/lib/x86_64-linux-gnu/libfltk_images.so /usr/lib/x86_64-linux-gnu/libfltk_forms.so /usr/lib/x86_64-linux-gnu/libfltk.so -lX11 -lm -ltiff ../../lib/librelion_lib.a -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -[ 99%] Built target display -[100%] Linking CXX executable ../../bin/relion +[ 98%] Built target manualpick +[ 99%] Linking CXX executable ../../bin/relion cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/relion.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/relion.dir/maingui.cpp.o -o ../../bin/relion ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gui_lib.a /usr/lib/x86_64-linux-gnu/libfltk_images.so /usr/lib/x86_64-linux-gnu/libfltk_forms.so /usr/lib/x86_64-linux-gnu/libfltk.so -lX11 -lm -ltiff ../../lib/librelion_lib.a -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -[100%] Built target manualpick +[ 99%] Built target relion +[100%] Linking CXX executable ../../bin/relion_prepare_subtomo +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/prepare_subtomo.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/prepare_subtomo.dir/prepare_subtomo.cpp.o -o ../../bin/relion_prepare_subtomo ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' +[100%] Built target prepare_subtomo +[100%] Linking CXX executable ../../bin/relion_star_handler +cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/star_handler.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/star_handler.dir/star_handler.cpp.o -o ../../bin/relion_star_handler ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' -[100%] Built target relion +[100%] Built target star_handler make[3]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/relion-3.1.3/build/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' @@ -11763,71 +11799,71 @@ /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin --- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_project --- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_convert_to_tiff_mpi --- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_star_datablock_singlefiles --- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_refine_mpi --- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_motion_refine_mpi --- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_import --- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_demodulate --- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_flex_analyse_mpi --- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_star_loopheader --- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_particle_reposition --- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_star_datablock_stack +-- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_display +-- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_preprocess_mpi -- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_scheduler --- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_reconstruct --- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_particle_select --- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_estimate_gain --- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_postprocess --- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_reconstruct_mpi --- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_plot_delocalisation --- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_manualpick --- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_stack_create --- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_tomo_test --- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_external_reconstruct --- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_particle_symmetry_expand --- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_ctf_refine +-- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_run_motioncorr -- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_mask_create --- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_particle_subtract_mpi +-- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_manualpick +-- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_image_handler -- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_tiltpair_plot --- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_run_motioncorr --- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_refine +-- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_localsym +-- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_star_datablock_ctfdat +-- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_convert_star +-- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_run_ctffind_mpi +-- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_estimate_gain +-- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_particle_FCC +-- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_flex_analyse_mpi +-- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_find_tiltpairs -- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_run_ctffind +-- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_star_printtable +-- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_pipeliner +-- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_refine -- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_localsym_mpi --- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_merge_particles --- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_align_symmetry +-- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_reconstruct_mpi +-- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_external_reconstruct +-- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_particle_subtract_mpi -- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_preprocess --- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion -- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_ctf_toolbox --- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_motion_refine --- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_run_ctffind_mpi --- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_qsub.csh --- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_preprocess_mpi --- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_helix_inimodel2d --- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_pipeliner -- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_ctf_refine_mpi --- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_convert_to_tiff --- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_star_plottable --- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_flex_analyse --- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_prepare_subtomo --- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_autopick --- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_image_handler --- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_star_datablock_ctfdat --- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_postprocess_mpi +-- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_plot_delocalisation +-- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_particle_select +-- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_helix_toolbox -- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_particle_subtract --- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_find_tiltpairs --- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_convert_star --- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_localsym --- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_star_handler --- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_particle_FCC --- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_ctf_mask_test +-- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_ctf_refine +-- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_reconstruct +-- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_motion_refine +-- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_convert_to_tiff +-- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_project +-- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_demodulate +-- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_motion_refine_mpi -- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_autopick_mpi --- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_display --- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_run_motioncorr_mpi --- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_star_printtable --- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_helix_toolbox -- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_reposition +-- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_star_datablock_singlefiles -- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_mrc2vtk +-- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_import +-- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion +-- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_star_handler +-- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_refine_mpi +-- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_particle_symmetry_expand +-- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_ctf_mask_test +-- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_star_datablock_stack +-- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_helix_inimodel2d +-- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_star_plottable +-- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_run_motioncorr_mpi +-- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_tomo_test +-- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_convert_to_tiff_mpi +-- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_particle_reposition +-- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_align_symmetry +-- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_postprocess +-- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_prepare_subtomo +-- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_star_loopheader +-- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_merge_particles +-- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_qsub.csh +-- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_flex_analyse +-- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_postprocess_mpi +-- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_autopick +-- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_stack_create -- Up-to-date: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_align_symmetry -- Up-to-date: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_autopick -- Up-to-date: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_autopick_mpi @@ -11913,8 +11949,8 @@ dh_builddeb dpkg-deb: building package 'relion' in '../relion_3.1.3-4_amd64.deb'. dpkg-deb: building package 'relion-dbgsym' in '../relion-dbgsym_3.1.3-4_amd64.deb'. -dpkg-deb: building package 'relion-gui' in '../relion-gui_3.1.3-4_amd64.deb'. dpkg-deb: building package 'relion-gui-dbgsym' in '../relion-gui-dbgsym_3.1.3-4_amd64.deb'. +dpkg-deb: building package 'relion-gui' in '../relion-gui_3.1.3-4_amd64.deb'. dpkg-genbuildinfo --build=binary -O../relion_3.1.3-4_amd64.buildinfo dpkg-genchanges --build=binary -O../relion_3.1.3-4_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -11922,12 +11958,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/1072322/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1072322/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/4041426 and its subdirectories -I: Current time: Tue Jan 27 23:09:22 -12 2026 -I: pbuilder-time-stamp: 1769598562 +I: removing directory /srv/workspace/pbuilder/1072322 and its subdirectories +I: Current time: Thu Dec 26 19:01:58 +14 2024 +I: pbuilder-time-stamp: 1735189318