Diff of the two buildlogs: -- --- b1/build.log 2023-04-12 19:03:07.831295699 +0000 +++ b2/build.log 2023-04-12 19:24:35.547246181 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Apr 12 05:56:25 -12 2023 -I: pbuilder-time-stamp: 1681322185 +I: Current time: Wed May 15 15:29:50 +14 2024 +I: pbuilder-time-stamp: 1715736590 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -16,7 +16,7 @@ I: copying [./relion_3.1.3.orig.tar.gz] I: copying [./relion_3.1.3-3.debian.tar.xz] I: Extracting source -gpgv: Signature made Mon Dec 5 23:51:10 2022 -12 +gpgv: Signature made Wed Dec 7 01:51:10 2022 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -29,11 +29,20 @@ dpkg-source: info: applying typos.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/20937/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1712/tmp/hooks/D01_modify_environment starting +debug: Running on codethink9-arm64. +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 +lrwxrwxrwx 1 root root 4 Jan 6 2023 /bin/sh -> dash +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/1712/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1712/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME='pbuilder2' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8' @@ -43,38 +52,38 @@ IFS=' ' LANG='C' - LANGUAGE='en_US:en' + LANGUAGE='nl_BE:nl' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' + 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' - PPID='20937' + PPID='1712' PS1='# ' PS2='> ' 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.mZN3SFvv/pbuilderrc_xmub --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.mZN3SFvv/b1 --logfile b1/build.log relion_3.1.3-3.dsc' + 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.mZN3SFvv/pbuilderrc_XxOi --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.mZN3SFvv/b2 --logfile b2/build.log --extrapackages usrmerge relion_3.1.3-3.dsc' SUDO_GID='117' SUDO_UID='110' SUDO_USER='jenkins' TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' + TZ='/usr/share/zoneinfo/Etc/GMT-14' USER='root' USERNAME='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.16:3128' I: uname -a - Linux codethink16-arm64 4.15.0-208-generic #220-Ubuntu SMP Mon Mar 20 14:28:12 UTC 2023 aarch64 GNU/Linux + Linux i-capture-the-hostname 4.15.0-208-generic #220-Ubuntu SMP Mon Mar 20 14:28:12 UTC 2023 aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Apr 10 22:26 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/20937/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 15 06:47 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1712/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -297,7 +306,7 @@ Get: 173 http://deb.debian.org/debian bookworm/main arm64 libtiff6 arm64 4.5.0-5 [300 kB] Get: 174 http://deb.debian.org/debian bookworm/main arm64 libtiffxx6 arm64 4.5.0-5 [144 kB] Get: 175 http://deb.debian.org/debian bookworm/main arm64 libtiff-dev arm64 4.5.0-5 [441 kB] -Fetched 101 MB in 2s (45.1 MB/s) +Fetched 101 MB in 2s (49.6 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libproc2-0:arm64. (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 ... 19616 files and directories currently installed.) @@ -1014,8 +1023,17 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +usrmerge is already the newest version (35). +0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/relion-3.1.3/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../relion_3.1.3-3_source.changes +I: user script /srv/workspace/pbuilder/1712/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +I: user script /srv/workspace/pbuilder/1712/tmp/hooks/A99_set_merged_usr finished +hostname: Temporary failure in name resolution +I: Running cd /build/relion-3.1.3/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../relion_3.1.3-3_source.changes dpkg-buildpackage: info: source package relion dpkg-buildpackage: info: source version 3.1.3-3 dpkg-buildpackage: info: source distribution unstable @@ -1159,27 +1177,27 @@ make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/relion_lib.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/relion_lib.dir/build.make src/apps/CMakeFiles/relion_lib.dir/build -make[4]: Leaving directory '/build/relion-3.1.3/build' /usr/bin/make -f CMakeFiles/copy_scripts.dir/build.make CMakeFiles/copy_scripts.dir/build make[4]: Entering directory '/build/relion-3.1.3/build' -make[4]: Entering directory '/build/relion-3.1.3/build' /usr/bin/cmake -E copy /build/relion-3.1.3/scripts/star_printtable /build/relion-3.1.3/build/bin/relion_star_printtable -[ 0%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/__/macros.cpp.o -[ 0%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/args.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/__/macros.cpp.o -MF CMakeFiles/relion_lib.dir/__/__/macros.cpp.o.d -o CMakeFiles/relion_lib.dir/__/__/macros.cpp.o -c /build/relion-3.1.3/build/macros.cpp -[ 1%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/CPlot2D.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/args.cpp.o -MF CMakeFiles/relion_lib.dir/__/args.cpp.o.d -o CMakeFiles/relion_lib.dir/__/args.cpp.o -c /build/relion-3.1.3/src/args.cpp -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/CPlot2D.cpp.o -MF CMakeFiles/relion_lib.dir/__/CPlot2D.cpp.o.d -o CMakeFiles/relion_lib.dir/__/CPlot2D.cpp.o -c /build/relion-3.1.3/src/CPlot2D.cpp +make[4]: Leaving directory '/build/relion-3.1.3/build' +/usr/bin/make -f src/apps/CMakeFiles/relion_lib.dir/build.make src/apps/CMakeFiles/relion_lib.dir/build +make[4]: Entering directory '/build/relion-3.1.3/build' /usr/bin/cmake -E copy /build/relion-3.1.3/scripts/star_plottable /build/relion-3.1.3/build/bin/relion_star_plottable -[ 1%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/autopicker_mpi.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/autopicker_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/autopicker_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/autopicker_mpi.cpp.o -c /build/relion-3.1.3/src/autopicker_mpi.cpp -[ 1%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/assembly.cpp.o +[ 2%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/__/macros.cpp.o +[ 2%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/assembly.cpp.o +[ 2%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/args.cpp.o +[ 2%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/autopicker_mpi.cpp.o +[ 2%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/autopicker.cpp.o +[ 2%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/CPlot2D.cpp.o +[ 3%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/backprojector.cpp.o /usr/bin/cmake -E copy /build/relion-3.1.3/scripts/star_loopheader /build/relion-3.1.3/build/bin/relion_star_loopheader cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/assembly.cpp.o -MF CMakeFiles/relion_lib.dir/__/assembly.cpp.o.d -o CMakeFiles/relion_lib.dir/__/assembly.cpp.o -c /build/relion-3.1.3/src/assembly.cpp -[ 2%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/autopicker.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/__/macros.cpp.o -MF CMakeFiles/relion_lib.dir/__/__/macros.cpp.o.d -o CMakeFiles/relion_lib.dir/__/__/macros.cpp.o -c /build/relion-3.1.3/build/macros.cpp +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/CPlot2D.cpp.o -MF CMakeFiles/relion_lib.dir/__/CPlot2D.cpp.o.d -o CMakeFiles/relion_lib.dir/__/CPlot2D.cpp.o -c /build/relion-3.1.3/src/CPlot2D.cpp +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/args.cpp.o -MF CMakeFiles/relion_lib.dir/__/args.cpp.o.d -o CMakeFiles/relion_lib.dir/__/args.cpp.o -c /build/relion-3.1.3/src/args.cpp cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/autopicker.cpp.o -MF CMakeFiles/relion_lib.dir/__/autopicker.cpp.o.d -o CMakeFiles/relion_lib.dir/__/autopicker.cpp.o -c /build/relion-3.1.3/src/autopicker.cpp -[ 3%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/backprojector.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/autopicker_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/autopicker_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/autopicker_mpi.cpp.o -c /build/relion-3.1.3/src/autopicker_mpi.cpp cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/backprojector.cpp.o -MF CMakeFiles/relion_lib.dir/__/backprojector.cpp.o.d -o CMakeFiles/relion_lib.dir/__/backprojector.cpp.o -c /build/relion-3.1.3/src/backprojector.cpp /usr/bin/cmake -E copy /build/relion-3.1.3/scripts/star_datablock_stack /build/relion-3.1.3/build/bin/relion_star_datablock_stack /usr/bin/cmake -E copy /build/relion-3.1.3/scripts/star_datablock_singlefiles /build/relion-3.1.3/build/bin/relion_star_datablock_singlefiles @@ -1194,8 +1212,9 @@ [ 4%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ctffind_runner.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/ctffind_runner.cpp.o -MF CMakeFiles/relion_lib.dir/__/ctffind_runner.cpp.o.d -o CMakeFiles/relion_lib.dir/__/ctffind_runner.cpp.o -c /build/relion-3.1.3/src/ctffind_runner.cpp In file included from /build/relion-3.1.3/src/image.h:455, - from /build/relion-3.1.3/src/autopicker.h:10, - from /build/relion-3.1.3/src/autopicker.cpp:20: + from /build/relion-3.1.3/src/projector.h:25, + from /build/relion-3.1.3/src/backprojector.h:33, + from /build/relion-3.1.3/src/backprojector.cpp:27: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -1254,9 +1273,8 @@ 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-3.1.3/src/image.h:455, - from /build/relion-3.1.3/src/projector.h:25, - from /build/relion-3.1.3/src/backprojector.h:33, - from /build/relion-3.1.3/src/backprojector.cpp:27: + from /build/relion-3.1.3/src/autopicker.h:10, + from /build/relion-3.1.3/src/autopicker.cpp:20: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -1610,6 +1628,8 @@ /usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +[ 6%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/filename.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/filename.cpp.o -MF CMakeFiles/relion_lib.dir/__/filename.cpp.o.d -o CMakeFiles/relion_lib.dir/__/filename.cpp.o -c /build/relion-3.1.3/src/filename.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/exp_model.h:24, from /build/relion-3.1.3/src/exp_model.cpp:20: @@ -1667,11 +1687,9 @@ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ -[ 6%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/filename.cpp.o /usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/filename.cpp.o -MF CMakeFiles/relion_lib.dir/__/filename.cpp.o.d -o CMakeFiles/relion_lib.dir/__/filename.cpp.o -c /build/relion-3.1.3/src/filename.cpp [ 6%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/flex_analyser.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/flex_analyser.cpp.o -MF CMakeFiles/relion_lib.dir/__/flex_analyser.cpp.o.d -o CMakeFiles/relion_lib.dir/__/flex_analyser.cpp.o -c /build/relion-3.1.3/src/flex_analyser.cpp [ 7%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/funcs.cpp.o @@ -2049,6 +2067,8 @@ | ^~~~~~ [ 9%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/local_symmetry_mpi.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/local_symmetry_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/local_symmetry_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/local_symmetry_mpi.cpp.o -c /build/relion-3.1.3/src/local_symmetry_mpi.cpp +[ 9%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/mask.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/mask.cpp.o -MF CMakeFiles/relion_lib.dir/__/mask.cpp.o.d -o CMakeFiles/relion_lib.dir/__/mask.cpp.o -c /build/relion-3.1.3/src/mask.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/local_symmetry.h:30, from /build/relion-3.1.3/src/local_symmetry_mpi.h:5, @@ -2110,8 +2130,6 @@ /usr/include/aarch64-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 -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/mask.cpp.o -MF CMakeFiles/relion_lib.dir/__/mask.cpp.o.d -o CMakeFiles/relion_lib.dir/__/mask.cpp.o -c /build/relion-3.1.3/src/mask.cpp [ 10%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/matrix1d.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/matrix1d.cpp.o -MF CMakeFiles/relion_lib.dir/__/matrix1d.cpp.o.d -o CMakeFiles/relion_lib.dir/__/matrix1d.cpp.o -c /build/relion-3.1.3/src/matrix1d.cpp [ 10%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/matrix2d.cpp.o @@ -2404,8 +2422,6 @@ | ^~~~~~ [ 14%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/motioncorr_runner.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/motioncorr_runner.cpp.o -MF CMakeFiles/relion_lib.dir/__/motioncorr_runner.cpp.o.d -o CMakeFiles/relion_lib.dir/__/motioncorr_runner.cpp.o -c /build/relion-3.1.3/src/motioncorr_runner.cpp -[ 14%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/motioncorr_runner_mpi.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/motioncorr_runner_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/motioncorr_runner_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/motioncorr_runner_mpi.cpp.o -c /build/relion-3.1.3/src/motioncorr_runner_mpi.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/motioncorr_runner.h:32, from /build/relion-3.1.3/src/motioncorr_runner.cpp:22: @@ -2466,6 +2482,8 @@ /usr/include/aarch64-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 +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/motioncorr_runner_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/motioncorr_runner_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/motioncorr_runner_mpi.cpp.o -c /build/relion-3.1.3/src/motioncorr_runner_mpi.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/motioncorr_runner.h:32, from /build/relion-3.1.3/src/motioncorr_runner_mpi.h:25, @@ -2535,8 +2553,6 @@ cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -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/relion-3.1.3/src/numerical_recipes.cpp [ 15%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/parallel.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/parallel.cpp.o -MF CMakeFiles/relion_lib.dir/__/parallel.cpp.o.d -o CMakeFiles/relion_lib.dir/__/parallel.cpp.o -c /build/relion-3.1.3/src/parallel.cpp -[ 16%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/particle_subtractor.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/particle_subtractor.cpp.o -MF CMakeFiles/relion_lib.dir/__/particle_subtractor.cpp.o.d -o CMakeFiles/relion_lib.dir/__/particle_subtractor.cpp.o -c /build/relion-3.1.3/src/particle_subtractor.cpp In file included from /build/relion-3.1.3/src/numerical_recipes.h:48, from /build/relion-3.1.3/src/numerical_recipes.cpp:49: In function 'void free_Tvector(T*&, int, int) [with T = double]', @@ -2575,8 +2591,14 @@ /build/relion-3.1.3/src/numerical_recipes.cpp:703:13: note: declared here 703 | RFLOAT *pt, *ptt, *xit; | ^~ +[ 16%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/particle_subtractor.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/particle_subtractor.cpp.o -MF CMakeFiles/relion_lib.dir/__/particle_subtractor.cpp.o.d -o CMakeFiles/relion_lib.dir/__/particle_subtractor.cpp.o -c /build/relion-3.1.3/src/particle_subtractor.cpp [ 16%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/pipeline_control.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/pipeline_control.cpp.o -MF CMakeFiles/relion_lib.dir/__/pipeline_control.cpp.o.d -o CMakeFiles/relion_lib.dir/__/pipeline_control.cpp.o -c /build/relion-3.1.3/src/pipeline_control.cpp +[ 17%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/pipeline_jobs.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/pipeline_jobs.cpp.o -MF CMakeFiles/relion_lib.dir/__/pipeline_jobs.cpp.o.d -o CMakeFiles/relion_lib.dir/__/pipeline_jobs.cpp.o -c /build/relion-3.1.3/src/pipeline_jobs.cpp +[ 17%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/pipeliner.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/pipeliner.cpp.o -MF CMakeFiles/relion_lib.dir/__/pipeliner.cpp.o.d -o CMakeFiles/relion_lib.dir/__/pipeliner.cpp.o -c /build/relion-3.1.3/src/pipeliner.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/projector.h:25, from /build/relion-3.1.3/src/ml_model.h:23, @@ -2640,10 +2662,6 @@ /usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 17%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/pipeline_jobs.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/pipeline_jobs.cpp.o -MF CMakeFiles/relion_lib.dir/__/pipeline_jobs.cpp.o.d -o CMakeFiles/relion_lib.dir/__/pipeline_jobs.cpp.o -c /build/relion-3.1.3/src/pipeline_jobs.cpp -[ 17%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/pipeliner.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/pipeliner.cpp.o -MF CMakeFiles/relion_lib.dir/__/pipeliner.cpp.o.d -o CMakeFiles/relion_lib.dir/__/pipeliner.cpp.o -c /build/relion-3.1.3/src/pipeliner.cpp [ 17%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/postprocessing.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/postprocessing.cpp.o -MF CMakeFiles/relion_lib.dir/__/postprocessing.cpp.o.d -o CMakeFiles/relion_lib.dir/__/postprocessing.cpp.o -c /build/relion-3.1.3/src/postprocessing.cpp In file included from /build/relion-3.1.3/src/image.h:455, @@ -2835,6 +2853,10 @@ cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/projector.cpp.o -MF CMakeFiles/relion_lib.dir/__/projector.cpp.o.d -o CMakeFiles/relion_lib.dir/__/projector.cpp.o -c /build/relion-3.1.3/src/projector.cpp [ 19%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/reconstructor.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/reconstructor.cpp.o -MF CMakeFiles/relion_lib.dir/__/reconstructor.cpp.o.d -o CMakeFiles/relion_lib.dir/__/reconstructor.cpp.o -c /build/relion-3.1.3/src/reconstructor.cpp +[ 19%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/reconstructor_mpi.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/reconstructor_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/reconstructor_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/reconstructor_mpi.cpp.o -c /build/relion-3.1.3/src/reconstructor_mpi.cpp +[ 20%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/renderEER.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/renderEER.cpp.o -MF CMakeFiles/relion_lib.dir/__/renderEER.cpp.o.d -o CMakeFiles/relion_lib.dir/__/renderEER.cpp.o -c /build/relion-3.1.3/src/renderEER.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/projector.h:25, from /build/relion-3.1.3/src/projector.cpp:20: @@ -2895,8 +2917,6 @@ /usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 19%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/reconstructor_mpi.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/reconstructor_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/reconstructor_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/reconstructor_mpi.cpp.o -c /build/relion-3.1.3/src/reconstructor_mpi.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/projector.h:25, from /build/relion-3.1.3/src/backprojector.h:33, @@ -3022,12 +3042,6 @@ /usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 20%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/renderEER.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/renderEER.cpp.o -MF CMakeFiles/relion_lib.dir/__/renderEER.cpp.o.d -o CMakeFiles/relion_lib.dir/__/renderEER.cpp.o -c /build/relion-3.1.3/src/renderEER.cpp -[ 20%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/scheduler.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/scheduler.cpp.o -MF CMakeFiles/relion_lib.dir/__/scheduler.cpp.o.d -o CMakeFiles/relion_lib.dir/__/scheduler.cpp.o -c /build/relion-3.1.3/src/scheduler.cpp -[ 20%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/strings.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/strings.cpp.o -MF CMakeFiles/relion_lib.dir/__/strings.cpp.o.d -o CMakeFiles/relion_lib.dir/__/strings.cpp.o -c /build/relion-3.1.3/src/strings.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/renderEER.cpp:10: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': @@ -3087,6 +3101,12 @@ /usr/include/aarch64-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/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/scheduler.cpp.o -MF CMakeFiles/relion_lib.dir/__/scheduler.cpp.o.d -o CMakeFiles/relion_lib.dir/__/scheduler.cpp.o -c /build/relion-3.1.3/src/scheduler.cpp +/build/relion-3.1.3/src/renderEER.cpp: In member function 'void EERRenderer::readLegacy(FILE*)': +/build/relion-3.1.3/src/renderEER.cpp:191:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 191 | fread(buf, sizeof(char), file_size, fh); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-3.1.3/src/scheduler.h:26, @@ -3148,18 +3168,14 @@ /usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -/build/relion-3.1.3/src/renderEER.cpp: In member function 'void EERRenderer::readLegacy(FILE*)': -/build/relion-3.1.3/src/renderEER.cpp:191:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 191 | fread(buf, sizeof(char), file_size, fh); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 20%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/strings.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/strings.cpp.o -MF CMakeFiles/relion_lib.dir/__/strings.cpp.o.d -o CMakeFiles/relion_lib.dir/__/strings.cpp.o -c /build/relion-3.1.3/src/strings.cpp [ 21%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/symmetries.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/symmetries.cpp.o -MF CMakeFiles/relion_lib.dir/__/symmetries.cpp.o.d -o CMakeFiles/relion_lib.dir/__/symmetries.cpp.o -c /build/relion-3.1.3/src/symmetries.cpp [ 21%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/tabfuncs.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/tabfuncs.cpp.o -MF CMakeFiles/relion_lib.dir/__/tabfuncs.cpp.o.d -o CMakeFiles/relion_lib.dir/__/tabfuncs.cpp.o -c /build/relion-3.1.3/src/tabfuncs.cpp [ 21%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/tiff_converter.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/tiff_converter.cpp.o -MF CMakeFiles/relion_lib.dir/__/tiff_converter.cpp.o.d -o CMakeFiles/relion_lib.dir/__/tiff_converter.cpp.o -c /build/relion-3.1.3/src/tiff_converter.cpp -[ 22%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/time.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/time.cpp.o -MF CMakeFiles/relion_lib.dir/__/time.cpp.o.d -o CMakeFiles/relion_lib.dir/__/time.cpp.o -c /build/relion-3.1.3/src/time.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/tiff_converter.cpp:24: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': @@ -3232,6 +3248,8 @@ | | | int | %10ld +[ 22%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/time.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/time.cpp.o -MF CMakeFiles/relion_lib.dir/__/time.cpp.o.d -o CMakeFiles/relion_lib.dir/__/time.cpp.o -c /build/relion-3.1.3/src/time.cpp /build/relion-3.1.3/src/tiff_converter.cpp: In member function 'int TIFFConverter::checkMRCtype(FileName)': /build/relion-3.1.3/src/tiff_converter.cpp:309:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 309 | fread(headers, sizeof(int), 24, mrcin); @@ -3318,6 +3336,10 @@ | ^~~~~~ [ 25%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/complex_io.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/complex_io.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/complex_io.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/complex_io.cpp.o -c /build/relion-3.1.3/src/jaz/complex_io.cpp +[ 25%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/convolution_helper.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/convolution_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/convolution_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/convolution_helper.cpp.o -c /build/relion-3.1.3/src/jaz/convolution_helper.cpp +[ 25%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf_helper.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf_helper.cpp.o -c /build/relion-3.1.3/src/jaz/ctf_helper.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/aberration_fit.h:24, from /build/relion-3.1.3/src/jaz/aberration_fit.cpp:21: @@ -3378,8 +3400,6 @@ /usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 25%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/convolution_helper.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/convolution_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/convolution_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/convolution_helper.cpp.o -c /build/relion-3.1.3/src/jaz/convolution_helper.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/complex_io.h:24, from /build/relion-3.1.3/src/jaz/complex_io.cpp:21: @@ -3440,8 +3460,6 @@ /usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 25%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf_helper.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf_helper.cpp.o -c /build/relion-3.1.3/src/jaz/ctf_helper.cpp [ 26%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/damage_helper.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/damage_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/damage_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/damage_helper.cpp.o -c /build/relion-3.1.3/src/jaz/damage_helper.cpp In file included from /build/relion-3.1.3/src/image.h:455, @@ -3504,8 +3522,6 @@ /usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 26%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/distribution_helper.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/distribution_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/distribution_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/distribution_helper.cpp.o -c /build/relion-3.1.3/src/jaz/distribution_helper.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-3.1.3/src/ctf.h:50, @@ -3630,6 +3646,12 @@ /usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +[ 26%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/distribution_helper.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/distribution_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/distribution_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/distribution_helper.cpp.o -c /build/relion-3.1.3/src/jaz/distribution_helper.cpp +[ 26%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/fftw_helper.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/fftw_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/fftw_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/fftw_helper.cpp.o -c /build/relion-3.1.3/src/jaz/fftw_helper.cpp +[ 27%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/fsc_helper.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/fsc_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/fsc_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/fsc_helper.cpp.o -c /build/relion-3.1.3/src/jaz/fsc_helper.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/distribution_helper.h:25, from /build/relion-3.1.3/src/jaz/distribution_helper.cpp:21: @@ -3690,10 +3712,6 @@ /usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 26%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/fftw_helper.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/fftw_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/fftw_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/fftw_helper.cpp.o -c /build/relion-3.1.3/src/jaz/fftw_helper.cpp -[ 27%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/fsc_helper.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/fsc_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/fsc_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/fsc_helper.cpp.o -c /build/relion-3.1.3/src/jaz/fsc_helper.cpp [ 27%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/image_log.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/image_log.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/image_log.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/image_log.cpp.o -c /build/relion-3.1.3/src/jaz/image_log.cpp In file included from /build/relion-3.1.3/src/image.h:455, @@ -3820,6 +3838,10 @@ | ^~~~~~ [ 28%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/interpolation.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/interpolation.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/interpolation.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/interpolation.cpp.o -c /build/relion-3.1.3/src/jaz/interpolation.cpp +[ 28%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/jaz_config.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/jaz_config.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/jaz_config.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/jaz_config.cpp.o -c /build/relion-3.1.3/src/jaz/jaz_config.cpp +[ 28%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/legacy_obs_model.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/legacy_obs_model.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/legacy_obs_model.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/legacy_obs_model.cpp.o -c /build/relion-3.1.3/src/jaz/legacy_obs_model.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/interpolation.h:24, from /build/relion-3.1.3/src/jaz/interpolation.cpp:21: @@ -3880,10 +3902,6 @@ /usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 28%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/jaz_config.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/jaz_config.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/jaz_config.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/jaz_config.cpp.o -c /build/relion-3.1.3/src/jaz/jaz_config.cpp -[ 28%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/legacy_obs_model.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/legacy_obs_model.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/legacy_obs_model.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/legacy_obs_model.cpp.o -c /build/relion-3.1.3/src/jaz/legacy_obs_model.cpp [ 29%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/local_motion_fit.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/local_motion_fit.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/local_motion_fit.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/local_motion_fit.cpp.o -c /build/relion-3.1.3/src/jaz/local_motion_fit.cpp In file included from /build/relion-3.1.3/src/image.h:455, @@ -3948,8 +3966,6 @@ | ^~~~~~ [ 29%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/micrograph_handler.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/micrograph_handler.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/micrograph_handler.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/micrograph_handler.cpp.o -c /build/relion-3.1.3/src/jaz/micrograph_handler.cpp -[ 29%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/new_ft.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/new_ft.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/new_ft.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/new_ft.cpp.o -c /build/relion-3.1.3/src/jaz/new_ft.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/local_motion_fit.h:24, from /build/relion-3.1.3/src/jaz/local_motion_fit.cpp:21: @@ -4010,6 +4026,14 @@ /usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +[ 29%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/new_ft.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/new_ft.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/new_ft.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/new_ft.cpp.o -c /build/relion-3.1.3/src/jaz/new_ft.cpp +[ 30%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/noise_helper.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/noise_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/noise_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/noise_helper.cpp.o -c /build/relion-3.1.3/src/jaz/noise_helper.cpp +[ 30%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/obs_model.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/obs_model.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/obs_model.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/obs_model.cpp.o -c /build/relion-3.1.3/src/jaz/obs_model.cpp +[ 31%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/parallel_ft.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/parallel_ft.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/parallel_ft.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/parallel_ft.cpp.o -c /build/relion-3.1.3/src/jaz/parallel_ft.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/micrograph_handler.h:31, from /build/relion-3.1.3/src/jaz/micrograph_handler.cpp:21: @@ -4070,12 +4094,6 @@ /usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 30%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/noise_helper.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/noise_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/noise_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/noise_helper.cpp.o -c /build/relion-3.1.3/src/jaz/noise_helper.cpp -[ 30%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/obs_model.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/obs_model.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/obs_model.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/obs_model.cpp.o -c /build/relion-3.1.3/src/jaz/obs_model.cpp -[ 31%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/parallel_ft.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/parallel_ft.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/parallel_ft.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/parallel_ft.cpp.o -c /build/relion-3.1.3/src/jaz/parallel_ft.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/projector.h:25, from /build/relion-3.1.3/src/jaz/noise_helper.h:25, @@ -4137,6 +4155,8 @@ /usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +[ 31%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/reference_map.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/reference_map.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/reference_map.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/reference_map.cpp.o -c /build/relion-3.1.3/src/jaz/reference_map.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-3.1.3/src/jaz/obs_model.cpp:21: @@ -4197,8 +4217,6 @@ /usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 31%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/reference_map.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/reference_map.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/reference_map.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/reference_map.cpp.o -c /build/relion-3.1.3/src/jaz/reference_map.cpp [ 31%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/refinement_helper.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/refinement_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/refinement_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/refinement_helper.cpp.o -c /build/relion-3.1.3/src/jaz/refinement_helper.cpp In file included from /build/relion-3.1.3/src/image.h:455, @@ -4261,10 +4279,6 @@ /usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 32%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/resampling_helper.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/resampling_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/resampling_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/resampling_helper.cpp.o -c /build/relion-3.1.3/src/jaz/resampling_helper.cpp -[ 32%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/slice_helper.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/slice_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/slice_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/slice_helper.cpp.o -c /build/relion-3.1.3/src/jaz/slice_helper.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-3.1.3/src/ctf.h:50, @@ -4327,6 +4341,12 @@ /usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +[ 32%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/resampling_helper.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/resampling_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/resampling_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/resampling_helper.cpp.o -c /build/relion-3.1.3/src/jaz/resampling_helper.cpp +[ 32%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/slice_helper.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/slice_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/slice_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/slice_helper.cpp.o -c /build/relion-3.1.3/src/jaz/slice_helper.cpp +[ 32%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/spectral_helper.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/spectral_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/spectral_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/spectral_helper.cpp.o -c /build/relion-3.1.3/src/jaz/spectral_helper.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/slice_helper.h:24, from /build/relion-3.1.3/src/jaz/slice_helper.cpp:21: @@ -4387,10 +4407,6 @@ /usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 32%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/spectral_helper.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/spectral_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/spectral_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/spectral_helper.cpp.o -c /build/relion-3.1.3/src/jaz/spectral_helper.cpp -[ 33%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/stack_helper.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/stack_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/stack_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/stack_helper.cpp.o -c /build/relion-3.1.3/src/jaz/stack_helper.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/spectral_helper.h:24, from /build/relion-3.1.3/src/jaz/spectral_helper.cpp:21: @@ -4451,6 +4467,8 @@ /usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +[ 33%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/stack_helper.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/stack_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/stack_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/stack_helper.cpp.o -c /build/relion-3.1.3/src/jaz/stack_helper.cpp [ 33%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/structure_tensor.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/structure_tensor.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/structure_tensor.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/structure_tensor.cpp.o -c /build/relion-3.1.3/src/jaz/structure_tensor.cpp In file included from /build/relion-3.1.3/src/image.h:455, @@ -4517,6 +4535,10 @@ | ^~~~~~ [ 34%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/svd_helper.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/svd_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/svd_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/svd_helper.cpp.o -c /build/relion-3.1.3/src/jaz/svd_helper.cpp +[ 34%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/t_complex.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/t_complex.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/t_complex.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/t_complex.cpp.o -c /build/relion-3.1.3/src/jaz/t_complex.cpp +[ 34%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/volume_converter.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/volume_converter.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/volume_converter.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/volume_converter.cpp.o -c /build/relion-3.1.3/src/jaz/volume_converter.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/img_proc/filter_helper.h:24, from /build/relion-3.1.3/src/jaz/structure_tensor.cpp:22: @@ -4577,22 +4599,8 @@ /usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 34%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/t_complex.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/t_complex.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/t_complex.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/t_complex.cpp.o -c /build/relion-3.1.3/src/jaz/t_complex.cpp -[ 34%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/volume_converter.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/volume_converter.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/volume_converter.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/volume_converter.cpp.o -c /build/relion-3.1.3/src/jaz/volume_converter.cpp [ 35%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/volume_integration.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/volume_integration.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/volume_integration.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/volume_integration.cpp.o -c /build/relion-3.1.3/src/jaz/volume_integration.cpp -[ 35%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/vtk_helper.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/vtk_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/vtk_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/vtk_helper.cpp.o -c /build/relion-3.1.3/src/jaz/vtk_helper.cpp -[ 36%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/gradient_descent.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/gradient_descent.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/optimization/gradient_descent.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/optimization/gradient_descent.cpp.o -c /build/relion-3.1.3/src/jaz/optimization/gradient_descent.cpp -[ 36%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/lbfgs.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/lbfgs.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/optimization/lbfgs.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/optimization/lbfgs.cpp.o -c /build/relion-3.1.3/src/jaz/optimization/lbfgs.cpp -[ 36%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/nelder_mead.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/nelder_mead.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/optimization/nelder_mead.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/optimization/nelder_mead.cpp.o -c /build/relion-3.1.3/src/jaz/optimization/nelder_mead.cpp -[ 37%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/optimization.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/optimization.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/optimization/optimization.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/optimization/optimization.cpp.o -c /build/relion-3.1.3/src/jaz/optimization/optimization.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/volume_converter.h:25, from /build/relion-3.1.3/src/jaz/volume_converter.cpp:21: @@ -4653,6 +4661,8 @@ /usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +[ 35%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/vtk_helper.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/vtk_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/vtk_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/vtk_helper.cpp.o -c /build/relion-3.1.3/src/jaz/vtk_helper.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/volume_integration.h:26, from /build/relion-3.1.3/src/jaz/volume_integration.cpp:21: @@ -4713,6 +4723,16 @@ /usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +[ 36%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/gradient_descent.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/gradient_descent.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/optimization/gradient_descent.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/optimization/gradient_descent.cpp.o -c /build/relion-3.1.3/src/jaz/optimization/gradient_descent.cpp +[ 36%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/lbfgs.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/lbfgs.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/optimization/lbfgs.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/optimization/lbfgs.cpp.o -c /build/relion-3.1.3/src/jaz/optimization/lbfgs.cpp +[ 36%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/nelder_mead.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/nelder_mead.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/optimization/nelder_mead.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/optimization/nelder_mead.cpp.o -c /build/relion-3.1.3/src/jaz/optimization/nelder_mead.cpp +[ 37%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/optimization.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/optimization.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/optimization/optimization.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/optimization/optimization.cpp.o -c /build/relion-3.1.3/src/jaz/optimization/optimization.cpp +[ 37%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/aberration_estimator.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/aberration_estimator.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/aberration_estimator.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/aberration_estimator.cpp.o -c /build/relion-3.1.3/src/jaz/ctf/aberration_estimator.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/vtk_helper.h:24, from /build/relion-3.1.3/src/jaz/vtk_helper.cpp:21: @@ -4773,16 +4793,12 @@ /usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 37%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/aberration_estimator.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/aberration_estimator.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/aberration_estimator.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/aberration_estimator.cpp.o -c /build/relion-3.1.3/src/jaz/ctf/aberration_estimator.cpp [ 37%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/bfactor_refiner.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/bfactor_refiner.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/bfactor_refiner.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/bfactor_refiner.cpp.o -c /build/relion-3.1.3/src/jaz/ctf/bfactor_refiner.cpp [ 38%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/ctf_refiner.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/ctf_refiner.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/ctf_refiner.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/ctf_refiner.cpp.o -c /build/relion-3.1.3/src/jaz/ctf/ctf_refiner.cpp [ 38%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/ctf_refiner_mpi.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/ctf_refiner_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/ctf_refiner_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/ctf_refiner_mpi.cpp.o -c /build/relion-3.1.3/src/jaz/ctf/ctf_refiner_mpi.cpp -[ 39%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/defocus_estimator.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/defocus_estimator.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/defocus_estimator.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/defocus_estimator.cpp.o -c /build/relion-3.1.3/src/jaz/ctf/defocus_estimator.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/ctf/aberration_estimator.h:4, from /build/relion-3.1.3/src/jaz/ctf/aberration_estimator.cpp:1: @@ -4843,6 +4859,8 @@ /usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +[ 39%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/defocus_estimator.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/defocus_estimator.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/defocus_estimator.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/defocus_estimator.cpp.o -c /build/relion-3.1.3/src/jaz/ctf/defocus_estimator.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/ctf/bfactor_refiner.h:4, from /build/relion-3.1.3/src/jaz/ctf/bfactor_refiner.cpp:1: @@ -5406,8 +5424,6 @@ /usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 42%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_helper.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_helper.cpp.o -c /build/relion-3.1.3/src/jaz/ctf/tilt_helper.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/ctf/tilt_estimator.h:24, from /build/relion-3.1.3/src/jaz/ctf/tilt_estimator.cpp:21: @@ -5468,6 +5484,8 @@ /usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +[ 42%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_helper.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_helper.cpp.o -c /build/relion-3.1.3/src/jaz/ctf/tilt_helper.cpp [ 42%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/alignment_set.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/alignment_set.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/alignment_set.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/alignment_set.cpp.o -c /build/relion-3.1.3/src/jaz/motion/alignment_set.cpp [ 42%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/frame_recombiner.cpp.o @@ -5784,8 +5802,6 @@ /usr/include/aarch64-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/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner.cpp.o -c /build/relion-3.1.3/src/jaz/motion/motion_refiner.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/motion/alignment_set.h:24, from /build/relion-3.1.3/src/jaz/motion/motion_param_estimator.h:24, @@ -5847,6 +5863,8 @@ /usr/include/aarch64-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/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner.cpp.o -c /build/relion-3.1.3/src/jaz/motion/motion_refiner.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-3.1.3/src/ctf.h:50, @@ -5914,9 +5932,11 @@ [ 45%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/three_hyperparameter_fit.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/three_hyperparameter_fit.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/three_hyperparameter_fit.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/three_hyperparameter_fit.cpp.o -c /build/relion-3.1.3/src/jaz/motion/three_hyperparameter_fit.cpp In file included from /build/relion-3.1.3/src/image.h:455, - from /build/relion-3.1.3/src/jaz/motion/alignment_set.h:24, - from /build/relion-3.1.3/src/jaz/motion/motion_param_estimator.h:24, - from /build/relion-3.1.3/src/jaz/motion/three_hyperparameter_fit.cpp:22: + from /build/relion-3.1.3/src/jaz/obs_model.h:24, + from /build/relion-3.1.3/src/ctf.h:50, + from /build/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, + from /build/relion-3.1.3/src/jaz/motion/motion_refiner_mpi.h:27, + from /build/relion-3.1.3/src/jaz/motion/motion_refiner_mpi.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -5975,11 +5995,9 @@ 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-3.1.3/src/image.h:455, - from /build/relion-3.1.3/src/jaz/obs_model.h:24, - from /build/relion-3.1.3/src/ctf.h:50, - from /build/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, - from /build/relion-3.1.3/src/jaz/motion/motion_refiner_mpi.h:27, - from /build/relion-3.1.3/src/jaz/motion/motion_refiner_mpi.cpp:21: + from /build/relion-3.1.3/src/jaz/motion/alignment_set.h:24, + from /build/relion-3.1.3/src/jaz/motion/motion_param_estimator.h:24, + from /build/relion-3.1.3/src/jaz/motion/three_hyperparameter_fit.cpp:22: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -6039,6 +6057,8 @@ | ^~~~~~ [ 45%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/two_hyperparameter_fit.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/two_hyperparameter_fit.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/two_hyperparameter_fit.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/two_hyperparameter_fit.cpp.o -c /build/relion-3.1.3/src/jaz/motion/two_hyperparameter_fit.cpp +[ 46%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/math/Zernike.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/math/Zernike.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/math/Zernike.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/math/Zernike.cpp.o -c /build/relion-3.1.3/src/jaz/math/Zernike.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/motion/alignment_set.h:24, from /build/relion-3.1.3/src/jaz/motion/motion_param_estimator.h:24, @@ -6100,8 +6120,6 @@ /usr/include/aarch64-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/math/Zernike.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/math/Zernike.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/math/Zernike.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/math/Zernike.cpp.o -c /build/relion-3.1.3/src/jaz/math/Zernike.cpp [ 46%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/img_proc/color_helper.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/img_proc/color_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/img_proc/color_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/img_proc/color_helper.cpp.o -c /build/relion-3.1.3/src/jaz/img_proc/color_helper.cpp [ 46%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/img_proc/filter_helper.cpp.o @@ -6232,6 +6250,8 @@ /usr/include/aarch64-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/projection_helper.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/projection_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/tomo/projection_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/tomo/projection_helper.cpp.o -c /build/relion-3.1.3/src/jaz/tomo/projection_helper.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/tomo/backprojection_helper.h:24, from /build/relion-3.1.3/src/jaz/tomo/backprojection_helper.cpp:23: @@ -6292,14 +6312,16 @@ /usr/include/aarch64-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/projection_helper.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/projection_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/tomo/projection_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/tomo/projection_helper.cpp.o -c /build/relion-3.1.3/src/jaz/tomo/projection_helper.cpp [ 48%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/tomo_stack.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/tomo_stack.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/tomo/tomo_stack.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/tomo/tomo_stack.cpp.o -c /build/relion-3.1.3/src/jaz/tomo/tomo_stack.cpp [ 49%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/io/star_converter.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/io/star_converter.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/io/star_converter.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/io/star_converter.cpp.o -c /build/relion-3.1.3/src/jaz/io/star_converter.cpp [ 49%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyev2.c.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyev2.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyev2.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyev2.c.o -c /build/relion-3.1.3/src/jaz/d3x3/dsyev2.c +[ 50%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevc3.c.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevc3.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevc3.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevc3.c.o -c /build/relion-3.1.3/src/jaz/d3x3/dsyevc3.c +[ 50%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevd3.c.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevd3.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevd3.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevd3.c.o -c /build/relion-3.1.3/src/jaz/d3x3/dsyevd3.c In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/tomo/tomo_stack.h:25, from /build/relion-3.1.3/src/jaz/tomo/tomo_stack.cpp:21: @@ -6360,10 +6382,6 @@ /usr/include/aarch64-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/relion-3.1.3/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevc3.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevc3.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevc3.c.o -c /build/relion-3.1.3/src/jaz/d3x3/dsyevc3.c -[ 50%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevd3.c.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevd3.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevd3.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevd3.c.o -c /build/relion-3.1.3/src/jaz/d3x3/dsyevd3.c [ 50%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevh3.c.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevh3.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevh3.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevh3.c.o -c /build/relion-3.1.3/src/jaz/d3x3/dsyevh3.c [ 51%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevj3.c.o @@ -6372,12 +6390,6 @@ cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevq3.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevq3.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevq3.c.o -c /build/relion-3.1.3/src/jaz/d3x3/dsyevq3.c [ 51%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevv3.c.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevv3.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevv3.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevv3.c.o -c /build/relion-3.1.3/src/jaz/d3x3/dsyevv3.c -[ 52%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsytrd3.c.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsytrd3.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsytrd3.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsytrd3.c.o -c /build/relion-3.1.3/src/jaz/d3x3/dsytrd3.c -[ 52%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/slvsec3.c.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/slvsec3.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/slvsec3.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/slvsec3.c.o -c /build/relion-3.1.3/src/jaz/d3x3/slvsec3.c -[ 53%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/lbfgs/lbfgs.c.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/lbfgs/lbfgs.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/lbfgs/lbfgs.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/lbfgs/lbfgs.c.o -c /build/relion-3.1.3/src/jaz/lbfgs/lbfgs.c In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/io/star_converter.h:5, from /build/relion-3.1.3/src/jaz/io/star_converter.cpp:1: @@ -6438,6 +6450,12 @@ /usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +[ 52%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsytrd3.c.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsytrd3.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsytrd3.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsytrd3.c.o -c /build/relion-3.1.3/src/jaz/d3x3/dsytrd3.c +[ 52%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/slvsec3.c.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/slvsec3.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/slvsec3.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/slvsec3.c.o -c /build/relion-3.1.3/src/jaz/d3x3/slvsec3.c +[ 53%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/lbfgs/lbfgs.c.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/lbfgs/lbfgs.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/lbfgs/lbfgs.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/lbfgs/lbfgs.c.o -c /build/relion-3.1.3/src/jaz/lbfgs/lbfgs.c [ 53%] Linking CXX static library ../../lib/librelion_lib.a cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -P CMakeFiles/relion_lib.dir/cmake_clean_target.cmake cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/relion_lib.dir/link.txt --verbose=1 @@ -6446,72 +6464,72 @@ make[4]: Leaving directory '/build/relion-3.1.3/build' [ 53%] Built target relion_lib /usr/bin/make -f src/apps/CMakeFiles/relion_gui_lib.dir/build.make src/apps/CMakeFiles/relion_gui_lib.dir/depend -make[4]: Entering directory '/build/relion-3.1.3/build' -cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/relion_gui_lib.dir/DependInfo.cmake --color= /usr/bin/make -f src/apps/CMakeFiles/align_symmetry.dir/build.make src/apps/CMakeFiles/align_symmetry.dir/depend /usr/bin/make -f src/apps/CMakeFiles/autopick.dir/build.make src/apps/CMakeFiles/autopick.dir/depend +/usr/bin/make -f src/apps/CMakeFiles/autopick_mpi.dir/build.make src/apps/CMakeFiles/autopick_mpi.dir/depend +/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/relion-3.1.3/build' +cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/relion_gui_lib.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/align_symmetry.dir/DependInfo.cmake --color= -/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_to_tiff_mpi.dir/build.make src/apps/CMakeFiles/convert_to_tiff_mpi.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/autopick.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/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/autopick_mpi.dir/DependInfo.cmake --color= -/usr/bin/make -f src/apps/CMakeFiles/convert_star.dir/build.make src/apps/CMakeFiles/convert_star.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/convert_star.dir/DependInfo.cmake --color= -/usr/bin/make -f src/apps/CMakeFiles/convert_to_tiff.dir/build.make src/apps/CMakeFiles/convert_to_tiff.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/convert_to_tiff.dir/DependInfo.cmake --color= -/usr/bin/make -f src/apps/CMakeFiles/convert_to_tiff_mpi.dir/build.make src/apps/CMakeFiles/convert_to_tiff_mpi.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/convert_to_tiff_mpi.dir/DependInfo.cmake --color= -/usr/bin/make -f src/apps/CMakeFiles/ctf_mask_test.dir/build.make src/apps/CMakeFiles/ctf_mask_test.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/ctf_mask_test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.3/build' +make[4]: Leaving directory '/build/relion-3.1.3/build' +make[4]: Leaving directory '/build/relion-3.1.3/build' +/usr/bin/make -f src/apps/CMakeFiles/autopick_mpi.dir/build.make src/apps/CMakeFiles/autopick_mpi.dir/build /usr/bin/make -f src/apps/CMakeFiles/align_symmetry.dir/build.make src/apps/CMakeFiles/align_symmetry.dir/build make[4]: Leaving directory '/build/relion-3.1.3/build' -make[4]: Entering directory '/build/relion-3.1.3/build' +make[4]: Leaving directory '/build/relion-3.1.3/build' /usr/bin/make -f src/apps/CMakeFiles/relion_gui_lib.dir/build.make src/apps/CMakeFiles/relion_gui_lib.dir/build -make[4]: Entering directory '/build/relion-3.1.3/build' make[4]: Leaving directory '/build/relion-3.1.3/build' /usr/bin/make -f src/apps/CMakeFiles/autopick.dir/build.make src/apps/CMakeFiles/autopick.dir/build +/usr/bin/make -f src/apps/CMakeFiles/convert_star.dir/build.make src/apps/CMakeFiles/convert_star.dir/build +make[4]: Entering directory '/build/relion-3.1.3/build' +make[4]: Entering directory '/build/relion-3.1.3/build' +/usr/bin/make -f src/apps/CMakeFiles/convert_to_tiff.dir/build.make src/apps/CMakeFiles/convert_to_tiff.dir/build +make[4]: Entering directory '/build/relion-3.1.3/build' +make[4]: Entering directory '/build/relion-3.1.3/build' make[4]: Entering directory '/build/relion-3.1.3/build' -[ 53%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/displayer.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_gui_lib.dir/__/displayer.cpp.o -MF CMakeFiles/relion_gui_lib.dir/__/displayer.cpp.o.d -o CMakeFiles/relion_gui_lib.dir/__/displayer.cpp.o -c /build/relion-3.1.3/src/displayer.cpp make[4]: Leaving directory '/build/relion-3.1.3/build' /usr/bin/make -f src/apps/CMakeFiles/ctf_mask_test.dir/build.make src/apps/CMakeFiles/ctf_mask_test.dir/build -make[4]: Leaving directory '/build/relion-3.1.3/build' make[4]: Entering directory '/build/relion-3.1.3/build' +make[4]: Leaving directory '/build/relion-3.1.3/build' /usr/bin/make -f src/apps/CMakeFiles/convert_to_tiff_mpi.dir/build.make src/apps/CMakeFiles/convert_to_tiff_mpi.dir/build make[4]: Entering directory '/build/relion-3.1.3/build' +make[4]: Entering directory '/build/relion-3.1.3/build' [ 53%] Building CXX object src/apps/CMakeFiles/align_symmetry.dir/align_symmetry.cpp.o -[ 54%] Building CXX object src/apps/CMakeFiles/convert_to_tiff_mpi.dir/convert_to_tiff_mpi.cpp.o -make[4]: Leaving directory '/build/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/convert_to_tiff.dir/build.make src/apps/CMakeFiles/convert_to_tiff.dir/build +[ 53%] Building CXX object src/apps/CMakeFiles/autopick_mpi.dir/autopick_mpi.cpp.o +[ 53%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/displayer.cpp.o +[ 53%] Building CXX object src/apps/CMakeFiles/convert_to_tiff.dir/convert_to_tiff.cpp.o +[ 54%] Building CXX object src/apps/CMakeFiles/autopick.dir/autopick.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/convert_to_tiff.dir/convert_to_tiff.cpp.o -MF CMakeFiles/convert_to_tiff.dir/convert_to_tiff.cpp.o.d -o CMakeFiles/convert_to_tiff.dir/convert_to_tiff.cpp.o -c /build/relion-3.1.3/src/apps/convert_to_tiff.cpp cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp 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-make[4]: Leaving directory '/build/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/autopick_mpi.dir/build.make src/apps/CMakeFiles/autopick_mpi.dir/build -make[4]: Leaving directory '/build/relion-3.1.3/build' -make[4]: Entering directory '/build/relion-3.1.3/build' -make[4]: Entering directory '/build/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/convert_star.dir/build.make src/apps/CMakeFiles/convert_star.dir/build -[ 54%] Building CXX object src/apps/CMakeFiles/ctf_mask_test.dir/ctf_mask_test.cpp.o -make[4]: Entering directory '/build/relion-3.1.3/build' -[ 55%] Building CXX object src/apps/CMakeFiles/autopick.dir/autopick.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/ctf_mask_test.dir/ctf_mask_test.cpp.o -MF CMakeFiles/ctf_mask_test.dir/ctf_mask_test.cpp.o.d -o CMakeFiles/ctf_mask_test.dir/ctf_mask_test.cpp.o -c /build/relion-3.1.3/src/apps/ctf_mask_test.cpp -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/autopick.dir/autopick.cpp.o -MF CMakeFiles/autopick.dir/autopick.cpp.o.d -o CMakeFiles/autopick.dir/autopick.cpp.o -c /build/relion-3.1.3/src/apps/autopick.cpp -[ 55%] Building CXX object src/apps/CMakeFiles/autopick_mpi.dir/autopick_mpi.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/autopick_mpi.dir/autopick_mpi.cpp.o -MF CMakeFiles/autopick_mpi.dir/autopick_mpi.cpp.o.d -o CMakeFiles/autopick_mpi.dir/autopick_mpi.cpp.o -c /build/relion-3.1.3/src/apps/autopick_mpi.cpp -[ 55%] Building CXX object src/apps/CMakeFiles/convert_to_tiff.dir/convert_to_tiff.cpp.o -[ 55%] Building CXX object src/apps/CMakeFiles/convert_star.dir/convert_star.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/convert_to_tiff.dir/convert_to_tiff.cpp.o -MF CMakeFiles/convert_to_tiff.dir/convert_to_tiff.cpp.o.d -o CMakeFiles/convert_to_tiff.dir/convert_to_tiff.cpp.o -c /build/relion-3.1.3/src/apps/convert_to_tiff.cpp +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_gui_lib.dir/__/displayer.cpp.o -MF CMakeFiles/relion_gui_lib.dir/__/displayer.cpp.o.d -o CMakeFiles/relion_gui_lib.dir/__/displayer.cpp.o -c /build/relion-3.1.3/src/displayer.cpp +[ 54%] Building CXX object src/apps/CMakeFiles/convert_star.dir/convert_star.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/autopick.dir/autopick.cpp.o -MF CMakeFiles/autopick.dir/autopick.cpp.o.d -o CMakeFiles/autopick.dir/autopick.cpp.o -c /build/relion-3.1.3/src/apps/autopick.cpp cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/convert_star.dir/convert_star.cpp.o -MF CMakeFiles/convert_star.dir/convert_star.cpp.o.d -o CMakeFiles/convert_star.dir/convert_star.cpp.o -c /build/relion-3.1.3/src/apps/convert_star.cpp +[ 54%] Building CXX object src/apps/CMakeFiles/ctf_mask_test.dir/ctf_mask_test.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/ctf_mask_test.dir/ctf_mask_test.cpp.o -MF CMakeFiles/ctf_mask_test.dir/ctf_mask_test.cpp.o.d -o CMakeFiles/ctf_mask_test.dir/ctf_mask_test.cpp.o -c /build/relion-3.1.3/src/apps/ctf_mask_test.cpp +[ 55%] Building CXX object src/apps/CMakeFiles/convert_to_tiff_mpi.dir/convert_to_tiff_mpi.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/convert_to_tiff_mpi.dir/convert_to_tiff_mpi.cpp.o -MF CMakeFiles/convert_to_tiff_mpi.dir/convert_to_tiff_mpi.cpp.o.d -o CMakeFiles/convert_to_tiff_mpi.dir/convert_to_tiff_mpi.cpp.o -c /build/relion-3.1.3/src/apps/convert_to_tiff_mpi.cpp In file included from /build/relion-3.1.3/src/image.h:455, - from /build/relion-3.1.3/src/tiff_converter.h:24, - from /build/relion-3.1.3/src/apps/convert_to_tiff_mpi.cpp:21: + from /build/relion-3.1.3/src/projector.h:25, + from /build/relion-3.1.3/src/apps/align_symmetry.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -6545,33 +6563,9 @@ /usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -/build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] - 185 | uint32 cur_width, cur_length; - | ^~~~~~~~~ -/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here - 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] - 185 | uint32 cur_width, cur_length; - | ^~~~~~~~~~ -/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here - 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 186 | uint16 cur_sampleFormat, cur_bitsPerSample; - | ^~~~~~~~~~~~~~~~ -/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 186 | uint16 cur_sampleFormat, cur_bitsPerSample; - | ^~~~~~~~~~~~~~~~~ -/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ In file included from /build/relion-3.1.3/src/image.h:455, - from /build/relion-3.1.3/src/projector.h:25, - from /build/relion-3.1.3/src/apps/align_symmetry.cpp:21: + from /build/relion-3.1.3/src/tiff_converter.h:24, + from /build/relion-3.1.3/src/apps/convert_to_tiff.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -6629,8 +6623,33 @@ /usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 185 | uint32 cur_width, cur_length; + | ^~~~~~~~~ +/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here + 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 185 | uint32 cur_width, cur_length; + | ^~~~~~~~~~ +/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here + 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 186 | uint16 cur_sampleFormat, cur_bitsPerSample; + | ^~~~~~~~~~~~~~~~ +/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 186 | uint16 cur_sampleFormat, cur_bitsPerSample; + | ^~~~~~~~~~~~~~~~~ +/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ In file included from /build/relion-3.1.3/src/image.h:455, - from /build/relion-3.1.3/src/apps/ctf_mask_test.cpp:7: + from /build/relion-3.1.3/src/autopicker.h:10, + from /build/relion-3.1.3/src/apps/autopick.cpp:20: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -6724,9 +6743,32 @@ /usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 185 | uint32 cur_width, cur_length; + | ^~~~~~~~~ +/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here + 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 185 | uint32 cur_width, cur_length; + | ^~~~~~~~~~ +/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here + 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 186 | uint16 cur_sampleFormat, cur_bitsPerSample; + | ^~~~~~~~~~~~~~~~ +/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 186 | uint16 cur_sampleFormat, cur_bitsPerSample; + | ^~~~~~~~~~~~~~~~~ +/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ In file included from /build/relion-3.1.3/src/image.h:455, - from /build/relion-3.1.3/src/autopicker.h:10, - from /build/relion-3.1.3/src/apps/autopick.cpp:20: + from /build/relion-3.1.3/src/apps/ctf_mask_test.cpp:7: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -6786,7 +6828,7 @@ | ^~~~~~ In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/tiff_converter.h:24, - from /build/relion-3.1.3/src/apps/convert_to_tiff.cpp:21: + from /build/relion-3.1.3/src/apps/convert_to_tiff_mpi.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -6844,30 +6886,6 @@ /usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -/build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] - 185 | uint32 cur_width, cur_length; - | ^~~~~~~~~ -/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here - 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] - 185 | uint32 cur_width, cur_length; - | ^~~~~~~~~~ -/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here - 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 186 | uint16 cur_sampleFormat, cur_bitsPerSample; - | ^~~~~~~~~~~~~~~~ -/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 186 | uint16 cur_sampleFormat, cur_bitsPerSample; - | ^~~~~~~~~~~~~~~~~ -/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/displayer.h:40, from /build/relion-3.1.3/src/displayer.cpp:21: @@ -7011,16 +7029,16 @@ make[4]: Leaving directory '/build/relion-3.1.3/build' [ 56%] Built target convert_star /usr/bin/make -f src/apps/CMakeFiles/ctf_refine_mpi.dir/build.make src/apps/CMakeFiles/ctf_refine_mpi.dir/depend +[ 56%] Linking CXX executable ../../bin/relion_convert_to_tiff_mpi make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/ctf_refine_mpi.dir/DependInfo.cmake --color= +cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/convert_to_tiff_mpi.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/convert_to_tiff_mpi.dir/convert_to_tiff_mpi.cpp.o -o ../../bin/relion_convert_to_tiff_mpi ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' /usr/bin/make -f src/apps/CMakeFiles/ctf_refine_mpi.dir/build.make src/apps/CMakeFiles/ctf_refine_mpi.dir/build make[4]: Entering directory '/build/relion-3.1.3/build' [ 56%] Building CXX object src/apps/CMakeFiles/ctf_refine_mpi.dir/ctf_refine_mpi.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/ctf_refine_mpi.dir/ctf_refine_mpi.cpp.o -MF CMakeFiles/ctf_refine_mpi.dir/ctf_refine_mpi.cpp.o.d -o CMakeFiles/ctf_refine_mpi.dir/ctf_refine_mpi.cpp.o -c /build/relion-3.1.3/src/apps/ctf_refine_mpi.cpp -[ 56%] Linking CXX executable ../../bin/relion_convert_to_tiff_mpi -cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/convert_to_tiff_mpi.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/convert_to_tiff_mpi.dir/convert_to_tiff_mpi.cpp.o -o ../../bin/relion_convert_to_tiff_mpi ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' [ 56%] Built target autopick /usr/bin/make -f src/apps/CMakeFiles/ctf_toolbox.dir/build.make src/apps/CMakeFiles/ctf_toolbox.dir/depend @@ -7168,12 +7186,16 @@ 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ make[4]: Leaving directory '/build/relion-3.1.3/build' +[ 58%] Built target autopick_mpi +/usr/bin/make -f src/apps/CMakeFiles/estimate_gain.dir/build.make src/apps/CMakeFiles/estimate_gain.dir/depend In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/apps/ctf_toolbox.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ +make[4]: Entering directory '/build/relion-3.1.3/build' +cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/estimate_gain.dir/DependInfo.cmake --color= In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here @@ -7203,7 +7225,6 @@ /usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 58%] Built target autopick_mpi /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ @@ -7228,9 +7249,6 @@ /usr/include/aarch64-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/estimate_gain.dir/build.make src/apps/CMakeFiles/estimate_gain.dir/depend -make[4]: Entering directory '/build/relion-3.1.3/build' -cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/estimate_gain.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.3/build' /usr/bin/make -f src/apps/CMakeFiles/estimate_gain.dir/build.make src/apps/CMakeFiles/estimate_gain.dir/build make[4]: Entering directory '/build/relion-3.1.3/build' @@ -7588,9 +7606,6 @@ /usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 62%] Linking CXX executable ../../bin/relion_demodulate -cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/demodulate.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/demodulate.dir/demodulate.cpp.o -o ../../bin/relion_demodulate ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In file included from /build/relion-3.1.3/src/numerical_recipes.h:48, from /build/relion-3.1.3/src/funcs.h:59, from /build/relion-3.1.3/src/args.h:56, @@ -7613,9 +7628,12 @@ /build/relion-3.1.3/src/numerical_recipes.h:198:26: note: declared here 198 | int *indxc, *indxr, *ipiv; | ^~~~ -[ 62%] Linking CXX executable ../../bin/relion_ctf_toolbox +[ 61%] Linking CXX executable ../../bin/relion_ctf_toolbox cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/ctf_toolbox.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ctf_toolbox.dir/ctf_toolbox.cpp.o -o ../../bin/relion_ctf_toolbox ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +[ 62%] Linking CXX executable ../../bin/relion_demodulate +cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/demodulate.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/demodulate.dir/demodulate.cpp.o -o ../../bin/relion_demodulate ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' [ 62%] Built target ctf_toolbox /usr/bin/make -f src/apps/CMakeFiles/helix_inimodel2d.dir/build.make src/apps/CMakeFiles/helix_inimodel2d.dir/depend @@ -7634,10 +7652,10 @@ make[4]: Leaving directory '/build/relion-3.1.3/build' /usr/bin/make -f src/apps/CMakeFiles/helix_toolbox.dir/build.make src/apps/CMakeFiles/helix_toolbox.dir/build make[4]: Entering directory '/build/relion-3.1.3/build' +[ 63%] Linking CXX executable ../../bin/relion_estimate_gain +cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/estimate_gain.dir/link.txt --verbose=1 [ 64%] Building CXX object src/apps/CMakeFiles/helix_toolbox.dir/helix_toolbox.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/helix_toolbox.dir/helix_toolbox.cpp.o -MF CMakeFiles/helix_toolbox.dir/helix_toolbox.cpp.o.d -o CMakeFiles/helix_toolbox.dir/helix_toolbox.cpp.o -c /build/relion-3.1.3/src/apps/helix_toolbox.cpp -[ 64%] Linking CXX executable ../../bin/relion_estimate_gain -cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/estimate_gain.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/estimate_gain.dir/estimate_gain.cpp.o -o ../../bin/relion_estimate_gain ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' [ 64%] Built target estimate_gain @@ -7712,6 +7730,9 @@ /usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +[ 66%] Linking CXX executable ../../bin/relion_find_tiltpairs +cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/find_tiltpairs.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/find_tiltpairs.dir/find_tiltpairs.cpp.o -o ../../bin/relion_find_tiltpairs ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/helix.h:30, from /build/relion-3.1.3/src/apps/helix_toolbox.cpp:22: @@ -7772,24 +7793,21 @@ /usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 65%] Linking CXX executable ../../bin/relion_external_reconstruct -cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/external_reconstruct.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/external_reconstruct.dir/external_reconstruct.cpp.o -o ../../bin/relion_external_reconstruct ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -[ 66%] Linking CXX executable ../../bin/relion_find_tiltpairs -cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/find_tiltpairs.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/find_tiltpairs.dir/find_tiltpairs.cpp.o -o ../../bin/relion_find_tiltpairs ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 66%] Built target flex_analyse +[ 66%] Built target find_tiltpairs /usr/bin/make -f src/apps/CMakeFiles/import.dir/build.make src/apps/CMakeFiles/import.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/import.dir/DependInfo.cmake --color= +[ 66%] Linking CXX executable ../../bin/relion_external_reconstruct +cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/external_reconstruct.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/external_reconstruct.dir/external_reconstruct.cpp.o -o ../../bin/relion_external_reconstruct ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' /usr/bin/make -f src/apps/CMakeFiles/import.dir/build.make src/apps/CMakeFiles/import.dir/build make[4]: Entering directory '/build/relion-3.1.3/build' [ 66%] Building CXX object src/apps/CMakeFiles/import.dir/import.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/import.dir/import.cpp.o -MF CMakeFiles/import.dir/import.cpp.o.d -o CMakeFiles/import.dir/import.cpp.o -c /build/relion-3.1.3/src/apps/import.cpp make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 66%] Built target external_reconstruct +[ 66%] Built target flex_analyse /usr/bin/make -f src/apps/CMakeFiles/localsym.dir/build.make src/apps/CMakeFiles/localsym.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/localsym.dir/DependInfo.cmake --color= @@ -7798,16 +7816,6 @@ make[4]: Entering directory '/build/relion-3.1.3/build' [ 67%] Building CXX object src/apps/CMakeFiles/localsym.dir/localsym.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/localsym.dir/localsym.cpp.o -MF CMakeFiles/localsym.dir/localsym.cpp.o.d -o CMakeFiles/localsym.dir/localsym.cpp.o -c /build/relion-3.1.3/src/apps/localsym.cpp -make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 67%] Built target find_tiltpairs -/usr/bin/make -f src/apps/CMakeFiles/localsym_mpi.dir/build.make src/apps/CMakeFiles/localsym_mpi.dir/depend -make[4]: Entering directory '/build/relion-3.1.3/build' -cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/localsym_mpi.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/localsym_mpi.dir/build.make src/apps/CMakeFiles/localsym_mpi.dir/build -make[4]: Entering directory '/build/relion-3.1.3/build' -[ 68%] Building CXX object src/apps/CMakeFiles/localsym_mpi.dir/localsym_mpi.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/localsym_mpi.dir/localsym_mpi.cpp.o -MF CMakeFiles/localsym_mpi.dir/localsym_mpi.cpp.o.d -o CMakeFiles/localsym_mpi.dir/localsym_mpi.cpp.o -c /build/relion-3.1.3/src/apps/localsym_mpi.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/apps/image_handler.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': @@ -7867,6 +7875,16 @@ /usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +make[4]: Leaving directory '/build/relion-3.1.3/build' +[ 67%] Built target external_reconstruct +/usr/bin/make -f src/apps/CMakeFiles/localsym_mpi.dir/build.make src/apps/CMakeFiles/localsym_mpi.dir/depend +make[4]: Entering directory '/build/relion-3.1.3/build' +cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/localsym_mpi.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/relion-3.1.3/build' +/usr/bin/make -f src/apps/CMakeFiles/localsym_mpi.dir/build.make src/apps/CMakeFiles/localsym_mpi.dir/build +make[4]: Entering directory '/build/relion-3.1.3/build' +[ 68%] Building CXX object src/apps/CMakeFiles/localsym_mpi.dir/localsym_mpi.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/localsym_mpi.dir/localsym_mpi.cpp.o -MF CMakeFiles/localsym_mpi.dir/localsym_mpi.cpp.o.d -o CMakeFiles/localsym_mpi.dir/localsym_mpi.cpp.o -c /build/relion-3.1.3/src/apps/localsym_mpi.cpp [ 68%] Linking CXX executable ../../bin/relion_helix_inimodel2d cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/helix_inimodel2d.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/helix_inimodel2d.dir/helix_inimodel2d.cpp.o -o ../../bin/relion_helix_inimodel2d ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff @@ -8000,9 +8018,6 @@ /usr/include/aarch64-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_flex_analyse_mpi -cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/flex_analyse_mpi.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/flex_analyse_mpi.dir/flex_analyse_mpi.cpp.o -o ../../bin/relion_flex_analyse_mpi ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/local_symmetry.h:30, from /build/relion-3.1.3/src/local_symmetry_mpi.h:5, @@ -8064,13 +8079,12 @@ /usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 68%] Built target flex_analyse_mpi [ 68%] Linking CXX executable ../../bin/relion_localsym -/usr/bin/make -f src/apps/CMakeFiles/merge_particles.dir/build.make src/apps/CMakeFiles/merge_particles.dir/depend -make[4]: Entering directory '/build/relion-3.1.3/build' -cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/merge_particles.dir/DependInfo.cmake --color= cd /build/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_flex_analyse_mpi +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/localsym.dir/localsym.cpp.o -o ../../bin/relion_localsym ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/flex_analyse_mpi.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/flex_analyse_mpi.dir/flex_analyse_mpi.cpp.o -o ../../bin/relion_flex_analyse_mpi ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/apps/mask_create.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': @@ -8130,14 +8144,18 @@ /usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/localsym.dir/localsym.cpp.o -o ../../bin/relion_localsym ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +make[4]: Leaving directory '/build/relion-3.1.3/build' +[ 68%] Built target localsym +/usr/bin/make -f src/apps/CMakeFiles/merge_particles.dir/build.make src/apps/CMakeFiles/merge_particles.dir/depend +make[4]: Entering directory '/build/relion-3.1.3/build' +cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/merge_particles.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.3/build' /usr/bin/make -f src/apps/CMakeFiles/merge_particles.dir/build.make src/apps/CMakeFiles/merge_particles.dir/build make[4]: Entering directory '/build/relion-3.1.3/build' [ 69%] Building CXX object src/apps/CMakeFiles/merge_particles.dir/merge_particles.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/merge_particles.dir/merge_particles.cpp.o -MF CMakeFiles/merge_particles.dir/merge_particles.cpp.o.d -o CMakeFiles/merge_particles.dir/merge_particles.cpp.o -c /build/relion-3.1.3/src/apps/merge_particles.cpp make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 69%] Built target localsym +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/merge_particles.dir/merge_particles.cpp.o -MF CMakeFiles/merge_particles.dir/merge_particles.cpp.o.d -o CMakeFiles/merge_particles.dir/merge_particles.cpp.o -c /build/relion-3.1.3/src/apps/merge_particles.cpp +[ 69%] Built target flex_analyse_mpi /usr/bin/make -f src/apps/CMakeFiles/motion_refine.dir/build.make src/apps/CMakeFiles/motion_refine.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/motion_refine.dir/DependInfo.cmake --color= @@ -8146,6 +8164,9 @@ make[4]: Entering directory '/build/relion-3.1.3/build' [ 70%] Building CXX object src/apps/CMakeFiles/motion_refine.dir/motion_refine.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/motion_refine.dir/motion_refine.cpp.o -MF CMakeFiles/motion_refine.dir/motion_refine.cpp.o.d -o CMakeFiles/motion_refine.dir/motion_refine.cpp.o -c /build/relion-3.1.3/src/apps/motion_refine.cpp +[ 70%] Linking CXX executable ../../bin/relion_localsym_mpi +cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/localsym_mpi.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/localsym_mpi.dir/localsym_mpi.cpp.o -o ../../bin/relion_localsym_mpi ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/io/star_converter.h:5, from /build/relion-3.1.3/src/apps/merge_particles.cpp:2: @@ -8206,9 +8227,6 @@ /usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 70%] Linking CXX executable ../../bin/relion_localsym_mpi -cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/localsym_mpi.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/localsym_mpi.dir/localsym_mpi.cpp.o -o ../../bin/relion_localsym_mpi ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-3.1.3/src/ctf.h:50, @@ -8360,7 +8378,17 @@ [ 70%] Linking CXX executable ../../bin/relion_import cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/import.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/import.dir/import.cpp.o -o ../../bin/relion_import ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -[ 70%] Linking CXX executable ../../bin/relion_motion_refine +make[4]: Leaving directory '/build/relion-3.1.3/build' +[ 70%] Built target import +/usr/bin/make -f src/apps/CMakeFiles/particle_FCC.dir/build.make src/apps/CMakeFiles/particle_FCC.dir/depend +make[4]: Entering directory '/build/relion-3.1.3/build' +cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/particle_FCC.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/relion-3.1.3/build' +/usr/bin/make -f src/apps/CMakeFiles/particle_FCC.dir/build.make src/apps/CMakeFiles/particle_FCC.dir/build +make[4]: Entering directory '/build/relion-3.1.3/build' +[ 71%] Building CXX object src/apps/CMakeFiles/particle_FCC.dir/particle_FCC.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/particle_FCC.dir/particle_FCC.cpp.o -MF CMakeFiles/particle_FCC.dir/particle_FCC.cpp.o.d -o CMakeFiles/particle_FCC.dir/particle_FCC.cpp.o -c /build/relion-3.1.3/src/apps/particle_FCC.cpp +[ 71%] Linking CXX executable ../../bin/relion_motion_refine cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/motion_refine.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/motion_refine.dir/motion_refine.cpp.o -o ../../bin/relion_motion_refine ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In file included from /build/relion-3.1.3/src/image.h:455, @@ -8423,16 +8451,6 @@ 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 70%] Built target import -/usr/bin/make -f src/apps/CMakeFiles/particle_FCC.dir/build.make src/apps/CMakeFiles/particle_FCC.dir/depend -make[4]: Entering directory '/build/relion-3.1.3/build' -cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/particle_FCC.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/particle_FCC.dir/build.make src/apps/CMakeFiles/particle_FCC.dir/build -make[4]: Entering directory '/build/relion-3.1.3/build' -[ 71%] Building CXX object src/apps/CMakeFiles/particle_FCC.dir/particle_FCC.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/particle_FCC.dir/particle_FCC.cpp.o -MF CMakeFiles/particle_FCC.dir/particle_FCC.cpp.o.d -o CMakeFiles/particle_FCC.dir/particle_FCC.cpp.o -c /build/relion-3.1.3/src/apps/particle_FCC.cpp -make[4]: Leaving directory '/build/relion-3.1.3/build' [ 71%] Built target motion_refine /usr/bin/make -f src/apps/CMakeFiles/particle_reposition.dir/build.make src/apps/CMakeFiles/particle_reposition.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' @@ -8442,6 +8460,8 @@ make[4]: Entering directory '/build/relion-3.1.3/build' [ 72%] Building CXX object src/apps/CMakeFiles/particle_reposition.dir/particle_reposition.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/particle_reposition.dir/particle_reposition.cpp.o -MF CMakeFiles/particle_reposition.dir/particle_reposition.cpp.o.d -o CMakeFiles/particle_reposition.dir/particle_reposition.cpp.o -c /build/relion-3.1.3/src/apps/particle_reposition.cpp +[ 73%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/gui_entries.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_gui_lib.dir/__/gui_entries.cpp.o -MF CMakeFiles/relion_gui_lib.dir/__/gui_entries.cpp.o.d -o CMakeFiles/relion_gui_lib.dir/__/gui_entries.cpp.o -c /build/relion-3.1.3/src/gui_entries.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/apps/particle_FCC.cpp:7: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': @@ -8501,8 +8521,6 @@ /usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 73%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/gui_entries.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_gui_lib.dir/__/gui_entries.cpp.o -MF CMakeFiles/relion_gui_lib.dir/__/gui_entries.cpp.o.d -o CMakeFiles/relion_gui_lib.dir/__/gui_entries.cpp.o -c /build/relion-3.1.3/src/gui_entries.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/projector.h:25, from /build/relion-3.1.3/src/ml_model.h:23, @@ -8565,14 +8583,14 @@ /usr/include/aarch64-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_mask_create +cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/mask_create.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/mask_create.dir/mask_create.cpp.o -o ../../bin/relion_mask_create ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 74%] Linking CXX executable ../../bin/relion_motion_refine_mpi cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/motion_refine_mpi.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/motion_refine_mpi.dir/motion_refine_mpi.cpp.o -o ../../bin/relion_motion_refine_mpi ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -[ 74%] Linking CXX executable ../../bin/relion_mask_create -cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/mask_create.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/mask_create.dir/mask_create.cpp.o -o ../../bin/relion_mask_create ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 74%] Built target motion_refine_mpi +[ 74%] Built target mask_create /usr/bin/make -f src/apps/CMakeFiles/particle_select.dir/build.make src/apps/CMakeFiles/particle_select.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/particle_select.dir/DependInfo.cmake --color= @@ -8581,44 +8599,44 @@ make[4]: Entering directory '/build/relion-3.1.3/build' [ 74%] Building CXX object src/apps/CMakeFiles/particle_select.dir/particle_select.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/particle_select.dir/particle_select.cpp.o -MF CMakeFiles/particle_select.dir/particle_select.cpp.o.d -o CMakeFiles/particle_select.dir/particle_select.cpp.o -c /build/relion-3.1.3/src/apps/particle_select.cpp -[ 74%] Linking CXX executable ../../bin/relion_mrc2vtk -cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/mrc2vtk.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/mrc2vtk.dir/mrc2vtk.cpp.o -o ../../bin/relion_mrc2vtk ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 74%] Built target mask_create +[ 74%] Built target motion_refine_mpi /usr/bin/make -f src/apps/CMakeFiles/particle_subtract.dir/build.make src/apps/CMakeFiles/particle_subtract.dir/depend +[ 74%] Linking CXX executable ../../bin/relion_particle_FCC +cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/particle_FCC.dir/link.txt --verbose=1 make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/particle_subtract.dir/DependInfo.cmake --color= +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/particle_FCC.dir/particle_FCC.cpp.o -o ../../bin/relion_particle_FCC ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' /usr/bin/make -f src/apps/CMakeFiles/particle_subtract.dir/build.make src/apps/CMakeFiles/particle_subtract.dir/build make[4]: Entering directory '/build/relion-3.1.3/build' [ 74%] Building CXX object src/apps/CMakeFiles/particle_subtract.dir/particle_subtract.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/particle_subtract.dir/particle_subtract.cpp.o -MF CMakeFiles/particle_subtract.dir/particle_subtract.cpp.o.d -o CMakeFiles/particle_subtract.dir/particle_subtract.cpp.o -c /build/relion-3.1.3/src/apps/particle_subtract.cpp -[ 74%] Linking CXX executable ../../bin/relion_particle_FCC -cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/particle_FCC.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/particle_FCC.dir/particle_FCC.cpp.o -o ../../bin/relion_particle_FCC ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +[ 74%] Linking CXX executable ../../bin/relion_mrc2vtk +cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/mrc2vtk.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/mrc2vtk.dir/mrc2vtk.cpp.o -o ../../bin/relion_mrc2vtk ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +[ 74%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/gui_jobwindow.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_gui_lib.dir/__/gui_jobwindow.cpp.o -MF CMakeFiles/relion_gui_lib.dir/__/gui_jobwindow.cpp.o.d -o CMakeFiles/relion_gui_lib.dir/__/gui_jobwindow.cpp.o -c /build/relion-3.1.3/src/gui_jobwindow.cpp +make[4]: Leaving directory '/build/relion-3.1.3/build' make[4]: Leaving directory '/build/relion-3.1.3/build' [ 74%] Built target mrc2vtk /usr/bin/make -f src/apps/CMakeFiles/particle_subtract_mpi.dir/build.make src/apps/CMakeFiles/particle_subtract_mpi.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/particle_subtract_mpi.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/particle_subtract_mpi.dir/build.make src/apps/CMakeFiles/particle_subtract_mpi.dir/build -make[4]: Entering directory '/build/relion-3.1.3/build' -[ 74%] Building CXX object src/apps/CMakeFiles/particle_subtract_mpi.dir/particle_subtract_mpi.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/particle_subtract_mpi.dir/particle_subtract_mpi.cpp.o -MF CMakeFiles/particle_subtract_mpi.dir/particle_subtract_mpi.cpp.o.d -o CMakeFiles/particle_subtract_mpi.dir/particle_subtract_mpi.cpp.o -c /build/relion-3.1.3/src/apps/particle_subtract_mpi.cpp -make[4]: Leaving directory '/build/relion-3.1.3/build' [ 74%] Built target particle_FCC /usr/bin/make -f src/apps/CMakeFiles/particle_symmetry_expand.dir/build.make src/apps/CMakeFiles/particle_symmetry_expand.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/particle_symmetry_expand.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.3/build' +/usr/bin/make -f src/apps/CMakeFiles/particle_subtract_mpi.dir/build.make src/apps/CMakeFiles/particle_subtract_mpi.dir/build +make[4]: Entering directory '/build/relion-3.1.3/build' +make[4]: Leaving directory '/build/relion-3.1.3/build' /usr/bin/make -f src/apps/CMakeFiles/particle_symmetry_expand.dir/build.make src/apps/CMakeFiles/particle_symmetry_expand.dir/build make[4]: Entering directory '/build/relion-3.1.3/build' +[ 74%] Building CXX object src/apps/CMakeFiles/particle_subtract_mpi.dir/particle_subtract_mpi.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/particle_subtract_mpi.dir/particle_subtract_mpi.cpp.o -MF CMakeFiles/particle_subtract_mpi.dir/particle_subtract_mpi.cpp.o.d -o CMakeFiles/particle_subtract_mpi.dir/particle_subtract_mpi.cpp.o -c /build/relion-3.1.3/src/apps/particle_subtract_mpi.cpp [ 75%] Building CXX object src/apps/CMakeFiles/particle_symmetry_expand.dir/particle_symmetry_expand.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/particle_symmetry_expand.dir/particle_symmetry_expand.cpp.o -MF CMakeFiles/particle_symmetry_expand.dir/particle_symmetry_expand.cpp.o.d -o CMakeFiles/particle_symmetry_expand.dir/particle_symmetry_expand.cpp.o -c /build/relion-3.1.3/src/apps/particle_symmetry_expand.cpp -[ 75%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/gui_jobwindow.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_gui_lib.dir/__/gui_jobwindow.cpp.o -MF CMakeFiles/relion_gui_lib.dir/__/gui_jobwindow.cpp.o.d -o CMakeFiles/relion_gui_lib.dir/__/gui_jobwindow.cpp.o -c /build/relion-3.1.3/src/gui_jobwindow.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-3.1.3/src/ctf.h:50, @@ -8893,6 +8911,22 @@ make[4]: Entering directory '/build/relion-3.1.3/build' [ 76%] Building CXX object src/apps/CMakeFiles/plot_delocalisation.dir/plot_delocalisation.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/plot_delocalisation.dir/plot_delocalisation.cpp.o -MF CMakeFiles/plot_delocalisation.dir/plot_delocalisation.cpp.o.d -o CMakeFiles/plot_delocalisation.dir/plot_delocalisation.cpp.o -c /build/relion-3.1.3/src/apps/plot_delocalisation.cpp +[ 76%] Linking CXX executable ../../bin/relion_helix_toolbox +cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/helix_toolbox.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/helix_toolbox.dir/helix_toolbox.cpp.o -o ../../bin/relion_helix_toolbox ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +[ 77%] Linking CXX executable ../../bin/relion_particle_subtract +cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/particle_subtract.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/particle_subtract.dir/particle_subtract.cpp.o -o ../../bin/relion_particle_subtract ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +make[4]: Leaving directory '/build/relion-3.1.3/build' +[ 77%] Built target helix_toolbox +/usr/bin/make -f src/apps/CMakeFiles/postprocess.dir/build.make src/apps/CMakeFiles/postprocess.dir/depend +make[4]: Entering directory '/build/relion-3.1.3/build' +cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/postprocess.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/relion-3.1.3/build' +/usr/bin/make -f src/apps/CMakeFiles/postprocess.dir/build.make src/apps/CMakeFiles/postprocess.dir/build +make[4]: Entering directory '/build/relion-3.1.3/build' +[ 77%] Building CXX object src/apps/CMakeFiles/postprocess.dir/postprocess.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/postprocess.dir/postprocess.cpp.o -MF CMakeFiles/postprocess.dir/postprocess.cpp.o.d -o CMakeFiles/postprocess.dir/postprocess.cpp.o -c /build/relion-3.1.3/src/apps/postprocess.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/apps/plot_delocalisation.cpp:7: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': @@ -8952,22 +8986,6 @@ /usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 77%] Linking CXX executable ../../bin/relion_particle_subtract -cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/particle_subtract.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/particle_subtract.dir/particle_subtract.cpp.o -o ../../bin/relion_particle_subtract ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -[ 77%] Linking CXX executable ../../bin/relion_helix_toolbox -cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/helix_toolbox.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/helix_toolbox.dir/helix_toolbox.cpp.o -o ../../bin/relion_helix_toolbox ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 77%] Built target helix_toolbox -/usr/bin/make -f src/apps/CMakeFiles/postprocess.dir/build.make src/apps/CMakeFiles/postprocess.dir/depend -make[4]: Entering directory '/build/relion-3.1.3/build' -cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/postprocess.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/postprocess.dir/build.make src/apps/CMakeFiles/postprocess.dir/build -make[4]: Entering directory '/build/relion-3.1.3/build' -[ 77%] Building CXX object src/apps/CMakeFiles/postprocess.dir/postprocess.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/postprocess.dir/postprocess.cpp.o -MF CMakeFiles/postprocess.dir/postprocess.cpp.o.d -o CMakeFiles/postprocess.dir/postprocess.cpp.o -c /build/relion-3.1.3/src/apps/postprocess.cpp make[4]: Leaving directory '/build/relion-3.1.3/build' [ 77%] Built target particle_subtract /usr/bin/make -f src/apps/CMakeFiles/postprocess_mpi.dir/build.make src/apps/CMakeFiles/postprocess_mpi.dir/depend @@ -8978,22 +8996,6 @@ make[4]: Entering directory '/build/relion-3.1.3/build' [ 78%] Building CXX object src/apps/CMakeFiles/postprocess_mpi.dir/postprocess_mpi.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/postprocess_mpi.dir/postprocess_mpi.cpp.o -MF CMakeFiles/postprocess_mpi.dir/postprocess_mpi.cpp.o.d -o CMakeFiles/postprocess_mpi.dir/postprocess_mpi.cpp.o -c /build/relion-3.1.3/src/apps/postprocess_mpi.cpp -[ 79%] Linking CXX executable ../../bin/relion_pipeliner -cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/pipeliner.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/pipeliner.dir/pipeliner.cpp.o -o ../../bin/relion_pipeliner ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 79%] Built target pipeliner -/usr/bin/make -f src/apps/CMakeFiles/prepare_subtomo.dir/build.make src/apps/CMakeFiles/prepare_subtomo.dir/depend -make[4]: Entering directory '/build/relion-3.1.3/build' -cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/prepare_subtomo.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/prepare_subtomo.dir/build.make src/apps/CMakeFiles/prepare_subtomo.dir/build -make[4]: Entering directory '/build/relion-3.1.3/build' -[ 79%] Building CXX object src/apps/CMakeFiles/prepare_subtomo.dir/prepare_subtomo.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/prepare_subtomo.dir/prepare_subtomo.cpp.o -MF CMakeFiles/prepare_subtomo.dir/prepare_subtomo.cpp.o.d -o CMakeFiles/prepare_subtomo.dir/prepare_subtomo.cpp.o -c /build/relion-3.1.3/src/apps/prepare_subtomo.cpp -[ 79%] Linking CXX executable ../../bin/relion_particle_subtract_mpi -cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/particle_subtract_mpi.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/particle_subtract_mpi.dir/particle_subtract_mpi.cpp.o -o ../../bin/relion_particle_subtract_mpi ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/postprocessing.h:24, from /build/relion-3.1.3/src/apps/postprocess.cpp:20: @@ -9054,6 +9056,9 @@ /usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +[ 79%] Linking CXX executable ../../bin/relion_pipeliner +cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/pipeliner.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/pipeliner.dir/pipeliner.cpp.o -o ../../bin/relion_pipeliner ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/postprocessing.h:24, from /build/relion-3.1.3/src/apps/postprocess_mpi.cpp:20: @@ -9114,11 +9119,24 @@ /usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +make[4]: Leaving directory '/build/relion-3.1.3/build' +[ 79%] Built target pipeliner +/usr/bin/make -f src/apps/CMakeFiles/prepare_subtomo.dir/build.make src/apps/CMakeFiles/prepare_subtomo.dir/depend +make[4]: Entering directory '/build/relion-3.1.3/build' +cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/prepare_subtomo.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/relion-3.1.3/build' +/usr/bin/make -f src/apps/CMakeFiles/prepare_subtomo.dir/build.make src/apps/CMakeFiles/prepare_subtomo.dir/build +make[4]: Entering directory '/build/relion-3.1.3/build' +[ 79%] Building CXX object src/apps/CMakeFiles/prepare_subtomo.dir/prepare_subtomo.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/prepare_subtomo.dir/prepare_subtomo.cpp.o -MF CMakeFiles/prepare_subtomo.dir/prepare_subtomo.cpp.o.d -o CMakeFiles/prepare_subtomo.dir/prepare_subtomo.cpp.o -c /build/relion-3.1.3/src/apps/prepare_subtomo.cpp +[ 79%] Linking CXX executable ../../bin/relion_particle_subtract_mpi +cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/particle_subtract_mpi.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/particle_subtract_mpi.dir/particle_subtract_mpi.cpp.o -o ../../bin/relion_particle_subtract_mpi ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 80%] Linking CXX executable ../../bin/relion_image_handler cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/image_handler.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/image_handler.dir/image_handler.cpp.o -o ../../bin/relion_image_handler ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 80%] Built target particle_subtract_mpi +[ 80%] Built target image_handler /usr/bin/make -f src/apps/CMakeFiles/preprocess.dir/build.make src/apps/CMakeFiles/preprocess.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/preprocess.dir/DependInfo.cmake --color= @@ -9127,19 +9145,6 @@ make[4]: Entering directory '/build/relion-3.1.3/build' [ 80%] Building CXX object src/apps/CMakeFiles/preprocess.dir/preprocess.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/preprocess.dir/preprocess.cpp.o -MF CMakeFiles/preprocess.dir/preprocess.cpp.o.d -o CMakeFiles/preprocess.dir/preprocess.cpp.o -c /build/relion-3.1.3/src/apps/preprocess.cpp -make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 80%] Built target image_handler -/usr/bin/make -f src/apps/CMakeFiles/preprocess_mpi.dir/build.make src/apps/CMakeFiles/preprocess_mpi.dir/depend -make[4]: Entering directory '/build/relion-3.1.3/build' -cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/preprocess_mpi.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/preprocess_mpi.dir/build.make src/apps/CMakeFiles/preprocess_mpi.dir/build -make[4]: Entering directory '/build/relion-3.1.3/build' -[ 80%] Building CXX object src/apps/CMakeFiles/preprocess_mpi.dir/preprocess_mpi.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/preprocess_mpi.dir/preprocess_mpi.cpp.o -MF CMakeFiles/preprocess_mpi.dir/preprocess_mpi.cpp.o.d -o CMakeFiles/preprocess_mpi.dir/preprocess_mpi.cpp.o -c /build/relion-3.1.3/src/apps/preprocess_mpi.cpp -[ 81%] Linking CXX executable ../../bin/relion_plot_delocalisation -cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/plot_delocalisation.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/plot_delocalisation.dir/plot_delocalisation.cpp.o -o ../../bin/relion_plot_delocalisation ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/helix.h:30, from /build/relion-3.1.3/src/apps/prepare_subtomo.cpp:22: @@ -9201,7 +9206,23 @@ 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 81%] Built target plot_delocalisation +[ 80%] Built target particle_subtract_mpi +/usr/bin/make -f src/apps/CMakeFiles/preprocess_mpi.dir/build.make src/apps/CMakeFiles/preprocess_mpi.dir/depend +make[4]: Entering directory '/build/relion-3.1.3/build' +cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/preprocess_mpi.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/relion-3.1.3/build' +/usr/bin/make -f src/apps/CMakeFiles/preprocess_mpi.dir/build.make src/apps/CMakeFiles/preprocess_mpi.dir/build +make[4]: Entering directory '/build/relion-3.1.3/build' +[ 81%] Linking CXX executable ../../bin/relion_plot_delocalisation +[ 81%] Building CXX object src/apps/CMakeFiles/preprocess_mpi.dir/preprocess_mpi.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/preprocess_mpi.dir/preprocess_mpi.cpp.o -MF CMakeFiles/preprocess_mpi.dir/preprocess_mpi.cpp.o.d -o CMakeFiles/preprocess_mpi.dir/preprocess_mpi.cpp.o -c /build/relion-3.1.3/src/apps/preprocess_mpi.cpp +cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/plot_delocalisation.dir/link.txt --verbose=1 +[ 81%] Linking CXX executable ../../bin/relion_postprocess +cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/postprocess.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/plot_delocalisation.dir/plot_delocalisation.cpp.o -o ../../bin/relion_plot_delocalisation ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/postprocess.dir/postprocess.cpp.o -o ../../bin/relion_postprocess ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +make[4]: Leaving directory '/build/relion-3.1.3/build' +[ 81%] Built target postprocess /usr/bin/make -f src/apps/CMakeFiles/project.dir/build.make src/apps/CMakeFiles/project.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/project.dir/DependInfo.cmake --color= @@ -9210,6 +9231,22 @@ make[4]: Entering directory '/build/relion-3.1.3/build' [ 82%] Building CXX object src/apps/CMakeFiles/project.dir/project.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/project.dir/project.cpp.o -MF CMakeFiles/project.dir/project.cpp.o.d -o CMakeFiles/project.dir/project.cpp.o -c /build/relion-3.1.3/src/apps/project.cpp +make[4]: Leaving directory '/build/relion-3.1.3/build' +[ 82%] Built target plot_delocalisation +/usr/bin/make -f src/apps/CMakeFiles/reconstruct.dir/build.make src/apps/CMakeFiles/reconstruct.dir/depend +make[4]: Entering directory '/build/relion-3.1.3/build' +cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/reconstruct.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/relion-3.1.3/build' +/usr/bin/make -f src/apps/CMakeFiles/reconstruct.dir/build.make src/apps/CMakeFiles/reconstruct.dir/build +make[4]: Entering directory '/build/relion-3.1.3/build' +[ 82%] Building CXX object src/apps/CMakeFiles/reconstruct.dir/reconstruct.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/reconstruct.dir/reconstruct.cpp.o -MF CMakeFiles/reconstruct.dir/reconstruct.cpp.o.d -o CMakeFiles/reconstruct.dir/reconstruct.cpp.o -c /build/relion-3.1.3/src/apps/reconstruct.cpp +[ 82%] Linking CXX executable ../../bin/relion_postprocess_mpi +cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/postprocess_mpi.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/postprocess_mpi.dir/postprocess_mpi.cpp.o -o ../../bin/relion_postprocess_mpi ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +[ 82%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/gui_mainwindow.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_gui_lib.dir/__/gui_mainwindow.cpp.o -MF CMakeFiles/relion_gui_lib.dir/__/gui_mainwindow.cpp.o.d -o CMakeFiles/relion_gui_lib.dir/__/gui_mainwindow.cpp.o -c /build/relion-3.1.3/src/gui_mainwindow.cpp +make[4]: Leaving directory '/build/relion-3.1.3/build' In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/preprocessing.h:29, from /build/relion-3.1.3/src/apps/preprocess.cpp:20: @@ -9270,6 +9307,15 @@ /usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +[ 82%] Built target postprocess_mpi +/usr/bin/make -f src/apps/CMakeFiles/reconstruct_mpi.dir/build.make src/apps/CMakeFiles/reconstruct_mpi.dir/depend +make[4]: Entering directory '/build/relion-3.1.3/build' +cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/reconstruct_mpi.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/relion-3.1.3/build' +/usr/bin/make -f src/apps/CMakeFiles/reconstruct_mpi.dir/build.make src/apps/CMakeFiles/reconstruct_mpi.dir/build +make[4]: Entering directory '/build/relion-3.1.3/build' +[ 82%] Building CXX object src/apps/CMakeFiles/reconstruct_mpi.dir/reconstruct_mpi.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/reconstruct_mpi.dir/reconstruct_mpi.cpp.o -MF CMakeFiles/reconstruct_mpi.dir/reconstruct_mpi.cpp.o.d -o CMakeFiles/reconstruct_mpi.dir/reconstruct_mpi.cpp.o -c /build/relion-3.1.3/src/apps/reconstruct_mpi.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/preprocessing.h:29, from /build/relion-3.1.3/src/preprocessing_mpi.h:24, @@ -9331,32 +9377,6 @@ /usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 82%] Linking CXX executable ../../bin/relion_postprocess -cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/postprocess.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/postprocess.dir/postprocess.cpp.o -o ../../bin/relion_postprocess ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -[ 82%] Linking CXX executable ../../bin/relion_postprocess_mpi -cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/postprocess_mpi.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/postprocess_mpi.dir/postprocess_mpi.cpp.o -o ../../bin/relion_postprocess_mpi ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 82%] Built target postprocess -/usr/bin/make -f src/apps/CMakeFiles/reconstruct.dir/build.make src/apps/CMakeFiles/reconstruct.dir/depend -make[4]: Entering directory '/build/relion-3.1.3/build' -cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/reconstruct.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/reconstruct.dir/build.make src/apps/CMakeFiles/reconstruct.dir/build -make[4]: Entering directory '/build/relion-3.1.3/build' -[ 82%] Building CXX object src/apps/CMakeFiles/reconstruct.dir/reconstruct.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/reconstruct.dir/reconstruct.cpp.o -MF CMakeFiles/reconstruct.dir/reconstruct.cpp.o.d -o CMakeFiles/reconstruct.dir/reconstruct.cpp.o -c /build/relion-3.1.3/src/apps/reconstruct.cpp -make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 82%] Built target postprocess_mpi -/usr/bin/make -f src/apps/CMakeFiles/reconstruct_mpi.dir/build.make src/apps/CMakeFiles/reconstruct_mpi.dir/depend -make[4]: Entering directory '/build/relion-3.1.3/build' -cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/reconstruct_mpi.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/reconstruct_mpi.dir/build.make src/apps/CMakeFiles/reconstruct_mpi.dir/build -make[4]: Entering directory '/build/relion-3.1.3/build' -[ 82%] Building CXX object src/apps/CMakeFiles/reconstruct_mpi.dir/reconstruct_mpi.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/reconstruct_mpi.dir/reconstruct_mpi.cpp.o -MF CMakeFiles/reconstruct_mpi.dir/reconstruct_mpi.cpp.o.d -o CMakeFiles/reconstruct_mpi.dir/reconstruct_mpi.cpp.o -c /build/relion-3.1.3/src/apps/reconstruct_mpi.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/projector.h:25, from /build/relion-3.1.3/src/apps/project.cpp:21: @@ -9417,21 +9437,6 @@ /usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 82%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/gui_mainwindow.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_gui_lib.dir/__/gui_mainwindow.cpp.o -MF CMakeFiles/relion_gui_lib.dir/__/gui_mainwindow.cpp.o.d -o CMakeFiles/relion_gui_lib.dir/__/gui_mainwindow.cpp.o -c /build/relion-3.1.3/src/gui_mainwindow.cpp -[ 83%] Linking CXX executable ../../bin/relion_preprocess -cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/preprocess.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/preprocess.dir/preprocess.cpp.o -o ../../bin/relion_preprocess ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 83%] Built target preprocess -/usr/bin/make -f src/apps/CMakeFiles/refine.dir/build.make src/apps/CMakeFiles/refine.dir/depend -make[4]: Entering directory '/build/relion-3.1.3/build' -cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/refine.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/refine.dir/build.make src/apps/CMakeFiles/refine.dir/build -make[4]: Entering directory '/build/relion-3.1.3/build' -[ 83%] Building CXX object src/apps/CMakeFiles/refine.dir/refine.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/refine.dir/refine.cpp.o -MF CMakeFiles/refine.dir/refine.cpp.o.d -o CMakeFiles/refine.dir/refine.cpp.o -c /build/relion-3.1.3/src/apps/refine.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/projector.h:25, from /build/relion-3.1.3/src/backprojector.h:33, @@ -9494,12 +9499,14 @@ /usr/include/aarch64-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_preprocess +cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/preprocess.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/preprocess.dir/preprocess.cpp.o -o ../../bin/relion_preprocess ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In file included from /build/relion-3.1.3/src/image.h:455, - from /build/relion-3.1.3/src/projector.h:25, - from /build/relion-3.1.3/src/backprojector.h:33, - from /build/relion-3.1.3/src/reconstructor.h:23, - from /build/relion-3.1.3/src/reconstructor_mpi.h:25, - from /build/relion-3.1.3/src/apps/reconstruct_mpi.cpp:21: + from /build/relion-3.1.3/src/jaz/obs_model.h:24, + from /build/relion-3.1.3/src/scheduler.h:26, + from /build/relion-3.1.3/src/gui_mainwindow.h:28, + from /build/relion-3.1.3/src/gui_mainwindow.cpp:22: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -9558,10 +9565,11 @@ 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-3.1.3/src/image.h:455, - from /build/relion-3.1.3/src/jaz/obs_model.h:24, - from /build/relion-3.1.3/src/scheduler.h:26, - from /build/relion-3.1.3/src/gui_mainwindow.h:28, - from /build/relion-3.1.3/src/gui_mainwindow.cpp:22: + from /build/relion-3.1.3/src/projector.h:25, + from /build/relion-3.1.3/src/backprojector.h:33, + from /build/relion-3.1.3/src/reconstructor.h:23, + from /build/relion-3.1.3/src/reconstructor_mpi.h:25, + from /build/relion-3.1.3/src/apps/reconstruct_mpi.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file @@ -9619,12 +9627,42 @@ /usr/include/aarch64-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_preprocess_mpi -cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/preprocess_mpi.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/preprocess_mpi.dir/preprocess_mpi.cpp.o -o ../../bin/relion_preprocess_mpi ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +make[4]: Leaving directory '/build/relion-3.1.3/build' +[ 83%] Built target preprocess +/usr/bin/make -f src/apps/CMakeFiles/refine.dir/build.make src/apps/CMakeFiles/refine.dir/depend +make[4]: Entering directory '/build/relion-3.1.3/build' +cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/refine.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/relion-3.1.3/build' +/usr/bin/make -f src/apps/CMakeFiles/refine.dir/build.make src/apps/CMakeFiles/refine.dir/build +make[4]: Entering directory '/build/relion-3.1.3/build' +[ 83%] Building CXX object src/apps/CMakeFiles/refine.dir/refine.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/refine.dir/refine.cpp.o -MF CMakeFiles/refine.dir/refine.cpp.o.d -o CMakeFiles/refine.dir/refine.cpp.o -c /build/relion-3.1.3/src/apps/refine.cpp [ 83%] Linking CXX executable ../../bin/relion_particle_reposition cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/particle_reposition.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/particle_reposition.dir/particle_reposition.cpp.o -o ../../bin/relion_particle_reposition ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +[ 83%] Linking CXX executable ../../bin/relion_preprocess_mpi +cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/preprocess_mpi.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/preprocess_mpi.dir/preprocess_mpi.cpp.o -o ../../bin/relion_preprocess_mpi ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +make[4]: Leaving directory '/build/relion-3.1.3/build' +[ 83%] Built target preprocess_mpi +/usr/bin/make -f src/apps/CMakeFiles/refine_mpi.dir/build.make src/apps/CMakeFiles/refine_mpi.dir/depend +make[4]: Entering directory '/build/relion-3.1.3/build' +cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/refine_mpi.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/relion-3.1.3/build' +/usr/bin/make -f src/apps/CMakeFiles/refine_mpi.dir/build.make src/apps/CMakeFiles/refine_mpi.dir/build +make[4]: Entering directory '/build/relion-3.1.3/build' +[ 84%] Building CXX object src/apps/CMakeFiles/refine_mpi.dir/refine_mpi.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/refine_mpi.dir/refine_mpi.cpp.o -MF CMakeFiles/refine_mpi.dir/refine_mpi.cpp.o.d -o CMakeFiles/refine_mpi.dir/refine_mpi.cpp.o -c /build/relion-3.1.3/src/apps/refine_mpi.cpp +make[4]: Leaving directory '/build/relion-3.1.3/build' +[ 84%] Built target particle_reposition +/usr/bin/make -f src/apps/CMakeFiles/reposition.dir/build.make src/apps/CMakeFiles/reposition.dir/depend +make[4]: Entering directory '/build/relion-3.1.3/build' +cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/reposition.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/relion-3.1.3/build' +/usr/bin/make -f src/apps/CMakeFiles/reposition.dir/build.make src/apps/CMakeFiles/reposition.dir/build +make[4]: Entering directory '/build/relion-3.1.3/build' +[ 84%] Building CXX object src/apps/CMakeFiles/reposition.dir/reposition.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/reposition.dir/reposition.cpp.o -MF CMakeFiles/reposition.dir/reposition.cpp.o.d -o CMakeFiles/reposition.dir/reposition.cpp.o -c /build/relion-3.1.3/src/apps/reposition.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/projector.h:25, from /build/relion-3.1.3/src/ml_model.h:23, @@ -9687,26 +9725,19 @@ /usr/include/aarch64-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_reconstruct +cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/reconstruct.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/reconstruct.dir/reconstruct.cpp.o -o ../../bin/relion_reconstruct ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 83%] Built target preprocess_mpi -/usr/bin/make -f src/apps/CMakeFiles/refine_mpi.dir/build.make src/apps/CMakeFiles/refine_mpi.dir/depend -make[4]: Entering directory '/build/relion-3.1.3/build' -cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/refine_mpi.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/refine_mpi.dir/build.make src/apps/CMakeFiles/refine_mpi.dir/build -make[4]: Entering directory '/build/relion-3.1.3/build' -[ 84%] Building CXX object src/apps/CMakeFiles/refine_mpi.dir/refine_mpi.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/refine_mpi.dir/refine_mpi.cpp.o -MF CMakeFiles/refine_mpi.dir/refine_mpi.cpp.o.d -o CMakeFiles/refine_mpi.dir/refine_mpi.cpp.o -c /build/relion-3.1.3/src/apps/refine_mpi.cpp -make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 84%] Built target particle_reposition -/usr/bin/make -f src/apps/CMakeFiles/reposition.dir/build.make src/apps/CMakeFiles/reposition.dir/depend +[ 85%] Built target reconstruct +/usr/bin/make -f src/apps/CMakeFiles/run_ctffind.dir/build.make src/apps/CMakeFiles/run_ctffind.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' -cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/reposition.dir/DependInfo.cmake --color= +cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/run_ctffind.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/reposition.dir/build.make src/apps/CMakeFiles/reposition.dir/build +/usr/bin/make -f src/apps/CMakeFiles/run_ctffind.dir/build.make src/apps/CMakeFiles/run_ctffind.dir/build make[4]: Entering directory '/build/relion-3.1.3/build' -[ 84%] Building CXX object src/apps/CMakeFiles/reposition.dir/reposition.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/reposition.dir/reposition.cpp.o -MF CMakeFiles/reposition.dir/reposition.cpp.o.d -o CMakeFiles/reposition.dir/reposition.cpp.o -c /build/relion-3.1.3/src/apps/reposition.cpp +[ 85%] Building CXX object src/apps/CMakeFiles/run_ctffind.dir/run_ctffind.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/run_ctffind.dir/run_ctffind.cpp.o -MF CMakeFiles/run_ctffind.dir/run_ctffind.cpp.o.d -o CMakeFiles/run_ctffind.dir/run_ctffind.cpp.o -c /build/relion-3.1.3/src/apps/run_ctffind.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/projector.h:25, from /build/relion-3.1.3/src/ml_model.h:23, @@ -9830,19 +9861,6 @@ /usr/include/aarch64-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_reconstruct -cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/reconstruct.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/reconstruct.dir/reconstruct.cpp.o -o ../../bin/relion_reconstruct ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 85%] Built target reconstruct -/usr/bin/make -f src/apps/CMakeFiles/run_ctffind.dir/build.make src/apps/CMakeFiles/run_ctffind.dir/depend -make[4]: Entering directory '/build/relion-3.1.3/build' -cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/run_ctffind.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/run_ctffind.dir/build.make src/apps/CMakeFiles/run_ctffind.dir/build -make[4]: Entering directory '/build/relion-3.1.3/build' -[ 85%] Building CXX object src/apps/CMakeFiles/run_ctffind.dir/run_ctffind.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/run_ctffind.dir/run_ctffind.cpp.o -MF CMakeFiles/run_ctffind.dir/run_ctffind.cpp.o.d -o CMakeFiles/run_ctffind.dir/run_ctffind.cpp.o -c /build/relion-3.1.3/src/apps/run_ctffind.cpp [ 86%] Linking CXX executable ../../bin/relion_reconstruct_mpi cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/reconstruct_mpi.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/reconstruct_mpi.dir/reconstruct_mpi.cpp.o -o ../../bin/relion_reconstruct_mpi ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff @@ -9916,22 +9934,14 @@ make[4]: Entering directory '/build/relion-3.1.3/build' [ 87%] Building CXX object src/apps/CMakeFiles/run_ctffind_mpi.dir/run_ctffind_mpi.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/run_ctffind_mpi.dir/run_ctffind_mpi.cpp.o -MF CMakeFiles/run_ctffind_mpi.dir/run_ctffind_mpi.cpp.o.d -o CMakeFiles/run_ctffind_mpi.dir/run_ctffind_mpi.cpp.o -c /build/relion-3.1.3/src/apps/run_ctffind_mpi.cpp -[ 87%] Linking CXX executable ../../bin/relion_refine -cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/refine.dir/link.txt --verbose=1 [ 87%] Linking CXX executable ../../bin/relion_run_ctffind cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/run_ctffind.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/refine.dir/refine.cpp.o -o ../../bin/relion_refine ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/run_ctffind.dir/run_ctffind.cpp.o -o ../../bin/relion_run_ctffind ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' [ 87%] Built target run_ctffind /usr/bin/make -f src/apps/CMakeFiles/run_motioncorr.dir/build.make src/apps/CMakeFiles/run_motioncorr.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/run_motioncorr.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/run_motioncorr.dir/build.make src/apps/CMakeFiles/run_motioncorr.dir/build -make[4]: Entering directory '/build/relion-3.1.3/build' -[ 88%] Building CXX object src/apps/CMakeFiles/run_motioncorr.dir/run_motioncorr.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/run_motioncorr.dir/run_motioncorr.cpp.o -MF CMakeFiles/run_motioncorr.dir/run_motioncorr.cpp.o.d -o CMakeFiles/run_motioncorr.dir/run_motioncorr.cpp.o -c /build/relion-3.1.3/src/apps/run_motioncorr.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/ctffind_runner.h:31, from /build/relion-3.1.3/src/ctffind_runner_mpi.h:25, @@ -9969,6 +9979,7 @@ /usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +make[4]: Leaving directory '/build/relion-3.1.3/build' /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ @@ -9981,6 +9992,7 @@ /usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ +/usr/bin/make -f src/apps/CMakeFiles/run_motioncorr.dir/build.make src/apps/CMakeFiles/run_motioncorr.dir/build /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ @@ -9993,6 +10005,12 @@ /usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +make[4]: Entering directory '/build/relion-3.1.3/build' +[ 88%] Building CXX object src/apps/CMakeFiles/run_motioncorr.dir/run_motioncorr.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/run_motioncorr.dir/run_motioncorr.cpp.o -MF CMakeFiles/run_motioncorr.dir/run_motioncorr.cpp.o.d -o CMakeFiles/run_motioncorr.dir/run_motioncorr.cpp.o -c /build/relion-3.1.3/src/apps/run_motioncorr.cpp +[ 88%] Linking CXX executable ../../bin/relion_refine +cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/refine.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/refine.dir/refine.cpp.o -o ../../bin/relion_refine ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' [ 88%] Built target refine /usr/bin/make -f src/apps/CMakeFiles/run_motioncorr_mpi.dir/build.make src/apps/CMakeFiles/run_motioncorr_mpi.dir/depend @@ -10065,7 +10083,13 @@ | ^~~~~~ [ 89%] Linking CXX executable ../../bin/relion_reposition cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/reposition.dir/link.txt --verbose=1 +[ 89%] Linking CXX executable ../../bin/relion_run_ctffind_mpi +cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/run_ctffind_mpi.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/reposition.dir/reposition.cpp.o -o ../../bin/relion_reposition ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/run_ctffind_mpi.dir/run_ctffind_mpi.cpp.o -o ../../bin/relion_run_ctffind_mpi ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff +[ 89%] Linking CXX executable ../../bin/relion_run_motioncorr +cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/run_motioncorr.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/run_motioncorr.dir/run_motioncorr.cpp.o -o ../../bin/relion_run_motioncorr ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/motioncorr_runner.h:32, from /build/relion-3.1.3/src/motioncorr_runner_mpi.h:25, @@ -10103,6 +10127,8 @@ /usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +[ 89%] Linking CXX executable ../../bin/relion_refine_mpi +cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/refine_mpi.dir/link.txt --verbose=1 /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ @@ -10127,8 +10153,9 @@ /usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/refine_mpi.dir/refine_mpi.cpp.o -o ../../bin/relion_refine_mpi ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 89%] Built target reposition +[ 89%] Built target run_ctffind_mpi /usr/bin/make -f src/apps/CMakeFiles/scheduler.dir/build.make src/apps/CMakeFiles/scheduler.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/scheduler.dir/DependInfo.cmake --color= @@ -10137,33 +10164,24 @@ make[4]: Entering directory '/build/relion-3.1.3/build' [ 89%] Building CXX object src/apps/CMakeFiles/scheduler.dir/scheduler.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/scheduler.dir/scheduler.cpp.o -MF CMakeFiles/scheduler.dir/scheduler.cpp.o.d -o CMakeFiles/scheduler.dir/scheduler.cpp.o -c /build/relion-3.1.3/src/apps/scheduler.cpp -[ 89%] Linking CXX executable ../../bin/relion_run_ctffind_mpi -cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/run_ctffind_mpi.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/run_ctffind_mpi.dir/run_ctffind_mpi.cpp.o -o ../../bin/relion_run_ctffind_mpi ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -[ 89%] Linking CXX executable ../../bin/relion_refine_mpi -cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/refine_mpi.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/refine_mpi.dir/refine_mpi.cpp.o -o ../../bin/relion_refine_mpi ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -[ 89%] Linking CXX executable ../../bin/relion_run_motioncorr -cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/run_motioncorr.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/run_motioncorr.dir/run_motioncorr.cpp.o -o ../../bin/relion_run_motioncorr ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 89%] Built target run_ctffind_mpi +make[4]: Leaving directory '/build/relion-3.1.3/build' +[ 89%] Built target run_motioncorr /usr/bin/make -f src/apps/CMakeFiles/stack_create.dir/build.make src/apps/CMakeFiles/stack_create.dir/depend +[ 89%] Built target reposition make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/stack_create.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/stack_create.dir/build.make src/apps/CMakeFiles/stack_create.dir/build -make[4]: Entering directory '/build/relion-3.1.3/build' -[ 90%] Building CXX object src/apps/CMakeFiles/stack_create.dir/stack_create.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/stack_create.dir/stack_create.cpp.o -MF CMakeFiles/stack_create.dir/stack_create.cpp.o.d -o CMakeFiles/stack_create.dir/stack_create.cpp.o -c /build/relion-3.1.3/src/apps/stack_create.cpp -make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 90%] Built target run_motioncorr /usr/bin/make -f src/apps/CMakeFiles/star_handler.dir/build.make src/apps/CMakeFiles/star_handler.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/star_handler.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.3/build' +/usr/bin/make -f src/apps/CMakeFiles/stack_create.dir/build.make src/apps/CMakeFiles/stack_create.dir/build +make[4]: Entering directory '/build/relion-3.1.3/build' +make[4]: Leaving directory '/build/relion-3.1.3/build' /usr/bin/make -f src/apps/CMakeFiles/star_handler.dir/build.make src/apps/CMakeFiles/star_handler.dir/build make[4]: Entering directory '/build/relion-3.1.3/build' +[ 90%] Building CXX object src/apps/CMakeFiles/stack_create.dir/stack_create.cpp.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/stack_create.dir/stack_create.cpp.o -MF CMakeFiles/stack_create.dir/stack_create.cpp.o.d -o CMakeFiles/stack_create.dir/stack_create.cpp.o -c /build/relion-3.1.3/src/apps/stack_create.cpp [ 91%] Building CXX object src/apps/CMakeFiles/star_handler.dir/star_handler.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/star_handler.dir/star_handler.cpp.o -MF CMakeFiles/star_handler.dir/star_handler.cpp.o.d -o CMakeFiles/star_handler.dir/star_handler.cpp.o -c /build/relion-3.1.3/src/apps/star_handler.cpp make[4]: Leaving directory '/build/relion-3.1.3/build' @@ -10296,9 +10314,6 @@ /usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 92%] Linking CXX executable ../../bin/relion_run_motioncorr_mpi -cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/run_motioncorr_mpi.dir/link.txt --verbose=1 -/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/run_motioncorr_mpi.dir/run_motioncorr_mpi.cpp.o -o ../../bin/relion_run_motioncorr_mpi ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/apps/star_handler.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': @@ -10358,6 +10373,9 @@ /usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +[ 92%] Linking CXX executable ../../bin/relion_run_motioncorr_mpi +cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/run_motioncorr_mpi.dir/link.txt --verbose=1 +/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/run_motioncorr_mpi.dir/run_motioncorr_mpi.cpp.o -o ../../bin/relion_run_motioncorr_mpi ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/apps/tiltpair_plot.cpp:25: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': @@ -10562,17 +10580,17 @@ /usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -[ 94%] Linking CXX executable ../../bin/relion_scheduler +[ 95%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/healpix_base.cc.o +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/healpix_base.cc.o -MF CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/healpix_base.cc.o.d -o CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/healpix_base.cc.o -c /build/relion-3.1.3/src/Healpix_2.15a/healpix_base.cc +[ 95%] Linking CXX executable ../../bin/relion_scheduler cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/scheduler.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/scheduler.dir/scheduler.cpp.o -o ../../bin/relion_scheduler ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff -[ 95%] Linking CXX executable ../../bin/relion_tomo_test +make[4]: Leaving directory '/build/relion-3.1.3/build' +[ 96%] Linking CXX executable ../../bin/relion_tomo_test cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/tomo_test.dir/link.txt --verbose=1 +[ 96%] Built target scheduler /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/tomo_test.dir/tomo_test.cpp.o -o ../../bin/relion_tomo_test ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 95%] Built target scheduler -[ 96%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/healpix_base.cc.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/healpix_base.cc.o -MF CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/healpix_base.cc.o.d -o CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/healpix_base.cc.o -c /build/relion-3.1.3/src/Healpix_2.15a/healpix_base.cc -make[4]: Leaving directory '/build/relion-3.1.3/build' [ 96%] Built target tomo_test [ 96%] Linking CXX executable ../../bin/relion_stack_create cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/stack_create.dir/link.txt --verbose=1 @@ -10593,28 +10611,34 @@ [ 97%] 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/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/display.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/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/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/manualpick.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/display.dir/build.make src/apps/CMakeFiles/display.dir/build -make[4]: Entering directory '/build/relion-3.1.3/build' make[4]: Leaving directory '/build/relion-3.1.3/build' -/usr/bin/make -f src/apps/CMakeFiles/manualpick.dir/build.make src/apps/CMakeFiles/manualpick.dir/build make[4]: Leaving directory '/build/relion-3.1.3/build' -make[4]: Entering directory '/build/relion-3.1.3/build' +/usr/bin/make -f src/apps/CMakeFiles/display.dir/build.make src/apps/CMakeFiles/display.dir/build /usr/bin/make -f src/apps/CMakeFiles/relion.dir/build.make src/apps/CMakeFiles/relion.dir/build +/usr/bin/make -f src/apps/CMakeFiles/manualpick.dir/build.make src/apps/CMakeFiles/manualpick.dir/build +make[4]: Entering directory '/build/relion-3.1.3/build' +make[4]: Entering directory '/build/relion-3.1.3/build' make[4]: Entering directory '/build/relion-3.1.3/build' +[ 97%] Building CXX object src/apps/CMakeFiles/manualpick.dir/manualpick.cpp.o [ 97%] Building CXX object src/apps/CMakeFiles/display.dir/display.cpp.o [ 97%] Building CXX object src/apps/CMakeFiles/relion.dir/maingui.cpp.o -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/display.dir/display.cpp.o -MF CMakeFiles/display.dir/display.cpp.o.d -o CMakeFiles/display.dir/display.cpp.o -c /build/relion-3.1.3/src/apps/display.cpp -cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion.dir/maingui.cpp.o -MF CMakeFiles/relion.dir/maingui.cpp.o.d -o CMakeFiles/relion.dir/maingui.cpp.o -c /build/relion-3.1.3/src/apps/maingui.cpp -[ 97%] Building CXX object src/apps/CMakeFiles/manualpick.dir/manualpick.cpp.o cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/manualpick.dir/manualpick.cpp.o -MF CMakeFiles/manualpick.dir/manualpick.cpp.o.d -o CMakeFiles/manualpick.dir/manualpick.cpp.o -c /build/relion-3.1.3/src/apps/manualpick.cpp +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion.dir/maingui.cpp.o -MF CMakeFiles/relion.dir/maingui.cpp.o.d -o CMakeFiles/relion.dir/maingui.cpp.o -c /build/relion-3.1.3/src/apps/maingui.cpp +cd /build/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.3/src/ -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/display.dir/display.cpp.o -MF CMakeFiles/display.dir/display.cpp.o.d -o CMakeFiles/display.dir/display.cpp.o -c /build/relion-3.1.3/src/apps/display.cpp +In file included from /build/relion-3.1.3/src/image.h:455, + from /build/relion-3.1.3/src/apps/display.cpp:25: +/build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': +/build/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 43 | uint32 width, length; // apparent dimensions in the file + | ^~~~~ In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/apps/manualpick.cpp:25: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': @@ -10626,113 +10650,107 @@ /usr/include/aarch64-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/aarch64-linux-gnu/tiffio.h:31, + from /build/relion-3.1.3/src/image.h:57: +/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here + 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 43 | uint32 width, length; // apparent dimensions in the file + | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ +/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here + 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; + | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ -/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] +/build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; - | ^~~~~~~~~~~~~ + | ^~~~~~~~~~~~ /usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -/build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; - | ^~~~~~~~~~~~~~ /usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -/build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] - 185 | uint32 cur_width, cur_length; - | ^~~~~~~~~ -/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here - 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] - 185 | uint32 cur_width, cur_length; - | ^~~~~~~~~~ -/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here - 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 186 | uint16 cur_sampleFormat, cur_bitsPerSample; - | ^~~~~~~~~~~~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; + | ^~~~~~~~~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; + | ^~~~~~~~~~~~~ /usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -/build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 186 | uint16 cur_sampleFormat, cur_bitsPerSample; - | ^~~~~~~~~~~~~~~~~ /usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -In file included from /build/relion-3.1.3/src/image.h:455, - from /build/relion-3.1.3/src/apps/display.cpp:25: -/build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': -/build/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] - 43 | uint32 width, length; // apparent dimensions in the file - | ^~~~~ -In file included from /usr/include/aarch64-linux-gnu/tiffio.h:31, - from /build/relion-3.1.3/src/image.h:57: -/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here - 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/relion-3.1.3/src/rwTIFF.h:43:23: warning: 'uint32' is deprecated [-Wdeprecated-declarations] - 43 | uint32 width, length; // apparent dimensions in the file - | ^~~~~~ -/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here - 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] +/build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; - | ^~~~~~~~~~~~ -/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here - 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; - | ^~~~~~ -/build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + | ^~~~~~~~~~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; - | ^~~~~~~~~~~~~ + | ^~~~~~~~~~~~~~ /usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ -/build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] - 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; - | ^~~~~~~~~~~~~~ /usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 185 | uint32 cur_width, cur_length; + | ^~~~~~~~~ +/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here + 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; + | ^~~~~~ /usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] + 185 | uint32 cur_width, cur_length; + | ^~~~~~~~~~ +/usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here + 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; + | ^~~~~~ /usr/include/aarch64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 186 | uint16 cur_sampleFormat, cur_bitsPerSample; + | ^~~~~~~~~~~~~~~~ /usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ +/build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] + 186 | uint16 cur_sampleFormat, cur_bitsPerSample; + | ^~~~~~~~~~~~~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ +/usr/include/aarch64-linux-gnu/tiff.h:83:38: note: declared here + 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; + | ^~~~~~ In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-3.1.3/src/scheduler.h:26, @@ -10803,12 +10821,12 @@ /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/manualpick.dir/manualpick.cpp.o -o ../../bin/relion_manualpick ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gui_lib.a /usr/lib/aarch64-linux-gnu/libfltk_images.so /usr/lib/aarch64-linux-gnu/libfltk_forms.so /usr/lib/aarch64-linux-gnu/libfltk.so -lX11 -lm -ltiff ../../lib/librelion_lib.a -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' [ 99%] Built target display -make[4]: Leaving directory '/build/relion-3.1.3/build' -[ 99%] Built target manualpick [100%] Linking CXX executable ../../bin/relion cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/relion.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/relion.dir/maingui.cpp.o -o ../../bin/relion ../../lib/librelion_lib.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gui_lib.a /usr/lib/aarch64-linux-gnu/libfltk_images.so /usr/lib/aarch64-linux-gnu/libfltk_forms.so /usr/lib/aarch64-linux-gnu/libfltk.so -lX11 -lm -ltiff ../../lib/librelion_lib.a -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' +[100%] Built target manualpick +make[4]: Leaving directory '/build/relion-3.1.3/build' [100%] Built target relion [100%] Linking CXX executable ../../bin/relion_star_handler cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/star_handler.dir/link.txt --verbose=1 @@ -11412,16 +11430,16 @@ -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_tiltpair_plot -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_project -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_run_motioncorr_mpi --- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_run_motioncorr -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_refine_mpi --- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_run_ctffind_mpi +-- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_run_motioncorr -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_reposition --- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_run_ctffind +-- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_run_ctffind_mpi -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_refine +-- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_run_ctffind -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_reconstruct_mpi -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_reconstruct --- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_particle_reposition -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_preprocess_mpi +-- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_particle_reposition -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_preprocess -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_postprocess_mpi -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_postprocess @@ -11429,27 +11447,27 @@ -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_image_handler -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_particle_subtract_mpi -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_pipeliner --- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_helix_toolbox -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_particle_subtract +-- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_helix_toolbox -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_particle_symmetry_expand -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_particle_select --- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_particle_FCC -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_mrc2vtk --- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_mask_create +-- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_particle_FCC -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_motion_refine_mpi +-- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_mask_create -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_motion_refine -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_import -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_merge_particles -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_localsym_mpi --- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_localsym -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_flex_analyse_mpi +-- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_localsym -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_helix_inimodel2d --- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_find_tiltpairs -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_external_reconstruct +-- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_find_tiltpairs -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_flex_analyse -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_estimate_gain --- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_ctf_toolbox -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_demodulate +-- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_ctf_toolbox -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_align_symmetry -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_ctf_mask_test -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_ctf_refine_mpi @@ -11553,12 +11571,14 @@ 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/1712/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1712/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/20937 and its subdirectories -I: Current time: Wed Apr 12 07:03:06 -12 2023 -I: pbuilder-time-stamp: 1681326186 +I: removing directory /srv/workspace/pbuilder/1712 and its subdirectories +I: Current time: Wed May 15 15:47:33 +14 2024 +I: pbuilder-time-stamp: 1715737653