Diff of the two buildlogs: -- --- b1/build.log 2025-02-07 10:12:25.174794442 +0000 +++ b2/build.log 2025-02-07 10:34:18.151445696 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Feb 6 21:30:52 -12 2025 -I: pbuilder-time-stamp: 1738920652 +I: Current time: Sat Feb 8 00:13:41 +14 2025 +I: pbuilder-time-stamp: 1738923221 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -27,52 +27,84 @@ dpkg-source: info: applying adjust-test-tolerance.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/29972/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/14933/tmp/hooks/D01_modify_environment starting +debug: Running on virt32a. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Feb 7 10:13 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/14933/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/14933/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='armhf' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=5 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='armhf' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='7f46dc66db5d4aef9d5fd97420b95f9c' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='29972' - PS1='# ' - PS2='> ' + INVOCATION_ID=6789413e6e8a4af794ae4aede5879007 + LANG=C + LANGUAGE=it_CH:it + LC_ALL=C + MACHTYPE=arm-unknown-linux-gnueabihf + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnueabihf + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=14933 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.ucbApmc2/pbuilderrc_njpw --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ucbApmc2/b1 --logfile b1/build.log gemmi_0.6.5+ds-3.dsc' - SUDO_GID='114' - SUDO_UID='109' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:3142/' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.ucbApmc2/pbuilderrc_gvxl --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ucbApmc2/b2 --logfile b2/build.log gemmi_0.6.5+ds-3.dsc' + SUDO_GID=113 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:3142/ I: uname -a - Linux ff64a 6.1.0-30-arm64 #1 SMP Debian 6.1.124-1 (2025-01-12) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-30-armmp-lpae #1 SMP Debian 6.1.124-1 (2025-01-12) armv7l GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/29972/tmp/hooks/D02_print_environment finished +I: user script /srv/workspace/pbuilder/14933/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -239,7 +271,7 @@ Get: 107 http://deb.debian.org/debian trixie/main armhf python3-pybind11 all 2.13.6-2 [215 kB] Get: 108 http://deb.debian.org/debian trixie/main armhf python3-pytest all 8.3.4-1 [250 kB] Get: 109 http://deb.debian.org/debian trixie/main armhf tao-pegtl-dev all 3.2.7-1 [69.4 kB] -Fetched 56.2 MB in 2s (34.9 MB/s) +Fetched 56.2 MB in 1s (63.9 MB/s) Preconfiguring packages ... Selecting previously unselected package liblocale-gettext-perl. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19567 files and directories currently installed.) @@ -601,8 +633,8 @@ Setting up tzdata (2024b-6) ... Current default time zone: 'Etc/UTC' -Local time is now: Fri Feb 7 09:32:41 UTC 2025. -Universal Time is now: Fri Feb 7 09:32:41 UTC 2025. +Local time is now: Fri Feb 7 10:14:30 UTC 2025. +Universal Time is now: Fri Feb 7 10:14:30 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... @@ -704,7 +736,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/gemmi-0.6.5+ds/ && 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 > ../gemmi_0.6.5+ds-3_source.changes +I: user script /srv/workspace/pbuilder/14933/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/14933/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/gemmi-0.6.5+ds/ && 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 > ../gemmi_0.6.5+ds-3_source.changes dpkg-buildpackage: info: source package gemmi dpkg-buildpackage: info: source version 0.6.5+ds-3 dpkg-buildpackage: info: source distribution unstable @@ -750,8 +786,8 @@ -- Performing Test HAS_FLTO - Success -- Found pybind11: /usr/lib/python3/dist-packages/pybind11/include (found version "2.13.6") -- Found pybind11 2.13.6: /usr/lib/python3/dist-packages/pybind11/include;/usr/include/python3.13 --- Configuring done (11.0s) --- Generating done (0.7s) +-- Configuring done (4.3s) +-- Generating done (0.3s) CMake Warning: Manually-specified variables were not used by the project: @@ -763,7 +799,7 @@ -- Build files have been written to: /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf make[1]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds' dh_auto_build -O--buildsystem=cmake - cd obj-arm-linux-gnueabihf && make -j5 "INSTALL=install --strip-program=true" VERBOSE=1 + cd obj-arm-linux-gnueabihf && make -j4 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' /usr/bin/cmake -S/build/reproducible-path/gemmi-0.6.5+ds -B/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf/CMakeFiles /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf//CMakeFiles/progress.marks @@ -772,35 +808,35 @@ make -f CMakeFiles/gemmi_cpp.dir/build.make CMakeFiles/gemmi_cpp.dir/depend make -f CMakeFiles/options.dir/build.make CMakeFiles/options.dir/depend make[3]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gemmi-0.6.5+ds /build/reproducible-path/gemmi-0.6.5+ds /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf/CMakeFiles/gemmi_cpp.dir/DependInfo.cmake "--color=" -make[3]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' cd /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gemmi-0.6.5+ds /build/reproducible-path/gemmi-0.6.5+ds /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf/CMakeFiles/options.dir/DependInfo.cmake "--color=" -make[3]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' -make -f CMakeFiles/gemmi_cpp.dir/build.make CMakeFiles/gemmi_cpp.dir/build +make[3]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gemmi-0.6.5+ds /build/reproducible-path/gemmi-0.6.5+ds /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf/CMakeFiles/gemmi_cpp.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' make -f CMakeFiles/options.dir/build.make CMakeFiles/options.dir/build +make[3]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' +make -f CMakeFiles/gemmi_cpp.dir/build.make CMakeFiles/gemmi_cpp.dir/build make[3]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' -[ 0%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/assembly.cpp.o -/usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/assembly.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/assembly.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/assembly.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/assembly.cpp [ 2%] Building CXX object CMakeFiles/options.dir/prog/options.cpp.o +[ 2%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/assembly.cpp.o +[ 4%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/align.cpp.o /usr/bin/c++ -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/options.dir/prog/options.cpp.o -MF CMakeFiles/options.dir/prog/options.cpp.o.d -o CMakeFiles/options.dir/prog/options.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/options.cpp -[ 4%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/calculate.cpp.o -[ 4%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/crd.cpp.o -/usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/calculate.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/calculate.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/calculate.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/calculate.cpp -[ 6%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/align.cpp.o -/usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/crd.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/crd.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/crd.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/crd.cpp +[ 6%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/calculate.cpp.o +/usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/assembly.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/assembly.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/assembly.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/assembly.cpp /usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/align.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/align.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/align.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/align.cpp +/usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/calculate.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/calculate.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/calculate.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/calculate.cpp In file included from /build/reproducible-path/gemmi-0.6.5+ds/prog/options.cpp:8: /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ +[ 6%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/crd.cpp.o +/usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/crd.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/crd.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/crd.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/crd.cpp [ 8%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/ddl.cpp.o /usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/ddl.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/ddl.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/ddl.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/ddl.cpp +make[3]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' +[ 8%] Built target options [ 10%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/eig3.cpp.o /usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/eig3.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/eig3.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/eig3.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/eig3.cpp -make[3]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' -[ 10%] Built target options [ 10%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/gz.cpp.o /usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/gz.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/gz.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/gz.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/gz.cpp In file included from /build/reproducible-path/gemmi-0.6.5+ds/src/gz.cpp:15: @@ -809,19 +845,12 @@ | ^ [ 12%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/intensit.cpp.o /usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/intensit.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/intensit.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/intensit.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/intensit.cpp -[ 12%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/json.cpp.o -/usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/json.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/json.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/json.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/json.cpp In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz.hpp:23, from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/intensit.hpp:14, from /build/reproducible-path/gemmi-0.6.5+ds/src/intensit.cpp:3: /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ -In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/json.hpp:10, - from /build/reproducible-path/gemmi-0.6.5+ds/src/json.cpp:3: -/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] - 37 | typedef std::unique_ptr fileptr_t; - | ^ In file included from /usr/include/c++/14/algorithm:61, from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/symmetry.hpp:15, from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/intensit.hpp:11: @@ -839,8 +868,13 @@ /usr/include/c++/14/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ -[ 14%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/mmcif.cpp.o -/usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/mmcif.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/mmcif.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/mmcif.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/mmcif.cpp +[ 12%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/json.cpp.o +/usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/json.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/json.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/json.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/json.cpp +In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/json.hpp:10, + from /build/reproducible-path/gemmi-0.6.5+ds/src/json.cpp:3: +/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] + 37 | typedef std::unique_ptr fileptr_t; + | ^ /usr/include/c++/14/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/14/bits/stl_algo.h:1876:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1876 | __introsort_loop(_RandomAccessIterator __first, @@ -871,17 +905,19 @@ /usr/include/c++/14/bits/stl_algo.h:1822:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1822 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +[ 14%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/mmcif.cpp.o +/usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/mmcif.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/mmcif.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/mmcif.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/mmcif.cpp [ 14%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/mmread_gz.cpp.o /usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/mmread_gz.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/mmread_gz.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/mmread_gz.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/mmread_gz.cpp [ 16%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/mtz.cpp.o /usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/mtz.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/mtz.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/mtz.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/mtz.cpp -[ 18%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/mtz2cif.cpp.o -/usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/mtz2cif.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/mtz2cif.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/mtz2cif.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/mtz2cif.cpp In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz.hpp:23, from /build/reproducible-path/gemmi-0.6.5+ds/src/mtz.cpp:3: /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ +[ 18%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/mtz2cif.cpp.o +/usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/mtz2cif.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/mtz2cif.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/mtz2cif.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/mtz2cif.cpp In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz.hpp:23, from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz2cif.hpp:14, from /build/reproducible-path/gemmi-0.6.5+ds/src/mtz2cif.cpp:3: @@ -894,8 +930,6 @@ /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ -[ 18%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/polyheur.cpp.o -/usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/polyheur.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/polyheur.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/polyheur.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/polyheur.cpp In file included from /usr/include/c++/14/algorithm:61, from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz.hpp:12: /usr/include/c++/14/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_less_iter]': @@ -942,30 +976,28 @@ /usr/include/c++/14/bits/stl_algo.h:1822:30: note: parameter passing for argument of type 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CMakeFiles/gemmi_cpp.dir/src/riding_h.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/riding_h.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/riding_h.cpp In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/json.hpp:10, from /build/reproducible-path/gemmi-0.6.5+ds/src/read_cif.cpp:5: /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ +[ 20%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/resinfo.cpp.o +/usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/resinfo.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/resinfo.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/resinfo.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/resinfo.cpp +[ 22%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/riding_h.cpp.o +/usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/riding_h.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/riding_h.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/riding_h.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/riding_h.cpp [ 22%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/sprintf.cpp.o /usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/sprintf.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/sprintf.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/sprintf.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/sprintf.cpp -[ 25%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/to_mmcif.cpp.o -/usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/to_mmcif.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/to_mmcif.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/to_mmcif.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/to_mmcif.cpp /build/reproducible-path/gemmi-0.6.5+ds/src/sprintf.cpp:30:86: note: '#pragma message: Using system stb_sprintf.h, not the bundled one. It may not work.' 30 | # pragma message("Using system stb_sprintf.h, not the bundled one. It may not work.") | ^ +[ 25%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/to_mmcif.cpp.o +/usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/to_mmcif.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/to_mmcif.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/to_mmcif.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/to_mmcif.cpp [ 27%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/to_pdb.cpp.o /usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/to_pdb.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/to_pdb.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/to_pdb.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/to_pdb.cpp -[ 27%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/monlib.cpp.o -/usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/monlib.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/monlib.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/monlib.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/monlib.cpp -[ 29%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/topo.cpp.o -/usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/topo.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/topo.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/topo.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/topo.cpp In file included from /usr/include/c++/14/algorithm:60, from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/model.hpp:8, from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/to_mmcif.hpp:8, @@ -975,6 +1007,8 @@ 2093 | __find_if(_RandomAccessIterator __first, _RandomAccessIterator __last, | ^~~~~~~~~ /usr/include/c++/14/bits/stl_algobase.h:2093:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +[ 27%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/monlib.cpp.o +/usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/monlib.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/monlib.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/monlib.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/monlib.cpp In file included from /usr/include/c++/14/algorithm:60, from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/model.hpp:8, from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/to_pdb.hpp:8, @@ -993,6 +1027,18 @@ | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2147 | std::__iterator_category(__first)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 29%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/topo.cpp.o +/usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/topo.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/topo.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/topo.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/topo.cpp +In function '_Iterator std::__find_if(_Iterator, _Iterator, _Predicate) [with _Iterator = __gnu_cxx::__normal_iterator >; _Predicate = __gnu_cxx::__ops::_Iter_pred >]', + inlined from '_IIter std::find_if(_IIter, _IIter, _Predicate) [with _IIter = __gnu_cxx::__normal_iterator >; _Predicate = gemmi::update_mmcif_block(const Structure&, cif::Block&, MmcifOutputGroups)::]' at /usr/include/c++/14/bits/stl_algo.h:3876:28, + inlined from 'bool std::none_of(_IIter, _IIter, _Predicate) [with _IIter = __gnu_cxx::__normal_iterator >; _Predicate = gemmi::update_mmcif_block(const Structure&, cif::Block&, MmcifOutputGroups)::]' at /usr/include/c++/14/bits/stl_algo.h:429:47, + inlined from 'bool std::any_of(_IIter, _IIter, _Predicate) [with _IIter = __gnu_cxx::__normal_iterator >; _Predicate = gemmi::update_mmcif_block(const Structure&, cif::Block&, MmcifOutputGroups)::]' at /usr/include/c++/14/bits/stl_algo.h:448:27, + inlined from 'void gemmi::update_mmcif_block(const Structure&, cif::Block&, MmcifOutputGroups)' at /build/reproducible-path/gemmi-0.6.5+ds/src/to_mmcif.cpp:626:20: +/usr/include/c++/14/bits/stl_algobase.h:2146:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2146 | return __find_if(__first, __last, __pred, + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ + 2147 | std::__iterator_category(__first)); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_tree.h:63, from /usr/include/c++/14/map:62, from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/monlib.hpp:9, @@ -1019,33 +1065,6 @@ /usr/include/c++/14/bits/stl_algobase.h:2093:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 [ 29%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/xds_ascii.cpp.o /usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/xds_ascii.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/xds_ascii.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/xds_ascii.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/xds_ascii.cpp -In file included from /usr/include/c++/14/bits/stl_algo.h:61, - from /usr/include/c++/14/algorithm:61, - from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/util.hpp:11, - from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/cifdoc.hpp:11, - from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/chemcomp.hpp:11, - from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/topo.hpp:12, - from /build/reproducible-path/gemmi-0.6.5+ds/src/topo.cpp:3: -/usr/include/c++/14/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = gemmi::Atom; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]': -/usr/include/c++/14/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, - | ^~~~~~~~~~~~~ -In file included from /usr/include/c++/14/vector:72, - from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/chemcomp.hpp:10: -/usr/include/c++/14/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(iterator, iterator) [with _Tp = gemmi::Atom; _Alloc = std::allocator]': -/usr/include/c++/14/bits/vector.tcc:195:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 195 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/14/bits/vector.tcc:195:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 -/usr/include/c++/14/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_comp_iter >]': -/usr/include/c++/14/bits/stl_algo.h:1750:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1750 | __unguarded_linear_insert(_RandomAccessIterator __last, - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/14/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]': -/usr/include/c++/14/bits/stl_algo.h:1770:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1770 | __insertion_sort(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/14/bits/stl_algo.h:1770:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/xds_ascii.hpp:11, from /build/reproducible-path/gemmi-0.6.5+ds/src/xds_ascii.cpp:3: /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] @@ -1089,6 +1108,43 @@ | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2147 | std::__iterator_category(__first)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/14/bits/stl_algo.h:61, + from /usr/include/c++/14/algorithm:61, + from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/util.hpp:11, + from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/cifdoc.hpp:11, + from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/chemcomp.hpp:11, + from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/topo.hpp:12, + from /build/reproducible-path/gemmi-0.6.5+ds/src/topo.cpp:3: +/usr/include/c++/14/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = gemmi::Atom; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]': +/usr/include/c++/14/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, + | ^~~~~~~~~~~~~ +In file included from /usr/include/c++/14/vector:72, + from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/chemcomp.hpp:10: +/usr/include/c++/14/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(iterator, iterator) [with _Tp = gemmi::Atom; _Alloc = std::allocator]': +/usr/include/c++/14/bits/vector.tcc:195:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 195 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/14/bits/vector.tcc:195:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 +/usr/include/c++/14/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_comp_iter >]': +/usr/include/c++/14/bits/stl_algo.h:1750:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1750 | __unguarded_linear_insert(_RandomAccessIterator __last, + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/14/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]': +/usr/include/c++/14/bits/stl_algo.h:1770:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1770 | __insertion_sort(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/14/bits/stl_algo.h:1770:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +In function '_Iterator std::__find_if(_Iterator, _Iterator, _Predicate) [with _Iterator = __gnu_cxx::__normal_iterator >; _Predicate = __gnu_cxx::__ops::_Iter_pred >]', + inlined from '_IIter std::find_if(_IIter, _IIter, _Predicate) [with _IIter = __gnu_cxx::__normal_iterator >; _Predicate = gemmi::ChemComp::find_atom(const std::string&)::]' at /usr/include/c++/14/bits/stl_algo.h:3876:28, + inlined from 'std::vector::iterator gemmi::ChemComp::find_atom(const std::string&)' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/chemcomp.hpp:429:24, + inlined from 'std::vector::const_iterator gemmi::ChemComp::find_atom(const std::string&) const' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/chemcomp.hpp:433:50, + inlined from 'std::string gemmi::MonLib::update_old_atom_names(gemmi::Structure&) const' at /build/reproducible-path/gemmi-0.6.5+ds/src/monlib.cpp:535:33: +/usr/include/c++/14/bits/stl_algobase.h:2146:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2146 | return __find_if(__first, __last, __pred, + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ + 2147 | std::__iterator_category(__first)); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(iterator) [with _Tp = gemmi::Atom; _Alloc = std::allocator]': /usr/include/c++/14/bits/vector.tcc:181:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 181 | vector<_Tp, _Alloc>:: @@ -1104,26 +1160,6 @@ /usr/include/c++/14/bits/stl_vector.h:1537:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1537 | { return _M_erase(begin() + (__position - cbegin())); } | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In function '_Iterator std::__find_if(_Iterator, _Iterator, _Predicate) [with _Iterator = __gnu_cxx::__normal_iterator >; _Predicate = __gnu_cxx::__ops::_Iter_pred >]', - inlined from '_IIter std::find_if(_IIter, _IIter, _Predicate) [with _IIter = __gnu_cxx::__normal_iterator >; _Predicate = gemmi::ChemComp::find_atom(const std::string&)::]' at /usr/include/c++/14/bits/stl_algo.h:3876:28, - inlined from 'std::vector::iterator gemmi::ChemComp::find_atom(const std::string&)' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/chemcomp.hpp:429:24, - inlined from 'std::vector::const_iterator gemmi::ChemComp::find_atom(const std::string&) const' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/chemcomp.hpp:433:50, - inlined from 'std::string gemmi::MonLib::update_old_atom_names(gemmi::Structure&) const' at /build/reproducible-path/gemmi-0.6.5+ds/src/monlib.cpp:535:33: -/usr/include/c++/14/bits/stl_algobase.h:2146:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2146 | return __find_if(__first, __last, __pred, - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ - 2147 | std::__iterator_category(__first)); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In function '_Iterator std::__find_if(_Iterator, _Iterator, _Predicate) [with _Iterator = __gnu_cxx::__normal_iterator >; _Predicate = __gnu_cxx::__ops::_Iter_pred >]', - inlined from '_IIter std::find_if(_IIter, _IIter, _Predicate) [with _IIter = __gnu_cxx::__normal_iterator >; _Predicate = gemmi::update_mmcif_block(const Structure&, cif::Block&, MmcifOutputGroups)::]' at /usr/include/c++/14/bits/stl_algo.h:3876:28, - inlined from 'bool std::none_of(_IIter, _IIter, _Predicate) [with _IIter = __gnu_cxx::__normal_iterator >; _Predicate = gemmi::update_mmcif_block(const Structure&, cif::Block&, MmcifOutputGroups)::]' at /usr/include/c++/14/bits/stl_algo.h:429:47, - inlined from 'bool std::any_of(_IIter, _IIter, _Predicate) [with _IIter = __gnu_cxx::__normal_iterator >; _Predicate = gemmi::update_mmcif_block(const Structure&, cif::Block&, MmcifOutputGroups)::]' at /usr/include/c++/14/bits/stl_algo.h:448:27, - inlined from 'void gemmi::update_mmcif_block(const Structure&, cif::Block&, MmcifOutputGroups)' at /build/reproducible-path/gemmi-0.6.5+ds/src/to_mmcif.cpp:626:20: -/usr/include/c++/14/bits/stl_algobase.h:2146:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2146 | return __find_if(__first, __last, __pred, - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ - 2147 | std::__iterator_category(__first)); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/vector:65, from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/monlib.hpp:11: /usr/include/c++/14/bits/stl_uninitialized.h: In function '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gemmi::Restraints::Plane*]': @@ -1229,41 +1265,31 @@ make -f CMakeFiles/gemmi_prog.dir/build.make CMakeFiles/gemmi_prog.dir/depend make -f CMakeFiles/gemmi_py.dir/build.make CMakeFiles/gemmi_py.dir/depend make[3]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gemmi-0.6.5+ds /build/reproducible-path/gemmi-0.6.5+ds /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf/CMakeFiles/gemmi_py.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gemmi-0.6.5+ds /build/reproducible-path/gemmi-0.6.5+ds /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf/CMakeFiles/gemmi_py.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gemmi-0.6.5+ds /build/reproducible-path/gemmi-0.6.5+ds /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf/CMakeFiles/gemmi_prog.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' -make -f CMakeFiles/gemmi_py.dir/build.make CMakeFiles/gemmi_py.dir/build -make[3]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' make[3]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' +make -f CMakeFiles/gemmi_py.dir/build.make CMakeFiles/gemmi_py.dir/build make -f CMakeFiles/gemmi_prog.dir/build.make CMakeFiles/gemmi_prog.dir/build make[3]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' -[ 31%] Building CXX object CMakeFiles/gemmi_py.dir/python/gemmi.cpp.o -[ 31%] Building CXX object CMakeFiles/gemmi_py.dir/python/ccp4.cpp.o -/usr/bin/c++ -Dgemmi_py_EXPORTS -I/build/reproducible-path/gemmi-0.6.5+ds/include -isystem /usr/include/python3.13 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/gemmi.cpp.o -MF CMakeFiles/gemmi_py.dir/python/gemmi.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/gemmi.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/python/gemmi.cpp -/usr/bin/c++ -Dgemmi_py_EXPORTS -I/build/reproducible-path/gemmi-0.6.5+ds/include -isystem /usr/include/python3.13 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/ccp4.cpp.o -MF CMakeFiles/gemmi_py.dir/python/ccp4.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/ccp4.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/python/ccp4.cpp +make[3]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' [ 35%] Building CXX object CMakeFiles/gemmi_py.dir/python/mol.cpp.o +[ 35%] Building CXX object CMakeFiles/gemmi_py.dir/python/gemmi.cpp.o [ 35%] Building CXX object CMakeFiles/gemmi_py.dir/python/align.cpp.o -/usr/bin/c++ -Dgemmi_py_EXPORTS -I/build/reproducible-path/gemmi-0.6.5+ds/include -isystem /usr/include/python3.13 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/align.cpp.o -MF CMakeFiles/gemmi_py.dir/python/align.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/align.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/python/align.cpp +/usr/bin/c++ -Dgemmi_py_EXPORTS -I/build/reproducible-path/gemmi-0.6.5+ds/include -isystem /usr/include/python3.13 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast 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CMakeFiles/gemmi_py.dir/python/mol.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/mol.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/python/mol.cpp +/usr/bin/c++ -Dgemmi_py_EXPORTS -I/build/reproducible-path/gemmi-0.6.5+ds/include -isystem /usr/include/python3.13 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/align.cpp.o -MF CMakeFiles/gemmi_py.dir/python/align.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/align.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/python/align.cpp [ 35%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/align.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/align.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/align.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/align.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/align.cpp -In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/ccp4.hpp:19, - from /build/reproducible-path/gemmi-0.6.5+ds/python/ccp4.cpp:3: -/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] - 37 | typedef std::unique_ptr fileptr_t; - | ^ +[ 35%] Building CXX object CMakeFiles/gemmi_py.dir/python/ccp4.cpp.o +/usr/bin/c++ -Dgemmi_py_EXPORTS -I/build/reproducible-path/gemmi-0.6.5+ds/include -isystem /usr/include/python3.13 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/ccp4.cpp.o -MF CMakeFiles/gemmi_py.dir/python/ccp4.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/ccp4.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/python/ccp4.cpp [ 37%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/blobs.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/blobs.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/blobs.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/blobs.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/blobs.cpp -[ 37%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/cif2mtz.cpp.o -/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/cif2mtz.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/cif2mtz.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/cif2mtz.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/cif2mtz.cpp [ 39%] Building CXX object CMakeFiles/gemmi_py.dir/python/chemcomp.cpp.o /usr/bin/c++ -Dgemmi_py_EXPORTS -I/build/reproducible-path/gemmi-0.6.5+ds/include -isystem /usr/include/python3.13 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/chemcomp.cpp.o -MF CMakeFiles/gemmi_py.dir/python/chemcomp.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/chemcomp.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/python/chemcomp.cpp -[ 41%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/cif2json.cpp.o -/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/cif2json.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/cif2json.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/cif2json.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/cif2json.cpp -In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz.hpp:23, - from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/cif2mtz.hpp:15, - from /build/reproducible-path/gemmi-0.6.5+ds/prog/cif2mtz.cpp:10: +In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/ccp4.hpp:19, + from /build/reproducible-path/gemmi-0.6.5+ds/python/ccp4.cpp:3: /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ @@ -1311,22 +1337,55 @@ /usr/include/c++/14/bits/stl_algo.h:1822:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1822 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -[ 43%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/cifdiff.cpp.o -/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/cifdiff.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/cifdiff.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/cifdiff.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/cifdiff.cpp -[ 43%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/contact.cpp.o -/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/contact.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/contact.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/contact.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/contact.cpp -[ 45%] Building CXX object CMakeFiles/gemmi_py.dir/python/cif.cpp.o +[ 41%] Building CXX object CMakeFiles/gemmi_py.dir/python/cif.cpp.o /usr/bin/c++ -Dgemmi_py_EXPORTS -I/build/reproducible-path/gemmi-0.6.5+ds/include -isystem /usr/include/python3.13 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 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/build/reproducible-path/gemmi-0.6.5+ds/prog/contents.cpp -[ 47%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/convert.cpp.o -/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/convert.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/convert.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/convert.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/convert.cpp -[ 47%] Building CXX object CMakeFiles/gemmi_py.dir/python/custom.cpp.o +[ 41%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/cif2mtz.cpp.o +/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/cif2mtz.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/cif2mtz.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/cif2mtz.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/cif2mtz.cpp +In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz.hpp:23, + from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/cif2mtz.hpp:15, + from /build/reproducible-path/gemmi-0.6.5+ds/prog/cif2mtz.cpp:10: +/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] + 37 | typedef std::unique_ptr fileptr_t; + | ^ +[ 41%] Building CXX object CMakeFiles/gemmi_py.dir/python/custom.cpp.o /usr/bin/c++ -Dgemmi_py_EXPORTS -I/build/reproducible-path/gemmi-0.6.5+ds/include -isystem /usr/include/python3.13 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/custom.cpp.o -MF CMakeFiles/gemmi_py.dir/python/custom.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/custom.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/python/custom.cpp -[ 50%] Building CXX object CMakeFiles/gemmi_py.dir/python/elem.cpp.o +[ 43%] Building CXX object CMakeFiles/gemmi_py.dir/python/elem.cpp.o /usr/bin/c++ -Dgemmi_py_EXPORTS -I/build/reproducible-path/gemmi-0.6.5+ds/include -isystem /usr/include/python3.13 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/elem.cpp.o -MF CMakeFiles/gemmi_py.dir/python/elem.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/elem.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/python/elem.cpp -[ 50%] Building CXX object CMakeFiles/gemmi_py.dir/python/grid.cpp.o +[ 43%] Building CXX object CMakeFiles/gemmi_py.dir/python/grid.cpp.o /usr/bin/c++ -Dgemmi_py_EXPORTS -I/build/reproducible-path/gemmi-0.6.5+ds/include -isystem /usr/include/python3.13 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/grid.cpp.o -MF CMakeFiles/gemmi_py.dir/python/grid.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/grid.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/python/grid.cpp +[ 45%] Building CXX object CMakeFiles/gemmi_py.dir/python/hkl.cpp.o +/usr/bin/c++ -Dgemmi_py_EXPORTS -I/build/reproducible-path/gemmi-0.6.5+ds/include -isystem /usr/include/python3.13 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong 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-fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/cif2json.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/cif2json.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/cif2json.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/cif2json.cpp +In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz.hpp:23, + from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/cif2mtz.hpp:15, + from /build/reproducible-path/gemmi-0.6.5+ds/python/hkl.cpp:9: +/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] + 37 | typedef std::unique_ptr fileptr_t; + | ^ +[ 47%] Building CXX object CMakeFiles/gemmi_py.dir/python/meta.cpp.o +/usr/bin/c++ -Dgemmi_py_EXPORTS -I/build/reproducible-path/gemmi-0.6.5+ds/include -isystem /usr/include/python3.13 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/meta.cpp.o -MF CMakeFiles/gemmi_py.dir/python/meta.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/meta.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/python/meta.cpp +[ 50%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/cifdiff.cpp.o +/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden 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Building CXX object CMakeFiles/gemmi_py.dir/python/monlib.cpp.o +/usr/bin/c++ -Dgemmi_py_EXPORTS -I/build/reproducible-path/gemmi-0.6.5+ds/include -isystem /usr/include/python3.13 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/monlib.cpp.o -MF CMakeFiles/gemmi_py.dir/python/monlib.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/monlib.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/python/monlib.cpp +[ 54%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/contents.cpp.o +/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/contents.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/contents.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/contents.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/contents.cpp +[ 54%] Building CXX object CMakeFiles/gemmi_py.dir/python/mtz.cpp.o +/usr/bin/c++ -Dgemmi_py_EXPORTS -I/build/reproducible-path/gemmi-0.6.5+ds/include -isystem /usr/include/python3.13 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -Wno-psabi -MD -MT CMakeFiles/gemmi_py.dir/python/mtz.cpp.o -MF CMakeFiles/gemmi_py.dir/python/mtz.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/mtz.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/python/mtz.cpp +In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz.hpp:23, + from /build/reproducible-path/gemmi-0.6.5+ds/python/mtz.cpp:3: +/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] + 37 | typedef std::unique_ptr fileptr_t; + | ^ +[ 54%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/convert.cpp.o +/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/convert.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/convert.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/convert.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/convert.cpp +[ 56%] Building CXX object CMakeFiles/gemmi_py.dir/python/read.cpp.o +/usr/bin/c++ -Dgemmi_py_EXPORTS -I/build/reproducible-path/gemmi-0.6.5+ds/include -isystem /usr/include/python3.13 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/read.cpp.o -MF CMakeFiles/gemmi_py.dir/python/read.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/read.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/python/read.cpp +[ 58%] Building CXX object CMakeFiles/gemmi_py.dir/python/recgrid.cpp.o +/usr/bin/c++ -Dgemmi_py_EXPORTS -I/build/reproducible-path/gemmi-0.6.5+ds/include -isystem /usr/include/python3.13 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -Wno-psabi -MD -MT CMakeFiles/gemmi_py.dir/python/recgrid.cpp.o -MF CMakeFiles/gemmi_py.dir/python/recgrid.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/recgrid.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/python/recgrid.cpp In file included from /usr/include/c++/14/vector:72, from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/iterator.hpp:10, from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/cifdoc.hpp:8, @@ -1337,10 +1396,11 @@ 195 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/vector.tcc:195:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 -[ 52%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/crd.cpp.o -/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/crd.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/crd.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/crd.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/crd.cpp -[ 54%] Building CXX object CMakeFiles/gemmi_py.dir/python/hkl.cpp.o -/usr/bin/c++ -Dgemmi_py_EXPORTS -I/build/reproducible-path/gemmi-0.6.5+ds/include -isystem /usr/include/python3.13 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -Wno-psabi -MD -MT CMakeFiles/gemmi_py.dir/python/hkl.cpp.o -MF CMakeFiles/gemmi_py.dir/python/hkl.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/hkl.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/python/hkl.cpp +In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/pdb.hpp:23, + from /build/reproducible-path/gemmi-0.6.5+ds/python/read.cpp:7: +/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] + 37 | typedef std::unique_ptr fileptr_t; + | ^ In file included from /usr/include/c++/14/vector:66: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(const_iterator, const_iterator) [with _Tp = gemmi::Atom; _Alloc = std::allocator]', inlined from 'void gemmi::vector_remove_if(std::vector&, F&&) [with T = Atom; F = remove_hydrogens(Residue&)::]' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/util.hpp:267:10, @@ -1351,12 +1411,6 @@ /usr/include/c++/14/bits/stl_vector.h:1568:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1568 | return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg)); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz.hpp:23, - from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/cif2mtz.hpp:15, - from /build/reproducible-path/gemmi-0.6.5+ds/python/hkl.cpp:9: -/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] - 37 | typedef std::unique_ptr fileptr_t; - | ^ /usr/include/c++/14/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const gemmi::Atom&}; _Tp = gemmi::Atom; _Alloc = std::allocator]': /usr/include/c++/14/bits/vector.tcc:452:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 452 | vector<_Tp, _Alloc>:: @@ -1374,10 +1428,8 @@ /usr/include/c++/14/bits/stl_vector.h:1568:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1568 | return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg)); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 54%] Building CXX object CMakeFiles/gemmi_py.dir/python/meta.cpp.o -/usr/bin/c++ -Dgemmi_py_EXPORTS -I/build/reproducible-path/gemmi-0.6.5+ds/include -isystem /usr/include/python3.13 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/meta.cpp.o -MF CMakeFiles/gemmi_py.dir/python/meta.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/meta.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/python/meta.cpp -[ 56%] Building CXX object CMakeFiles/gemmi_py.dir/python/monlib.cpp.o -/usr/bin/c++ -Dgemmi_py_EXPORTS -I/build/reproducible-path/gemmi-0.6.5+ds/include -isystem /usr/include/python3.13 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/monlib.cpp.o -MF CMakeFiles/gemmi_py.dir/python/monlib.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/monlib.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/python/monlib.cpp +[ 58%] Building CXX object CMakeFiles/gemmi_py.dir/python/scaling.cpp.o +/usr/bin/c++ -Dgemmi_py_EXPORTS -I/build/reproducible-path/gemmi-0.6.5+ds/include -isystem /usr/include/python3.13 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/scaling.cpp.o -MF CMakeFiles/gemmi_py.dir/python/scaling.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/scaling.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/python/scaling.cpp In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(const_iterator, const_iterator) [with _Tp = gemmi::Atom; _Alloc = std::allocator]', inlined from 'void gemmi::vector_remove_if(std::vector&, F&&) [with T = Atom; F = Selection::remove_not_selected(gemmi::Residue&) const::]' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/util.hpp:267:10, inlined from 'void gemmi::Selection::remove_not_selected(T&) const [with T = gemmi::Residue]' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/select.hpp:290:21, @@ -1396,8 +1448,16 @@ /usr/include/c++/14/bits/stl_vector.h:1568:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1568 | return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg)); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 56%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/ecalc.cpp.o +[ 60%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/crd.cpp.o +/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/crd.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/crd.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/crd.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/crd.cpp +[ 62%] Building CXX object CMakeFiles/gemmi_py.dir/python/search.cpp.o +/usr/bin/c++ -Dgemmi_py_EXPORTS -I/build/reproducible-path/gemmi-0.6.5+ds/include -isystem /usr/include/python3.13 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/search.cpp.o -MF CMakeFiles/gemmi_py.dir/python/search.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/search.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/python/search.cpp +[ 62%] Building CXX object CMakeFiles/gemmi_py.dir/python/sf.cpp.o +/usr/bin/c++ -Dgemmi_py_EXPORTS -I/build/reproducible-path/gemmi-0.6.5+ds/include -isystem /usr/include/python3.13 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/sf.cpp.o -MF CMakeFiles/gemmi_py.dir/python/sf.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/sf.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/python/sf.cpp +[ 62%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/ecalc.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/ecalc.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/ecalc.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/ecalc.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/ecalc.cpp +[ 64%] Building CXX object CMakeFiles/gemmi_py.dir/python/sym.cpp.o +/usr/bin/c++ -Dgemmi_py_EXPORTS -I/build/reproducible-path/gemmi-0.6.5+ds/include -isystem /usr/include/python3.13 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/sym.cpp.o -MF CMakeFiles/gemmi_py.dir/python/sym.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/sym.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/python/sym.cpp In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz.hpp:23, from /build/reproducible-path/gemmi-0.6.5+ds/prog/ecalc.cpp:5: /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] @@ -1426,13 +1486,6 @@ 1770 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algo.h:1770:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -[ 56%] Building CXX object CMakeFiles/gemmi_py.dir/python/mtz.cpp.o -/usr/bin/c++ -Dgemmi_py_EXPORTS -I/build/reproducible-path/gemmi-0.6.5+ds/include -isystem /usr/include/python3.13 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -Wno-psabi -MD -MT CMakeFiles/gemmi_py.dir/python/mtz.cpp.o -MF CMakeFiles/gemmi_py.dir/python/mtz.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/mtz.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/python/mtz.cpp -In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz.hpp:23, - from /build/reproducible-path/gemmi-0.6.5+ds/python/mtz.cpp:3: -/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] - 37 | typedef std::unique_ptr fileptr_t; - | ^ In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/14/bits/stl_algo.h:4772:18, inlined from 'void gemmi::Binner::setup_from_1_d2(int, Method, std::vector&&, const gemmi::UnitCell*)' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/binner.hpp:36:16, @@ -1455,38 +1508,6 @@ /usr/include/c++/14/bits/stl_algo.h:1822:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1822 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -[ 58%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/fprime.cpp.o -/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/fprime.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/fprime.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/fprime.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/fprime.cpp -[ 60%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/grep.cpp.o -/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/grep.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/grep.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/grep.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/grep.cpp -[ 60%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/h.cpp.o 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-fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/read.cpp.o -MF CMakeFiles/gemmi_py.dir/python/read.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/read.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/python/read.cpp -In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/pdb.hpp:23, - from /build/reproducible-path/gemmi-0.6.5+ds/python/read.cpp:7: -/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] - 37 | typedef std::unique_ptr fileptr_t; - | ^ -[ 64%] Building CXX object CMakeFiles/gemmi_py.dir/python/recgrid.cpp.o -/usr/bin/c++ -Dgemmi_py_EXPORTS -I/build/reproducible-path/gemmi-0.6.5+ds/include -isystem 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-fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/scaling.cpp.o -MF CMakeFiles/gemmi_py.dir/python/scaling.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/scaling.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/python/scaling.cpp -[ 66%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/json2cif.cpp.o -/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/json2cif.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/json2cif.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/json2cif.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/json2cif.cpp -[ 66%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/main.cpp.o -/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/main.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/main.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/main.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/main.cpp -[ 68%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/map.cpp.o -/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/map.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/map.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/map.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/map.cpp -[ 70%] Building CXX object CMakeFiles/gemmi_py.dir/python/search.cpp.o -/usr/bin/c++ -Dgemmi_py_EXPORTS -I/build/reproducible-path/gemmi-0.6.5+ds/include -isystem /usr/include/python3.13 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/search.cpp.o -MF CMakeFiles/gemmi_py.dir/python/search.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/search.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/python/search.cpp -[ 70%] Building CXX object CMakeFiles/gemmi_py.dir/python/sf.cpp.o -/usr/bin/c++ -Dgemmi_py_EXPORTS -I/build/reproducible-path/gemmi-0.6.5+ds/include -isystem /usr/include/python3.13 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/sf.cpp.o -MF CMakeFiles/gemmi_py.dir/python/sf.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/sf.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/python/sf.cpp -In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/ccp4.hpp:19, - from /build/reproducible-path/gemmi-0.6.5+ds/prog/map.cpp:6: -/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] - 37 | typedef std::unique_ptr fileptr_t; - | ^ In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/it92.hpp:16, from /build/reproducible-path/gemmi-0.6.5+ds/python/sf.cpp:6: /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/formfact.hpp: In instantiation of 'std::pair gemmi::ExpSum::calculate_with_derivative(float) const [with int N = 5]': @@ -1543,31 +1564,56 @@ /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/formfact.hpp:73:26: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 73 | std::pair calculate_with_derivative(float r) const { | ^~~~~~~~~~~~~~~~~~~~~~~~~ -[ 70%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/map2sf.cpp.o +[ 66%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/fprime.cpp.o +/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/fprime.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/fprime.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/fprime.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/fprime.cpp +[ 68%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/grep.cpp.o +/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/grep.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/grep.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/grep.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/grep.cpp +[ 68%] Building CXX object CMakeFiles/gemmi_py.dir/python/topo.cpp.o +/usr/bin/c++ -Dgemmi_py_EXPORTS -I/build/reproducible-path/gemmi-0.6.5+ds/include -isystem /usr/include/python3.13 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/topo.cpp.o -MF CMakeFiles/gemmi_py.dir/python/topo.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/topo.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/python/topo.cpp +[ 68%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/h.cpp.o +/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/h.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/h.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/h.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/h.cpp +[ 70%] Building CXX object CMakeFiles/gemmi_py.dir/python/unitcell.cpp.o +/usr/bin/c++ -Dgemmi_py_EXPORTS -I/build/reproducible-path/gemmi-0.6.5+ds/include -isystem /usr/include/python3.13 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/unitcell.cpp.o -MF CMakeFiles/gemmi_py.dir/python/unitcell.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/unitcell.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/python/unitcell.cpp +[ 72%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/json2cif.cpp.o +/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/json2cif.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/json2cif.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/json2cif.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/json2cif.cpp +[ 72%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/main.cpp.o +/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/main.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/main.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/main.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/main.cpp +[ 75%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/map.cpp.o +/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/map.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/map.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/map.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/map.cpp +In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/ccp4.hpp:19, + from /build/reproducible-path/gemmi-0.6.5+ds/prog/map.cpp:6: +/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] + 37 | typedef std::unique_ptr fileptr_t; + | ^ +[ 75%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/map2sf.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/map2sf.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/map2sf.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/map2sf.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/map2sf.cpp +[ 77%] Building CXX object CMakeFiles/gemmi_py.dir/python/write.cpp.o +/usr/bin/c++ -Dgemmi_py_EXPORTS -I/build/reproducible-path/gemmi-0.6.5+ds/include -isystem /usr/include/python3.13 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/write.cpp.o -MF CMakeFiles/gemmi_py.dir/python/write.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/write.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/python/write.cpp In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz.hpp:23, from /build/reproducible-path/gemmi-0.6.5+ds/prog/map2sf.cpp:10: /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ -[ 72%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/mapcoef.cpp.o +[ 79%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/mapcoef.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/mapcoef.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/mapcoef.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/mapcoef.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/mapcoef.cpp In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz.hpp:23, from /build/reproducible-path/gemmi-0.6.5+ds/prog/mapcoef.cpp:11: /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ -[ 75%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/mask.cpp.o +[ 81%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/mask.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/mask.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/mask.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/mask.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/mask.cpp -[ 75%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/merge.cpp.o -/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/merge.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/merge.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/merge.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/merge.cpp In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/ccp4.hpp:19, from /build/reproducible-path/gemmi-0.6.5+ds/prog/mask.cpp:5: /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ -[ 77%] Building CXX object CMakeFiles/gemmi_py.dir/python/sym.cpp.o -/usr/bin/c++ -Dgemmi_py_EXPORTS -I/build/reproducible-path/gemmi-0.6.5+ds/include -isystem /usr/include/python3.13 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/sym.cpp.o -MF CMakeFiles/gemmi_py.dir/python/sym.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/sym.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/python/sym.cpp +[ 81%] Linking CXX shared module gemmi.cpython-313-arm-linux-gnueabihf.so +/usr/bin/cmake -E cmake_link_script CMakeFiles/gemmi_py.dir/link.txt --verbose=1 +[ 81%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/merge.cpp.o +/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/merge.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/merge.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/merge.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/merge.cpp +[ 83%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/mondiff.cpp.o +/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/mondiff.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/mondiff.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/mondiff.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/mondiff.cpp In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz.hpp:23, from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz2cif.hpp:14, from /build/reproducible-path/gemmi-0.6.5+ds/prog/merge.cpp:12: @@ -1590,10 +1636,6 @@ /usr/include/c++/14/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ -[ 79%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/mondiff.cpp.o -/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/mondiff.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/mondiff.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/mondiff.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/mondiff.cpp -[ 79%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/monlib_opt.cpp.o -/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/monlib_opt.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/monlib_opt.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/monlib_opt.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/monlib_opt.cpp In file included from /usr/include/c++/14/bits/stl_tree.h:63, from /usr/include/c++/14/set:62, from /build/reproducible-path/gemmi-0.6.5+ds/prog/mondiff.cpp:7: @@ -1602,50 +1644,11 @@ 2093 | __find_if(_RandomAccessIterator __first, _RandomAccessIterator __last, | ^~~~~~~~~ /usr/include/c++/14/bits/stl_algobase.h:2093:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/14/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/14/bits/stl_algo.h:1876:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1876 | __introsort_loop(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/14/bits/stl_algo.h:1876:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/14/bits/stl_algo.h:1890:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1890 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 83%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/monlib_opt.cpp.o +/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/monlib_opt.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/monlib_opt.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/monlib_opt.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/monlib_opt.cpp /usr/include/c++/14/bits/stl_algobase.h: In function '_RandomAccessIterator std::__find_if(_RandomAccessIterator, _RandomAccessIterator, _Predicate, random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Predicate = __gnu_cxx::__ops::_Iter_pred(const AtomId&, const AtomId&, const AtomId&, const AtomId&):: >]': /usr/include/c++/14/bits/stl_algobase.h:2093:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/14/bits/stl_algobase.h:2093:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -[ 79%] Building CXX object CMakeFiles/gemmi_py.dir/python/topo.cpp.o -/usr/bin/c++ -Dgemmi_py_EXPORTS -I/build/reproducible-path/gemmi-0.6.5+ds/include -isystem /usr/include/python3.13 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/topo.cpp.o -MF CMakeFiles/gemmi_py.dir/python/topo.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/topo.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/python/topo.cpp -In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', - inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/14/bits/stl_algo.h:4772:18, - inlined from 'void gemmi::Intensities::sort()' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/intensit.hpp:95:26, - inlined from 'void {anonymous}::compare_intensities(gemmi::Intensities&, gemmi::Intensities&, bool)' at /build/reproducible-path/gemmi-0.6.5+ds/prog/merge.cpp:176:11, - inlined from 'int merge_main(int, char**)' at /build/reproducible-path/gemmi-0.6.5+ds/prog/merge.cpp:303:26: -/usr/include/c++/14/bits/stl_algo.h:1905:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1905 | std::__introsort_loop(__first, __last, - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ - 1906 | std::__lg(__last - __first) * 2, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1907 | __comp); - | ~~~~~~~ -In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', - inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/14/bits/stl_algo.h:1908:31, - inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/14/bits/stl_algo.h:4772:18, - inlined from 'void gemmi::Intensities::sort()' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/intensit.hpp:95:26, - inlined from 'void {anonymous}::compare_intensities(gemmi::Intensities&, gemmi::Intensities&, bool)' at /build/reproducible-path/gemmi-0.6.5+ds/prog/merge.cpp:176:11, - inlined from 'int merge_main(int, char**)' at /build/reproducible-path/gemmi-0.6.5+ds/prog/merge.cpp:303:26: -/usr/include/c++/14/bits/stl_algo.h:1817:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1817 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/14/bits/stl_algo.h:1822:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1822 | std::__insertion_sort(__first, __last, __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -[ 81%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/mtz.cpp.o -/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -Wno-psabi -MD -MT CMakeFiles/gemmi_prog.dir/prog/mtz.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/mtz.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/mtz.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/mtz.cpp -In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz.hpp:23, - from /build/reproducible-path/gemmi-0.6.5+ds/prog/mtz.cpp:8: -/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] - 37 | typedef std::unique_ptr fileptr_t; - | ^ In function '_Iterator std::__find_if(_Iterator, _Iterator, _Predicate) [with _Iterator = __gnu_cxx::__normal_iterator >; _Predicate = __gnu_cxx::__ops::_Iter_pred(const AtomId&, const AtomId&):: >]', inlined from '_IIter std::find_if(_IIter, _IIter, _Predicate) [with _IIter = __gnu_cxx::__normal_iterator >; _Predicate = gemmi::Restraints::find_bond(const AtomId&, const AtomId&)::]' at /usr/include/c++/14/bits/stl_algo.h:3876:28, inlined from 'std::vector::iterator gemmi::Restraints::find_bond(const T&, const T&) [with T = AtomId]' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/chemcomp.hpp:154:24, @@ -1690,8 +1693,16 @@ | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2147 | std::__iterator_category(__first)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 81%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/mtz2cif.cpp.o -/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/mtz2cif.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/mtz2cif.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/mtz2cif.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/mtz2cif.cpp +[ 85%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/mtz.cpp.o +/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -Wno-psabi -MD -MT CMakeFiles/gemmi_prog.dir/prog/mtz.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/mtz.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/mtz.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/mtz.cpp +/usr/include/c++/14/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/14/bits/stl_algo.h:1876:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1876 | __introsort_loop(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/14/bits/stl_algo.h:1876:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/14/bits/stl_algo.h:1890:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1890 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/map:62, from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/monlib.hpp:9, from /build/reproducible-path/gemmi-0.6.5+ds/prog/monlib_opt.h:5, @@ -1701,13 +1712,34 @@ 2454 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz.hpp:23, - from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz2cif.hpp:14, - from /build/reproducible-path/gemmi-0.6.5+ds/prog/mtz2cif.cpp:8: + from /build/reproducible-path/gemmi-0.6.5+ds/prog/mtz.cpp:8: /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ -[ 83%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/reindex.cpp.o -/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/reindex.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/reindex.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/reindex.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/reindex.cpp +In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', + inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/14/bits/stl_algo.h:4772:18, + inlined from 'void gemmi::Intensities::sort()' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/intensit.hpp:95:26, + inlined from 'void {anonymous}::compare_intensities(gemmi::Intensities&, gemmi::Intensities&, bool)' at /build/reproducible-path/gemmi-0.6.5+ds/prog/merge.cpp:176:11, + inlined from 'int merge_main(int, char**)' at /build/reproducible-path/gemmi-0.6.5+ds/prog/merge.cpp:303:26: +/usr/include/c++/14/bits/stl_algo.h:1905:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1905 | std::__introsort_loop(__first, __last, + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ + 1906 | std::__lg(__last - __first) * 2, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1907 | __comp); + | ~~~~~~~ +In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', + inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/14/bits/stl_algo.h:1908:31, + inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/14/bits/stl_algo.h:4772:18, + inlined from 'void gemmi::Intensities::sort()' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/intensit.hpp:95:26, + inlined from 'void {anonymous}::compare_intensities(gemmi::Intensities&, gemmi::Intensities&, bool)' at /build/reproducible-path/gemmi-0.6.5+ds/prog/merge.cpp:176:11, + inlined from 'int merge_main(int, char**)' at /build/reproducible-path/gemmi-0.6.5+ds/prog/merge.cpp:303:26: +/usr/include/c++/14/bits/stl_algo.h:1817:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1817 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/14/bits/stl_algo.h:1822:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1822 | std::__insertion_sort(__first, __last, __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/map:63: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::iterator std::map<_Key, _Tp, _Compare, _Alloc>::emplace_hint(const_iterator, _Args&& ...) [with _Args = {const std::__cxx11::basic_string, std::allocator >&, gemmi::EnerLib::Atom}; _Key = std::__cxx11::basic_string; _Tp = gemmi::EnerLib::Atom; _Compare = std::less >; _Alloc = std::allocator, gemmi::EnerLib::Atom> >]', inlined from 'std::pair, std::_Select1st >, _Compare, typename __gnu_cxx::__alloc_traits<_Alloc>::rebind >::other>::iterator, bool> std::map<_Key, _Tp, _Compare, _Alloc>::emplace(_Args&& ...) [with _Args = {const std::__cxx11::basic_string, std::allocator >&, gemmi::EnerLib::Atom}; _Key = std::__cxx11::basic_string; _Tp = gemmi::EnerLib::Atom; _Compare = std::less >; _Alloc = std::allocator, gemmi::EnerLib::Atom> >]' at /usr/include/c++/14/bits/stl_map.h:601:22, @@ -1717,26 +1749,32 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ 641 | std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 85%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/mtz2cif.cpp.o +/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/mtz2cif.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/mtz2cif.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/mtz2cif.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/mtz2cif.cpp +[ 87%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/reindex.cpp.o +/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/reindex.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/reindex.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/reindex.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/reindex.cpp +In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz.hpp:23, + from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz2cif.hpp:14, + from /build/reproducible-path/gemmi-0.6.5+ds/prog/mtz2cif.cpp:8: +/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] + 37 | typedef std::unique_ptr fileptr_t; + | ^ In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz.hpp:23, from /build/reproducible-path/gemmi-0.6.5+ds/prog/reindex.cpp:9: /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ -[ 83%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/residues.cpp.o +[ 87%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/residues.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/residues.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/residues.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/residues.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/residues.cpp -[ 85%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/rmsz.cpp.o +[ 89%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/rmsz.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/rmsz.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/rmsz.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/rmsz.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/rmsz.cpp -[ 87%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/sf2map.cpp.o +[ 91%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/sf2map.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/sf2map.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/sf2map.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/sf2map.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/sf2map.cpp In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/ccp4.hpp:19, from /build/reproducible-path/gemmi-0.6.5+ds/prog/sf2map.cpp:6: /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ -[ 89%] Building CXX object CMakeFiles/gemmi_py.dir/python/unitcell.cpp.o -/usr/bin/c++ -Dgemmi_py_EXPORTS -I/build/reproducible-path/gemmi-0.6.5+ds/include -isystem /usr/include/python3.13 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/unitcell.cpp.o -MF CMakeFiles/gemmi_py.dir/python/unitcell.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/unitcell.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/python/unitcell.cpp -[ 89%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/sfcalc.cpp.o -/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/sfcalc.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/sfcalc.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/sfcalc.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/sfcalc.cpp In file included from /usr/include/c++/14/bits/specfun.h:43, from /usr/include/c++/14/cmath:3906, from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/ccp4.hpp:9: @@ -1745,13 +1783,50 @@ 2093 | __find_if(_RandomAccessIterator __first, _RandomAccessIterator __last, | ^~~~~~~~~ /usr/include/c++/14/bits/stl_algobase.h:2093:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +[ 91%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/sfcalc.cpp.o +/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/sfcalc.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/sfcalc.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/sfcalc.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/sfcalc.cpp +[ 93%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/sg.cpp.o +/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/sg.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/sg.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/sg.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/sg.cpp In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/ccp4.hpp:19, from /build/reproducible-path/gemmi-0.6.5+ds/prog/sfcalc.cpp:9: /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ -[ 91%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/sg.cpp.o -/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/sg.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/sg.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/sg.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/sg.cpp +In file included from /usr/include/c++/14/algorithm:61, + from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/symmetry.hpp:15, + from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/ccp4.hpp:17: +In function '_InputIterator std::__find_if_not(_InputIterator, _InputIterator, _Predicate) [with _InputIterator = __gnu_cxx::__normal_iterator >; _Predicate = __gnu_cxx::__ops::_Iter_pred >]', + inlined from '_IIter std::find_if_not(_IIter, _IIter, _Predicate) [with _IIter = __gnu_cxx::__normal_iterator >; _Predicate = gemmi::Selection::matches(const gemmi::Atom&) const::]' at /usr/include/c++/14/bits/stl_algo.h:471:32, + inlined from 'bool std::all_of(_IIter, _IIter, _Predicate) [with _IIter = __gnu_cxx::__normal_iterator >; _Predicate = gemmi::Selection::matches(const gemmi::Atom&) const::]' at /usr/include/c++/14/bits/stl_algo.h:411:40, + inlined from 'bool gemmi::Selection::matches(const gemmi::Atom&) const' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/select.hpp:200:23, + inlined from 'bool gemmi::FilterIterPolicy::matches(std::size_t) const [with Filter = gemmi::Selection; Vector = std::vector; Value = gemmi::Atom]' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/iterator.hpp:191:62, + inlined from 'gemmi::FilterIterPolicy::FilterIterPolicy(const Filter*, Vector*, std::size_t) [with Filter = gemmi::Selection; Vector = std::vector; Value = gemmi::Atom]' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/iterator.hpp:188:44, + inlined from 'gemmi::FilterProxy::iterator gemmi::FilterProxy::begin() [with Filter = gemmi::Selection; Value = gemmi::Atom]' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/iterator.hpp:211:48, + inlined from 'void {anonymous}::transform_sf_to_map(OptParser&)' at /build/reproducible-path/gemmi-0.6.5+ds/prog/sf2map.cpp:84:51: +/usr/include/c++/14/bits/stl_algo.h:112:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 112 | return std::__find_if(__first, __last, + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ + 113 | __gnu_cxx::__ops::__negate(__pred), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 114 | std::__iterator_category(__first)); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In function '_InputIterator std::__find_if_not(_InputIterator, _InputIterator, _Predicate) [with _InputIterator = __gnu_cxx::__normal_iterator >; _Predicate = __gnu_cxx::__ops::_Iter_pred >]', + inlined from '_IIter std::find_if_not(_IIter, _IIter, _Predicate) [with _IIter = __gnu_cxx::__normal_iterator >; _Predicate = gemmi::Selection::matches(const gemmi::Atom&) const::]' at /usr/include/c++/14/bits/stl_algo.h:471:32, + inlined from 'bool std::all_of(_IIter, _IIter, _Predicate) [with _IIter = __gnu_cxx::__normal_iterator >; _Predicate = gemmi::Selection::matches(const gemmi::Atom&) const::]' at /usr/include/c++/14/bits/stl_algo.h:411:40, + inlined from 'bool gemmi::Selection::matches(const gemmi::Atom&) const' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/select.hpp:200:23, + inlined from 'bool gemmi::FilterIterPolicy::matches(std::size_t) const [with Filter = gemmi::Selection; Vector = std::vector; Value = gemmi::Atom]' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/iterator.hpp:191:62, + inlined from 'void gemmi::FilterIterPolicy::increment() [with Filter = gemmi::Selection; Vector = std::vector; Value = gemmi::Atom]' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/iterator.hpp:192:62, + inlined from 'gemmi::BidirIterator& gemmi::BidirIterator::operator++() [with Policy = gemmi::FilterIterPolicy, gemmi::Atom>]' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/iterator.hpp:37:50, + inlined from 'void {anonymous}::transform_sf_to_map(OptParser&)' at /build/reproducible-path/gemmi-0.6.5+ds/prog/sf2map.cpp:84:51: +/usr/include/c++/14/bits/stl_algo.h:112:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 112 | return std::__find_if(__first, __last, + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ + 113 | __gnu_cxx::__ops::__negate(__pred), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 114 | std::__iterator_category(__first)); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 93%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/tags.cpp.o +/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/tags.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/tags.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/tags.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/tags.cpp In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/it92.hpp:16, from /build/reproducible-path/gemmi-0.6.5+ds/prog/sfcalc.cpp:14: /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/formfact.hpp: In instantiation of 'std::pair gemmi::ExpSum::calculate_with_derivative(float) const [with int N = 5]': @@ -1827,43 +1902,6 @@ /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/dencalc.hpp:19:54: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 19 | std::tie(y1, dy) = precal.calculate_with_derivative(x1); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /usr/include/c++/14/algorithm:61, - from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/symmetry.hpp:15, - from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/ccp4.hpp:17: -In function '_InputIterator std::__find_if_not(_InputIterator, _InputIterator, _Predicate) [with _InputIterator = __gnu_cxx::__normal_iterator >; _Predicate = __gnu_cxx::__ops::_Iter_pred >]', - inlined from '_IIter std::find_if_not(_IIter, _IIter, _Predicate) [with _IIter = __gnu_cxx::__normal_iterator >; _Predicate = gemmi::Selection::matches(const gemmi::Atom&) const::]' at /usr/include/c++/14/bits/stl_algo.h:471:32, - inlined from 'bool std::all_of(_IIter, _IIter, _Predicate) [with _IIter = __gnu_cxx::__normal_iterator >; _Predicate = gemmi::Selection::matches(const gemmi::Atom&) const::]' at /usr/include/c++/14/bits/stl_algo.h:411:40, - inlined from 'bool gemmi::Selection::matches(const gemmi::Atom&) const' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/select.hpp:200:23, - inlined from 'bool gemmi::FilterIterPolicy::matches(std::size_t) const [with Filter = gemmi::Selection; Vector = std::vector; Value = gemmi::Atom]' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/iterator.hpp:191:62, - inlined from 'gemmi::FilterIterPolicy::FilterIterPolicy(const Filter*, Vector*, std::size_t) [with Filter = gemmi::Selection; Vector = std::vector; Value = gemmi::Atom]' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/iterator.hpp:188:44, - inlined from 'gemmi::FilterProxy::iterator gemmi::FilterProxy::begin() [with Filter = gemmi::Selection; Value = gemmi::Atom]' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/iterator.hpp:211:48, - inlined from 'void {anonymous}::transform_sf_to_map(OptParser&)' at /build/reproducible-path/gemmi-0.6.5+ds/prog/sf2map.cpp:84:51: -/usr/include/c++/14/bits/stl_algo.h:112:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 112 | return std::__find_if(__first, __last, - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ - 113 | __gnu_cxx::__ops::__negate(__pred), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 114 | std::__iterator_category(__first)); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In function '_InputIterator std::__find_if_not(_InputIterator, _InputIterator, _Predicate) [with _InputIterator = __gnu_cxx::__normal_iterator >; _Predicate = __gnu_cxx::__ops::_Iter_pred >]', - inlined from '_IIter std::find_if_not(_IIter, _IIter, _Predicate) [with _IIter = __gnu_cxx::__normal_iterator >; _Predicate = gemmi::Selection::matches(const gemmi::Atom&) const::]' at /usr/include/c++/14/bits/stl_algo.h:471:32, - inlined from 'bool std::all_of(_IIter, _IIter, _Predicate) [with _IIter = __gnu_cxx::__normal_iterator >; _Predicate = gemmi::Selection::matches(const gemmi::Atom&) const::]' at /usr/include/c++/14/bits/stl_algo.h:411:40, - inlined from 'bool gemmi::Selection::matches(const gemmi::Atom&) const' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/select.hpp:200:23, - inlined from 'bool gemmi::FilterIterPolicy::matches(std::size_t) const [with Filter = gemmi::Selection; Vector = std::vector; Value = gemmi::Atom]' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/iterator.hpp:191:62, - inlined from 'void gemmi::FilterIterPolicy::increment() [with Filter = gemmi::Selection; Vector = std::vector; Value = gemmi::Atom]' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/iterator.hpp:192:62, - inlined from 'gemmi::BidirIterator& gemmi::BidirIterator::operator++() [with Policy = gemmi::FilterIterPolicy, gemmi::Atom>]' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/iterator.hpp:37:50, - inlined from 'void {anonymous}::transform_sf_to_map(OptParser&)' at /build/reproducible-path/gemmi-0.6.5+ds/prog/sf2map.cpp:84:51: -/usr/include/c++/14/bits/stl_algo.h:112:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 112 | return std::__find_if(__first, __last, - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ - 113 | __gnu_cxx::__ops::__negate(__pred), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 114 | std::__iterator_category(__first)); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 93%] Building CXX object CMakeFiles/gemmi_py.dir/python/write.cpp.o -/usr/bin/c++ -Dgemmi_py_EXPORTS -I/build/reproducible-path/gemmi-0.6.5+ds/include -isystem /usr/include/python3.13 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/write.cpp.o -MF CMakeFiles/gemmi_py.dir/python/write.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/write.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/python/write.cpp -[ 93%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/tags.cpp.o -/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/tags.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/tags.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/tags.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/tags.cpp [ 95%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/validate.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/validate.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/validate.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/validate.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/validate.cpp [ 95%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/validate_mon.cpp.o @@ -1934,16 +1972,14 @@ /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 95%] Linking CXX shared module gemmi.cpython-313-arm-linux-gnueabihf.so -/usr/bin/cmake -E cmake_link_script CMakeFiles/gemmi_py.dir/link.txt --verbose=1 [ 97%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/wcn.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/wcn.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/wcn.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/wcn.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/wcn.cpp -[100%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/xds2mtz.cpp.o -/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/xds2mtz.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/xds2mtz.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/xds2mtz.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/xds2mtz.cpp In file included from /build/reproducible-path/gemmi-0.6.5+ds/prog/wcn.cpp:10: /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ +[100%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/xds2mtz.cpp.o +/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/xds2mtz.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/xds2mtz.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/xds2mtz.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/xds2mtz.cpp In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/xds_ascii.hpp:11, from /build/reproducible-path/gemmi-0.6.5+ds/prog/xds2mtz.cpp:8: /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] @@ -1972,13 +2008,13 @@ /usr/include/c++/14/bits/stl_vector.h:1568:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1568 | return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg)); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +./include/gemmi/dencalc.hpp: In member function 'calculate_with_derivative': +./include/gemmi/dencalc.hpp:19:54: note: parameter passing for argument of type 'struct pair' when C++17 is enabled changed to match C++14 in GCC 10.1 [100%] Linking CXX executable gemmi /usr/bin/cmake -E cmake_link_script CMakeFiles/gemmi_prog.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,--dependency-file=CMakeFiles/gemmi_prog.dir/link.d CMakeFiles/gemmi_prog.dir/prog/align.cpp.o CMakeFiles/gemmi_prog.dir/prog/blobs.cpp.o CMakeFiles/gemmi_prog.dir/prog/cif2mtz.cpp.o CMakeFiles/gemmi_prog.dir/prog/cif2json.cpp.o CMakeFiles/gemmi_prog.dir/prog/cifdiff.cpp.o CMakeFiles/gemmi_prog.dir/prog/contact.cpp.o CMakeFiles/gemmi_prog.dir/prog/contents.cpp.o CMakeFiles/gemmi_prog.dir/prog/convert.cpp.o CMakeFiles/gemmi_prog.dir/prog/crd.cpp.o CMakeFiles/gemmi_prog.dir/prog/ecalc.cpp.o CMakeFiles/gemmi_prog.dir/prog/fprime.cpp.o CMakeFiles/gemmi_prog.dir/prog/grep.cpp.o CMakeFiles/gemmi_prog.dir/prog/h.cpp.o CMakeFiles/gemmi_prog.dir/prog/json2cif.cpp.o CMakeFiles/gemmi_prog.dir/prog/main.cpp.o CMakeFiles/gemmi_prog.dir/prog/map.cpp.o CMakeFiles/gemmi_prog.dir/prog/map2sf.cpp.o CMakeFiles/gemmi_prog.dir/prog/mapcoef.cpp.o CMakeFiles/gemmi_prog.dir/prog/mask.cpp.o CMakeFiles/gemmi_prog.dir/prog/merge.cpp.o CMakeFiles/gemmi_prog.dir/prog/mondiff.cpp.o CMakeFiles/gemmi_prog.dir/prog/monlib_opt.cpp.o CMakeFiles/gemmi_prog.dir/prog/mtz.cpp.o CMakeFiles/gemmi_prog.dir/prog/mtz2cif.cpp.o CMakeFiles/gemmi_prog.dir/prog/reindex.cpp.o CMakeFiles/gemmi_prog.dir/prog/residues.cpp.o CMakeFiles/gemmi_prog.dir/prog/rmsz.cpp.o CMakeFiles/gemmi_prog.dir/prog/sf2map.cpp.o CMakeFiles/gemmi_prog.dir/prog/sfcalc.cpp.o CMakeFiles/gemmi_prog.dir/prog/sg.cpp.o CMakeFiles/gemmi_prog.dir/prog/tags.cpp.o CMakeFiles/gemmi_prog.dir/prog/validate.cpp.o CMakeFiles/gemmi_prog.dir/prog/validate_mon.cpp.o CMakeFiles/gemmi_prog.dir/prog/wcn.cpp.o CMakeFiles/gemmi_prog.dir/prog/xds2mtz.cpp.o CMakeFiles/options.dir/prog/options.cpp.o -o gemmi libgemmi_cpp.a /usr/lib/arm-linux-gnueabihf/libz.so make[3]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' [100%] Built target gemmi_prog -./include/gemmi/dencalc.hpp: In member function 'calculate_with_derivative': -./include/gemmi/dencalc.hpp:19:54: note: parameter passing for argument of type 'struct pair' when C++17 is enabled changed to match C++14 in GCC 10.1 /usr/lib/python3/dist-packages/pybind11/include/pybind11/pybind11.h: In member function 'operator()': /usr/lib/python3/dist-packages/pybind11/include/pybind11/pybind11.h:249: note: parameter passing for argument of type 'struct pair' when C++17 is enabled changed to match C++14 in GCC 10.1 249 | rec->impl = [](function_call &call) -> handle { @@ -1992,7 +2028,7 @@ debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds' dh_auto_build -- check - cd obj-arm-linux-gnueabihf && make -j5 "INSTALL=install --strip-program=true" check VERBOSE=1 + cd obj-arm-linux-gnueabihf && make -j4 "INSTALL=install --strip-program=true" check VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' /usr/bin/cmake -S/build/reproducible-path/gemmi-0.6.5+ds -B/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 check @@ -2003,121 +2039,164 @@ make[4]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' make -f CMakeFiles/gemmi_cpp.dir/build.make CMakeFiles/gemmi_cpp.dir/depend make -f CMakeFiles/cpptest.dir/build.make CMakeFiles/cpptest.dir/depend -make -f CMakeFiles/hello.dir/build.make CMakeFiles/hello.dir/depend -make -f CMakeFiles/doc_example.dir/build.make CMakeFiles/doc_example.dir/depend make -f CMakeFiles/options.dir/build.make CMakeFiles/options.dir/depend -make[5]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gemmi-0.6.5+ds /build/reproducible-path/gemmi-0.6.5+ds /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf 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directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' +[ 6%] Building CXX object CMakeFiles/doc_example.dir/docs/code/sym.cpp.o +/usr/bin/c++ -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -UNDEBUG -MD -MT CMakeFiles/doc_example.dir/docs/code/sym.cpp.o -MF CMakeFiles/doc_example.dir/docs/code/sym.cpp.o.d -o CMakeFiles/doc_example.dir/docs/code/sym.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/docs/code/sym.cpp Consolidate compiler generated dependencies of target gemmi_cpp make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' make -f CMakeFiles/gemmi_cpp.dir/build.make CMakeFiles/gemmi_cpp.dir/build -[ 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CMakeFiles/doc_maybegz.dir/build.make CMakeFiles/doc_maybegz.dir/build +make[5]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' +[ 41%] Building CXX object CMakeFiles/doc_maybegz.dir/docs/code/maybegz.cpp.o +/usr/bin/c++ -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/doc_maybegz.dir/docs/code/maybegz.cpp.o -MF CMakeFiles/doc_maybegz.dir/docs/code/maybegz.cpp.o.d -o CMakeFiles/doc_maybegz.dir/docs/code/maybegz.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/docs/code/maybegz.cpp +[ 43%] Linking CXX executable doc_example +/usr/bin/cmake -E cmake_link_script CMakeFiles/doc_example.dir/link.txt --verbose=1 +[ 45%] Linking CXX executable doc_example2 +/usr/bin/cmake -E cmake_link_script CMakeFiles/doc_example2.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,--dependency-file=CMakeFiles/doc_example.dir/link.d CMakeFiles/doc_example.dir/docs/code/sym.cpp.o CMakeFiles/doc_example.dir/docs/code/elem.cpp.o CMakeFiles/doc_example.dir/docs/code/resinfo.cpp.o CMakeFiles/doc_example.dir/docs/code/cell.cpp.o CMakeFiles/doc_example.dir/src/resinfo.cpp.o -o doc_example +make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' +[ 45%] Built target doc_example +make -f CMakeFiles/doc_newmtz.dir/build.make CMakeFiles/doc_newmtz.dir/depend +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,--dependency-file=CMakeFiles/doc_example2.dir/link.d CMakeFiles/doc_example2.dir/docs/code/cif_cc.cpp.o -o doc_example2 +make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' +[ 45%] Built target doc_example2 make -f CMakeFiles/test_disulf.dir/build.make CMakeFiles/test_disulf.dir/depend make[5]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' cd /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gemmi-0.6.5+ds /build/reproducible-path/gemmi-0.6.5+ds /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf 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'/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' +[ 47%] Building CXX object CMakeFiles/test_disulf.dir/tests/disulf.cpp.o /usr/bin/c++ -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/test_disulf.dir/tests/disulf.cpp.o -MF CMakeFiles/test_disulf.dir/tests/disulf.cpp.o.d -o CMakeFiles/test_disulf.dir/tests/disulf.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/tests/disulf.cpp -[ 45%] Linking CXX executable doc_example -/usr/bin/cmake -E cmake_link_script CMakeFiles/doc_example.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,--dependency-file=CMakeFiles/doc_example.dir/link.d CMakeFiles/doc_example.dir/docs/code/sym.cpp.o CMakeFiles/doc_example.dir/docs/code/elem.cpp.o CMakeFiles/doc_example.dir/docs/code/resinfo.cpp.o CMakeFiles/doc_example.dir/docs/code/cell.cpp.o CMakeFiles/doc_example.dir/src/resinfo.cpp.o -o doc_example make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' -[ 45%] Built target doc_example +make -f CMakeFiles/doc_newmtz.dir/build.make CMakeFiles/doc_newmtz.dir/build +make[5]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' +[ 47%] Building CXX object CMakeFiles/doc_newmtz.dir/docs/code/newmtz.cpp.o +/usr/bin/c++ -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/doc_newmtz.dir/docs/code/newmtz.cpp.o -MF CMakeFiles/doc_newmtz.dir/docs/code/newmtz.cpp.o.d -o CMakeFiles/doc_newmtz.dir/docs/code/newmtz.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/docs/code/newmtz.cpp +In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz.hpp:23, + from /build/reproducible-path/gemmi-0.6.5+ds/docs/code/newmtz.cpp:1: +/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] + 37 | typedef std::unique_ptr fileptr_t; + | ^ +In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/json.hpp:10, + from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mmread.hpp:12, + from /build/reproducible-path/gemmi-0.6.5+ds/docs/code/maybegz.cpp:2: +/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] + 37 | typedef std::unique_ptr fileptr_t; + | ^ +In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/json.hpp:10, + from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mmread.hpp:12, + from /build/reproducible-path/gemmi-0.6.5+ds/tests/disulf.cpp:11: +/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] + 37 | typedef std::unique_ptr fileptr_t; + | ^ +[ 50%] Building CXX object CMakeFiles/cpptest.dir/tests/cif.cpp.o +/usr/bin/c++ -DUSE_STD_SNPRINTF=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/cpptest.dir/tests/cif.cpp.o -MF CMakeFiles/cpptest.dir/tests/cif.cpp.o.d -o CMakeFiles/cpptest.dir/tests/cif.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/tests/cif.cpp +[ 52%] Linking CXX executable doc_newmtz +/usr/bin/cmake -E cmake_link_script CMakeFiles/doc_newmtz.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,--dependency-file=CMakeFiles/doc_newmtz.dir/link.d CMakeFiles/doc_newmtz.dir/docs/code/newmtz.cpp.o -o doc_newmtz libgemmi_cpp.a /usr/lib/arm-linux-gnueabihf/libz.so +make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' +[ 52%] Built target doc_newmtz make -f CMakeFiles/check_conn.dir/build.make CMakeFiles/check_conn.dir/depend make[5]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' cd /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gemmi-0.6.5+ds /build/reproducible-path/gemmi-0.6.5+ds /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf/CMakeFiles/check_conn.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' make -f CMakeFiles/check_conn.dir/build.make CMakeFiles/check_conn.dir/build make[5]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' -[ 45%] Building CXX object CMakeFiles/check_conn.dir/examples/check_conn.cpp.o +[ 52%] Building CXX object CMakeFiles/check_conn.dir/examples/check_conn.cpp.o /usr/bin/c++ -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/check_conn.dir/examples/check_conn.cpp.o -MF CMakeFiles/check_conn.dir/examples/check_conn.cpp.o.d -o CMakeFiles/check_conn.dir/examples/check_conn.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/examples/check_conn.cpp -[ 47%] Linking CXX executable doc_example2 -/usr/bin/cmake -E cmake_link_script CMakeFiles/doc_example2.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,--dependency-file=CMakeFiles/doc_example2.dir/link.d CMakeFiles/doc_example2.dir/docs/code/cif_cc.cpp.o -o doc_example2 +[ 52%] Linking CXX executable cpptest +/usr/bin/cmake -E cmake_link_script CMakeFiles/cpptest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,--dependency-file=CMakeFiles/cpptest.dir/link.d CMakeFiles/cpptest.dir/tests/main.cpp.o CMakeFiles/cpptest.dir/tests/cif.cpp.o -o cpptest make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' -[ 47%] Built target doc_example2 +[ 52%] Built target cpptest make -f CMakeFiles/gemmi_prog.dir/build.make CMakeFiles/gemmi_prog.dir/depend make[5]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' cd /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gemmi-0.6.5+ds /build/reproducible-path/gemmi-0.6.5+ds /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf/CMakeFiles/gemmi_prog.dir/DependInfo.cmake "--color=" @@ -2163,68 +2242,25 @@ make[5]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' make[5]: Nothing to be done for 'CMakeFiles/gemmi_prog.dir/build'. make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' -[ 89%] Built target gemmi_prog -make -f CMakeFiles/doc_maybegz.dir/build.make CMakeFiles/doc_maybegz.dir/depend -make[5]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gemmi-0.6.5+ds /build/reproducible-path/gemmi-0.6.5+ds /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf/CMakeFiles/doc_maybegz.dir/DependInfo.cmake "--color=" -make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' -make -f CMakeFiles/doc_maybegz.dir/build.make CMakeFiles/doc_maybegz.dir/build -make[5]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' -[ 91%] Building CXX object CMakeFiles/doc_maybegz.dir/docs/code/maybegz.cpp.o -/usr/bin/c++ -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/doc_maybegz.dir/docs/code/maybegz.cpp.o -MF CMakeFiles/doc_maybegz.dir/docs/code/maybegz.cpp.o.d -o CMakeFiles/doc_maybegz.dir/docs/code/maybegz.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/docs/code/maybegz.cpp -In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/json.hpp:10, - from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mmread.hpp:12, - from /build/reproducible-path/gemmi-0.6.5+ds/tests/disulf.cpp:11: -/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] - 37 | typedef std::unique_ptr fileptr_t; - | ^ -[ 91%] Building CXX object CMakeFiles/doc_maybegz.dir/docs/code/mutate.cpp.o +[ 93%] Built target gemmi_prog +[ 93%] Building CXX object CMakeFiles/doc_maybegz.dir/docs/code/mutate.cpp.o /usr/bin/c++ -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/doc_maybegz.dir/docs/code/mutate.cpp.o -MF CMakeFiles/doc_maybegz.dir/docs/code/mutate.cpp.o.d -o CMakeFiles/doc_maybegz.dir/docs/code/mutate.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/docs/code/mutate.cpp -In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/json.hpp:10, - from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mmread.hpp:12, - from /build/reproducible-path/gemmi-0.6.5+ds/docs/code/maybegz.cpp:2: -/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] - 37 | typedef std::unique_ptr fileptr_t; - | ^ -[ 91%] Linking CXX executable cpptest -make -f CMakeFiles/doc_newmtz.dir/build.make CMakeFiles/doc_newmtz.dir/depend -/usr/bin/cmake -E cmake_link_script CMakeFiles/cpptest.dir/link.txt --verbose=1 -make[5]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gemmi-0.6.5+ds /build/reproducible-path/gemmi-0.6.5+ds /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf/CMakeFiles/doc_newmtz.dir/DependInfo.cmake "--color=" -make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' -make -f CMakeFiles/doc_newmtz.dir/build.make CMakeFiles/doc_newmtz.dir/build -make[5]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' -[ 91%] Building CXX object CMakeFiles/doc_newmtz.dir/docs/code/newmtz.cpp.o -/usr/bin/c++ -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/doc_newmtz.dir/docs/code/newmtz.cpp.o -MF CMakeFiles/doc_newmtz.dir/docs/code/newmtz.cpp.o.d -o CMakeFiles/doc_newmtz.dir/docs/code/newmtz.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/docs/code/newmtz.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,--dependency-file=CMakeFiles/cpptest.dir/link.d CMakeFiles/cpptest.dir/tests/main.cpp.o CMakeFiles/cpptest.dir/tests/cif.cpp.o -o cpptest +[ 95%] Linking CXX executable check_conn +/usr/bin/cmake -E cmake_link_script CMakeFiles/check_conn.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,--dependency-file=CMakeFiles/check_conn.dir/link.d CMakeFiles/check_conn.dir/examples/check_conn.cpp.o -o check_conn libgemmi_cpp.a /usr/lib/arm-linux-gnueabihf/libz.so make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' -[ 91%] Built target cpptest +[ 95%] Built target check_conn make -f CMakeFiles/print-version.dir/build.make CMakeFiles/print-version.dir/depend make[5]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' cd /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gemmi-0.6.5+ds /build/reproducible-path/gemmi-0.6.5+ds /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf/CMakeFiles/print-version.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' make -f CMakeFiles/print-version.dir/build.make CMakeFiles/print-version.dir/build make[5]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' -[ 91%] gemmi --version +[ 95%] gemmi --version cd /build/reproducible-path/gemmi-0.6.5+ds && /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf/gemmi --version gemmi 0.6.5 make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' -[ 91%] Built target print-version -In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz.hpp:23, - from /build/reproducible-path/gemmi-0.6.5+ds/docs/code/newmtz.cpp:1: -/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] - 37 | typedef std::unique_ptr fileptr_t; - | ^ -[ 93%] Linking CXX executable check_conn -/usr/bin/cmake -E cmake_link_script CMakeFiles/check_conn.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,--dependency-file=CMakeFiles/check_conn.dir/link.d CMakeFiles/check_conn.dir/examples/check_conn.cpp.o -o check_conn libgemmi_cpp.a /usr/lib/arm-linux-gnueabihf/libz.so -make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' -[ 93%] Built target check_conn -[ 95%] Linking CXX executable doc_newmtz -/usr/bin/cmake -E cmake_link_script CMakeFiles/doc_newmtz.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,--dependency-file=CMakeFiles/doc_newmtz.dir/link.d CMakeFiles/doc_newmtz.dir/docs/code/newmtz.cpp.o -o doc_newmtz libgemmi_cpp.a /usr/lib/arm-linux-gnueabihf/libz.so -make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' -[ 95%] Built target doc_newmtz +[ 95%] Built target print-version [ 97%] Linking CXX executable doc_maybegz /usr/bin/cmake -E cmake_link_script CMakeFiles/doc_maybegz.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,--dependency-file=CMakeFiles/doc_maybegz.dir/link.d CMakeFiles/doc_maybegz.dir/docs/code/maybegz.cpp.o CMakeFiles/doc_maybegz.dir/docs/code/mutate.cpp.o -o doc_maybegz libgemmi_cpp.a /usr/lib/arm-linux-gnueabihf/libz.so @@ -2249,7 +2285,7 @@ 100% tests passed, 0 tests failed out of 1 -Total Test time (real) = 0.03 sec +Total Test time (real) = 0.01 sec make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' [100%] Built target check make[4]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' @@ -2278,13 +2314,13 @@ SKIPPED [1] tests/test_seq.py:146: BioPython not installed. SKIPPED [1] tests/test_seq.py:105: BioPython not installed. SKIPPED [1] tests/test_seq.py:114: BioPython not installed. -172 passed, 17 skipped, 2 deselected in 8.02s +172 passed, 17 skipped, 2 deselected in 3.45s make[1]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=cmake dh_prep -O--buildsystem=cmake dh_auto_install -O--buildsystem=cmake - cd obj-arm-linux-gnueabihf && make -j5 install DESTDIR=/build/reproducible-path/gemmi-0.6.5\+ds/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd obj-arm-linux-gnueabihf && make -j4 install DESTDIR=/build/reproducible-path/gemmi-0.6.5\+ds/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' /usr/bin/cmake -S/build/reproducible-path/gemmi-0.6.5+ds -B/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -2296,110 +2332,110 @@ -- Install configuration: "None" -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/bin/gemmi -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/addends.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/smcif.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/twin.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/binner.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/asudata.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/seqid.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/it92.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/ddl.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/to_cif.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/intensit.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/symmetry.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/contact.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/model.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/blob.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/neutron92.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/asumask.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/to_chemcomp.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/serialize.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/ccp4.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/resinfo.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/calculate.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/chemcomp.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/fail.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/fileutil.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/version.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/formfact.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/fprime.hpp --- Installing: 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/build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/c4322.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/read_map.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/formfact.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/mmcif.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/mmread_gz.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/monlib.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/remarks.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/metadata.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/to_json.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/third_party -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/third_party/fast_float.h -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/third_party/pocketfft_hdronly.h -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/third_party/tinydir.h --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/topo.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/align.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/elem.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/neighbor.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/floodfill.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/linkhunt.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/modify.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/atox.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/cif2mtz.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/fprime.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/read_cif.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/it92.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/ddl.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/unitcell.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/neighbor.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/polyheur.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/json.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/pdb_id.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/to_mmcif.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/numb.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/mtz.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/mmread.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/dirwalk.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/iterator.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/sprintf.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/to_cif.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/mmcif_impl.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/reciproc.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/select.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/ecalc.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/assembly.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/cifdoc.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/atof.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/resinfo.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/c4322.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/pdb.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/twin.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/serialize.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/gz.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/seqtools.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/math.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/to_chemcomp.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/input.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/fstream.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/align.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/eig3.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/solmask.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/blob.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/span.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/mtz2cif.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/topo.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/mmdb.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/addends.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/fileutil.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/fail.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/grid.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/linkhunt.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/modify.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/elem.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/bessel.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/seqtools.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/cif.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/chemcomp_xyz.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/metadata.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/unitcell.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/polyheur.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/qcp.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/math.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/interop.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/scaling.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/to_pdb.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/mtz.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/mtz2cif.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/mmcif.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/enumstr.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/intensit.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/pirfasta.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/levmar.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/ecalc.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/iterator.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/to_json.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/input.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/atox.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/seqalign.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/asumask.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/bond_idx.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/riding_h.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/dencalc.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/neutron92.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/recgrid.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/xds_ascii.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/sfcalc.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/fourier.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/mmread.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/pdb.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/cellred.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/utf.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/refln.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/enumstr.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/crd.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/arm-linux-gnueabihf/libgemmi_cpp.a -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/arm-linux-gnueabihf/cmake/gemmi/gemmi-targets.cmake -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/arm-linux-gnueabihf/cmake/gemmi/gemmi-targets-none.cmake @@ -2407,30 +2443,30 @@ -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/arm-linux-gnueabihf/cmake/gemmi/gemmi-config-version.cmake -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi.cpython-313-arm-linux-gnueabihf.so -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/merge_mtz_mmcif.py --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/multiproc.py --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/ccd_subgraph.py --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/refln-stats.py -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/rama_plot.py --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/monomers.py +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/mtz_i_sigi.py +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/long_geom.py -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/from_json.py --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/maskcheck.py --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/maskdiff.py -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/cif_i_sigi.py +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/multiproc.py +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/merge_mtz_mmcif.py +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/hello.py +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/refln-stats.py -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/weight.py --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/col_order.py --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/mtz_i_sigi.py +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/patterson_slice.py -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/simple_search.py --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/long_geom.py --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/aafreq.py --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/mtrix_iso.py --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/map2mtz.py --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/ccd_gi.py --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/matthews.py -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/rama_gather.py +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/mtrix_iso.py +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/maskcheck.py +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/col_order.py +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/monomers.py -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/sub_ccd.py --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/patterson_slice.py --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/hello.py +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/matthews.py +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/ccd_gi.py +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/ccd_subgraph.py +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/map2mtz.py +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/maskdiff.py +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/aafreq.py make[1]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' dh_install -O--buildsystem=cmake dh_installdocs -O--buildsystem=cmake @@ -2471,9 +2507,9 @@ dpkg-gencontrol: warning: Provides field of package python3-gemmi: substitution variable ${python3:Provides} used, but is not defined dh_md5sums -O--buildsystem=cmake dh_builddeb -O--buildsystem=cmake +dpkg-deb: building package 'gemmi' in '../gemmi_0.6.5+ds-3_armhf.deb'. dpkg-deb: building package 'gemmi-dbgsym' in '../gemmi-dbgsym_0.6.5+ds-3_armhf.deb'. dpkg-deb: building package 'gemmi-dev' in '../gemmi-dev_0.6.5+ds-3_armhf.deb'. -dpkg-deb: building package 'gemmi' in '../gemmi_0.6.5+ds-3_armhf.deb'. dpkg-deb: building package 'python3-gemmi' in '../python3-gemmi_0.6.5+ds-3_armhf.deb'. dpkg-genbuildinfo --build=binary -O../gemmi_0.6.5+ds-3_armhf.buildinfo dpkg-genchanges --build=binary -O../gemmi_0.6.5+ds-3_armhf.changes @@ -2482,12 +2518,14 @@ 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/14933/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/14933/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/29972 and its subdirectories -I: Current time: Thu Feb 6 22:12:20 -12 2025 -I: pbuilder-time-stamp: 1738923140 +I: removing directory /srv/workspace/pbuilder/14933 and its subdirectories +I: Current time: Sat Feb 8 00:34:12 +14 2025 +I: pbuilder-time-stamp: 1738924452