Diff of the two buildlogs: -- --- b1/build.log 2025-02-04 18:17:04.893501558 +0000 +++ b2/build.log 2025-02-04 18:24:45.056849680 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Mar 9 12:35:57 -12 2026 -I: pbuilder-time-stamp: 1773102957 +I: Current time: Wed Feb 5 08:17:08 +14 2025 +I: pbuilder-time-stamp: 1738693028 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-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/2121061/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/4103583/tmp/hooks/D01_modify_environment starting +debug: Running on codethink04-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Feb 4 18:17 /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/4103583/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/4103583/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='arm64' - DEBIAN_FRONTEND='noninteractive' + 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]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='a017b1de05cb4e5b9d06274adc2c732e' - 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='2121061' - PS1='# ' - PS2='> ' + INVOCATION_ID=6948956be9ef4200a390e96ea24c5696 + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=4103583 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.QLsf0LRP/pbuilderrc_d1LH --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.QLsf0LRP/b1 --logfile b1/build.log gemmi_0.6.5+ds-3.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.QLsf0LRP/pbuilderrc_Qcj6 --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.QLsf0LRP/b2 --logfile b2/build.log gemmi_0.6.5+ds-3.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink03-arm64 6.1.0-30-cloud-arm64 #1 SMP Debian 6.1.124-1 (2025-01-12) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-30-cloud-arm64 #1 SMP Debian 6.1.124-1 (2025-01-12) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2121061/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/4103583/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -240,7 +272,7 @@ Get: 108 http://deb.debian.org/debian unstable/main arm64 python3-pybind11 all 2.13.6-2 [215 kB] Get: 109 http://deb.debian.org/debian unstable/main arm64 python3-pytest all 8.3.4-1 [250 kB] Get: 110 http://deb.debian.org/debian unstable/main arm64 tao-pegtl-dev all 3.2.7-1 [69.4 kB] -Fetched 62.6 MB in 0s (178 MB/s) +Fetched 62.6 MB in 1s (106 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 ... 19920 files and directories currently installed.) @@ -605,8 +637,8 @@ Setting up tzdata (2025a-1) ... Current default time zone: 'Etc/UTC' -Local time is now: Tue Mar 10 00:36:25 UTC 2026. -Universal Time is now: Tue Mar 10 00:36:25 UTC 2026. +Local time is now: Tue Feb 4 18:18:01 UTC 2025. +Universal Time is now: Tue Feb 4 18:18:01 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... @@ -709,7 +741,11 @@ 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/4103583/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/4103583/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 @@ -755,8 +791,8 @@ -- 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 (3.6s) --- Generating done (0.1s) +-- Configuring done (6.8s) +-- Generating done (0.2s) CMake Warning: Manually-specified variables were not used by the project: @@ -775,36 +811,36 @@ make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu' 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-aarch64-linux-gnu' -cd /build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu && /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-aarch64-linux-gnu /build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu /build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu/CMakeFiles/options.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu' +make -f CMakeFiles/options.dir/build.make CMakeFiles/options.dir/depend cd /build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu && /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-aarch64-linux-gnu /build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu /build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu/CMakeFiles/gemmi_cpp.dir/DependInfo.cmake "--color=" -make[3]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu' -make -f CMakeFiles/options.dir/build.make CMakeFiles/options.dir/build make[3]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu' +cd /build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu && /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-aarch64-linux-gnu /build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu /build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu/CMakeFiles/options.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu' make -f CMakeFiles/gemmi_cpp.dir/build.make CMakeFiles/gemmi_cpp.dir/build +make[3]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu' +make[3]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu' +make -f CMakeFiles/options.dir/build.make CMakeFiles/options.dir/build make[3]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu' -[ 2%] Building CXX object CMakeFiles/options.dir/prog/options.cpp.o +[ 2%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/align.cpp.o +[ 4%] Building CXX object CMakeFiles/options.dir/prog/options.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 -mbranch-protection=standard -fexcess-precision=fast -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 -[ 2%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/assembly.cpp.o -[ 4%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/align.cpp.o -[ 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 -mbranch-protection=standard -fexcess-precision=fast -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 +[ 4%] 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 -mbranch-protection=standard -fexcess-precision=fast -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 +[ 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 -mbranch-protection=standard -fexcess-precision=fast -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/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 -mbranch-protection=standard -fexcess-precision=fast -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/crd.cpp.o [ 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 -mbranch-protection=standard -fexcess-precision=fast -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 +/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 -mbranch-protection=standard -fexcess-precision=fast -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 [ 10%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/eig3.cpp.o [ 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 -mbranch-protection=standard 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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 -mbranch-protection=standard -fexcess-precision=fast -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 /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 -mbranch-protection=standard 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/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 -mbranch-protection=standard -fexcess-precision=fast -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 [ 14%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/mmcif.cpp.o [ 14%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/mmread_gz.cpp.o @@ -818,13 +854,13 @@ /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; | ^ -[ 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 -mbranch-protection=standard -fexcess-precision=fast -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 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; | ^ +[ 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 -mbranch-protection=standard -fexcess-precision=fast -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 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/read_cif.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/read_cif.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/read_cif.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/read_cif.cpp -make[3]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu' -[ 20%] Built target options [ 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 -mbranch-protection=standard -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 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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, @@ -925,41 +961,41 @@ make[3]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu' [ 31%] Built target gemmi_cpp 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-aarch64-linux-gnu' +make -f CMakeFiles/gemmi_py.dir/build.make CMakeFiles/gemmi_py.dir/depend cd /build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu && /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-aarch64-linux-gnu /build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu 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-ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fexcess-precision=fast -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 -/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 -mbranch-protection=standard -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects 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43%] 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 -mbranch-protection=standard -fexcess-precision=fast -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/cif.cpp.o -MF CMakeFiles/gemmi_py.dir/python/cif.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/cif.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/python/cif.cpp -/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 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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 +/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 -mbranch-protection=standard -fexcess-precision=fast -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 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] @@ -971,159 +1007,223 @@ /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_prog.dir/prog/contents.cpp.o +[ 45%] 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 -mbranch-protection=standard -fexcess-precision=fast -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 +[ 47%] 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 -mbranch-protection=standard -fexcess-precision=fast -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_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 -mbranch-protection=standard -fexcess-precision=fast -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 -[ 47%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/convert.cpp.o +[ 50%] 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 -mbranch-protection=standard -fexcess-precision=fast -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 -[ 50%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/crd.cpp.o +[ 50%] 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 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/build/reproducible-path/gemmi-0.6.5+ds/python/custom.cpp -[ 50%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/ecalc.cpp.o +[ 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 -mbranch-protection=standard -fexcess-precision=fast -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 +[ 54%] 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 -mbranch-protection=standard -fexcess-precision=fast -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 -[ 52%] 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 -mbranch-protection=standard -fexcess-precision=fast -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 -[ 54%] 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 -mbranch-protection=standard -fexcess-precision=fast -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 -[ 54%] 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 -mbranch-protection=standard -fexcess-precision=fast -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 +[ 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 -mbranch-protection=standard -fexcess-precision=fast -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 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] 37 | typedef std::unique_ptr fileptr_t; | ^ -[ 56%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/grep.cpp.o +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; + | ^ +[ 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 -mbranch-protection=standard -fexcess-precision=fast -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 +[ 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 -mbranch-protection=standard -fexcess-precision=fast -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 +[ 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 -mbranch-protection=standard -fexcess-precision=fast -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 +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; + | ^ +[ 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 -mbranch-protection=standard -fexcess-precision=fast -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 -[ 56%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/h.cpp.o +[ 60%] 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 -mbranch-protection=standard -fexcess-precision=fast -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 -[ 58%] 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 -mbranch-protection=standard -fexcess-precision=fast -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 -[ 60%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/json2cif.cpp.o +[ 62%] 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 -mbranch-protection=standard -fexcess-precision=fast -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 -[ 60%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/main.cpp.o +[ 62%] 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 -mbranch-protection=standard -fexcess-precision=fast -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 -[ 60%] 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 -mbranch-protection=standard -fexcess-precision=fast -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 -[ 62%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/map.cpp.o +[ 64%] 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 -mbranch-protection=standard -fexcess-precision=fast -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; | ^ -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; - | ^ -[ 62%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/map2sf.cpp.o +[ 64%] 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 -mbranch-protection=standard -fexcess-precision=fast -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 -[ 64%] 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 -mbranch-protection=standard -fexcess-precision=fast -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 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; | ^ -[ 66%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/mapcoef.cpp.o +[ 66%] 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 -mbranch-protection=standard -fexcess-precision=fast -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 +[ 68%] 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 -mbranch-protection=standard -fexcess-precision=fast -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 -[ 68%] 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 -mbranch-protection=standard -fexcess-precision=fast -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 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; | ^ -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: +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; | ^ -[ 68%] 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 -mbranch-protection=standard -fexcess-precision=fast -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 -[ 68%] 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 -mbranch-protection=standard -fexcess-precision=fast -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/mtz.hpp:23, - from /build/reproducible-path/gemmi-0.6.5+ds/python/mtz.cpp:3: +[ 70%] 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 -mbranch-protection=standard -fexcess-precision=fast -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 +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; | ^ -[ 70%] 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 -mbranch-protection=standard -fexcess-precision=fast -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 +[ 70%] 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 -mbranch-protection=standard -fexcess-precision=fast -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/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: /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_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 -mbranch-protection=standard -fexcess-precision=fast -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 -[ 75%] Building CXX object CMakeFiles/gemmi_py.dir/python/recgrid.cpp.o +[ 72%] 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 -mbranch-protection=standard -fexcess-precision=fast -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 -[ 75%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/monlib_opt.cpp.o +[ 72%] 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 -mbranch-protection=standard -fexcess-precision=fast -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 +[ 75%] 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 -mbranch-protection=standard -fexcess-precision=fast -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 +[ 75%] 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 -mbranch-protection=standard -fexcess-precision=fast -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 +[ 77%] 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 -mbranch-protection=standard -fexcess-precision=fast -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 +[ 77%] 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 -mbranch-protection=standard -fexcess-precision=fast -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 -[ 77%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/mtz.cpp.o +[ 79%] 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 -mbranch-protection=standard -fexcess-precision=fast -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/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; - | ^ +[ 81%] 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 -mbranch-protection=standard -fexcess-precision=fast -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/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]': +/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/dencalc.hpp:19:54: required from 'Real gemmi::determine_cutoff_radius(Real, const ExpSum&, Real) [with int N = 5; Real = float]' + 19 | std::tie(y1, dy) = precal.calculate_with_derivative(x1); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/dencalc.hpp:136:35: required from 'gemmi::DensityCalculator::CReal gemmi::DensityCalculator::estimate_radius(const gemmi::ExpSum&, CReal) const [with int N = 5; Table = gemmi::IT92; GReal = float; CReal = float; typename Table::Coef::coef_type = float; typename Table::Coef = gemmi::GaussianCoef<4, 1, float>]' + 136 | return determine_cutoff_radius(x1, precal, (CReal)cutoff); + | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/gemmi-0.6.5+ds/python/sf.cpp:60:36: required from 'void add_dencalc(pybind11::module&, const char*) [with Table = gemmi::IT92; pybind11::module = pybind11::module_]' + 60 | return self.estimate_radius(precal, bb); + | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +/build/reproducible-path/gemmi-0.6.5+ds/python/sf.cpp:83:20: required from here + 83 | add_dencalc(m, "DensityCalculatorX"); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +/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 { + | ^~~~~~~~~~~~~~~~~~~~~~~~~ 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; | ^ -[ 77%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/mtz2cif.cpp.o +/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/formfact.hpp: In instantiation of 'std::pair<_ForwardIterator, _ForwardIterator> gemmi::ExpSum::calculate_with_derivative(Real) const [with int N = 1; Real = double]': +/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/dencalc.hpp:19:54: required from 'Real gemmi::determine_cutoff_radius(Real, const ExpSum&, Real) [with int N = 1; Real = double]' + 19 | std::tie(y1, dy) = precal.calculate_with_derivative(x1); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/dencalc.hpp:136:35: required from 'gemmi::DensityCalculator::CReal gemmi::DensityCalculator::estimate_radius(const gemmi::ExpSum&, CReal) const [with int N = 1; Table = gemmi::Neutron92; GReal = float; CReal = double; typename Table::Coef::coef_type = double; typename Table::Coef = gemmi::GaussianCoef<0, 1, double>]' + 136 | return determine_cutoff_radius(x1, precal, (CReal)cutoff); + | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/gemmi-0.6.5+ds/python/sf.cpp:60:36: required from 'void add_dencalc(pybind11::module&, const char*) [with Table = gemmi::Neutron92; pybind11::module = pybind11::module_]' + 60 | return self.estimate_radius(precal, bb); + | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +/build/reproducible-path/gemmi-0.6.5+ds/python/sf.cpp:85:25: required from here + 85 | add_dencalc(m, "DensityCalculatorN"); + | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/formfact.hpp:48:24: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 48 | std::pair calculate_with_derivative(Real r) const { + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +/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 = 1]': +/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/dencalc.hpp:19:54: required from 'Real gemmi::determine_cutoff_radius(Real, const ExpSum&, Real) [with int N = 1; Real = float]' + 19 | std::tie(y1, dy) = precal.calculate_with_derivative(x1); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/dencalc.hpp:136:35: required from 'gemmi::DensityCalculator::CReal gemmi::DensityCalculator::estimate_radius(const gemmi::ExpSum&, CReal) const [with int N = 1; Table = gemmi::IT92; GReal = float; CReal = float; typename Table::Coef::coef_type = float; typename Table::Coef = gemmi::GaussianCoef<4, 1, float>]' + 136 | return determine_cutoff_radius(x1, precal, (CReal)cutoff); + | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/dencalc.hpp:149:37: required from 'void gemmi::DensityCalculator::do_add_atom_density_to_grid(const gemmi::Atom&, const Coef&, float) [with Coef = gemmi::GaussianCoef<0, 1, float>; Table = gemmi::IT92; GReal = float]' + 149 | CReal radius = estimate_radius(precal, b); + | ~~~~~~~~~~~~~~~^~~~~~~~~~~ +/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/dencalc.hpp:128:32: required from 'void gemmi::DensityCalculator::add_c_contribution_to_grid(const gemmi::Atom&, float) [with Table = gemmi::IT92; GReal = float]' + 128 | do_add_atom_density_to_grid(atom, GaussianCoef<0, 1, CReal>{0}, c); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/gemmi-0.6.5+ds/python/sf.cpp:47:40: required from 'void add_dencalc(pybind11::module&, const char*) [with Table = gemmi::IT92; pybind11::module = pybind11::module_]' + 47 | .def("add_c_contribution_to_grid", &DenCalc::add_c_contribution_to_grid) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/gemmi-0.6.5+ds/python/sf.cpp:83:20: required from here + 83 | add_dencalc(m, "DensityCalculatorX"); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +/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 { + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +[ 81%] 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 -mbranch-protection=standard -fexcess-precision=fast -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 +[ 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 -mbranch-protection=standard -fexcess-precision=fast -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 -[ 79%] 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 -mbranch-protection=standard -fexcess-precision=fast -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 +[ 83%] 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 -mbranch-protection=standard -fexcess-precision=fast -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 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; | ^ +[ 85%] 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 -mbranch-protection=standard -fexcess-precision=fast -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/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; | ^ -[ 79%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/residues.cpp.o +[ 85%] 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 -mbranch-protection=standard -fexcess-precision=fast -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 -[ 79%] 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 -mbranch-protection=standard -fexcess-precision=fast -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 -[ 81%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/rmsz.cpp.o +[ 87%] 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 -mbranch-protection=standard -fexcess-precision=fast -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 +[ 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 -mbranch-protection=standard -fexcess-precision=fast -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 -[ 83%] 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 -mbranch-protection=standard -fexcess-precision=fast -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 -[ 85%] 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 -mbranch-protection=standard -fexcess-precision=fast -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; | ^ -[ 85%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/sfcalc.cpp.o +[ 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 -mbranch-protection=standard -fexcess-precision=fast -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 -[ 85%] 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 -mbranch-protection=standard -fexcess-precision=fast -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 -[ 87%] 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 -mbranch-protection=standard -fexcess-precision=fast -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 +[ 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 -mbranch-protection=standard -fexcess-precision=fast -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 +[ 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 -mbranch-protection=standard -fexcess-precision=fast -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/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; | ^ -[ 89%] 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 -mbranch-protection=standard -fexcess-precision=fast -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 -[ 89%] 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 -mbranch-protection=standard -fexcess-precision=fast -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 -[ 91%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/validate.cpp.o +[ 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 -mbranch-protection=standard -fexcess-precision=fast -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 -[ 91%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/validate_mon.cpp.o +[ 95%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/validate_mon.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 -mbranch-protection=standard -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/validate_mon.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/validate_mon.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/validate_mon.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/validate_mon.cpp +[ 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 -mbranch-protection=standard -fexcess-precision=fast -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 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]': @@ -1194,81 +1294,17 @@ /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/formfact.hpp:48:24: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 48 | std::pair calculate_with_derivative(Real r) const { | ^~~~~~~~~~~~~~~~~~~~~~~~~ -[ 93%] 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 -mbranch-protection=standard -fexcess-precision=fast -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 In file included from /build/reproducible-path/gemmi-0.6.5+ds/prog/sfcalc.cpp:19: /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/dencalc.hpp: In function 'Real gemmi::determine_cutoff_radius(Real, const ExpSum&, Real) [with int N = 5; Real = float]': /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 /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]': -/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/dencalc.hpp:19:54: required from 'Real gemmi::determine_cutoff_radius(Real, const ExpSum&, Real) [with int N = 5; Real = float]' - 19 | std::tie(y1, dy) = precal.calculate_with_derivative(x1); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/dencalc.hpp:136:35: required from 'gemmi::DensityCalculator::CReal gemmi::DensityCalculator::estimate_radius(const gemmi::ExpSum&, CReal) const [with int N = 5; Table = gemmi::IT92; GReal = float; CReal = float; typename Table::Coef::coef_type = float; typename Table::Coef = gemmi::GaussianCoef<4, 1, float>]' - 136 | return determine_cutoff_radius(x1, precal, (CReal)cutoff); - | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/gemmi-0.6.5+ds/python/sf.cpp:60:36: required from 'void add_dencalc(pybind11::module&, const char*) [with Table = gemmi::IT92; pybind11::module = pybind11::module_]' - 60 | return self.estimate_radius(precal, bb); - | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -/build/reproducible-path/gemmi-0.6.5+ds/python/sf.cpp:83:20: required from here - 83 | add_dencalc(m, "DensityCalculatorX"); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -/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 { - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -[ 93%] 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 -mbranch-protection=standard -fexcess-precision=fast -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 -/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/formfact.hpp: In instantiation of 'std::pair<_ForwardIterator, _ForwardIterator> gemmi::ExpSum::calculate_with_derivative(Real) const [with int N = 1; Real = double]': -/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/dencalc.hpp:19:54: required from 'Real gemmi::determine_cutoff_radius(Real, const ExpSum&, Real) [with int N = 1; Real = double]' - 19 | std::tie(y1, dy) = precal.calculate_with_derivative(x1); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/dencalc.hpp:136:35: required from 'gemmi::DensityCalculator::CReal gemmi::DensityCalculator::estimate_radius(const gemmi::ExpSum&, CReal) const [with int N = 1; Table = gemmi::Neutron92; GReal = float; CReal = double; typename Table::Coef::coef_type = double; typename Table::Coef = gemmi::GaussianCoef<0, 1, double>]' - 136 | return determine_cutoff_radius(x1, precal, (CReal)cutoff); - | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/gemmi-0.6.5+ds/python/sf.cpp:60:36: required from 'void add_dencalc(pybind11::module&, const char*) [with Table = gemmi::Neutron92; pybind11::module = pybind11::module_]' - 60 | return self.estimate_radius(precal, bb); - | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -/build/reproducible-path/gemmi-0.6.5+ds/python/sf.cpp:85:25: required from here - 85 | add_dencalc(m, "DensityCalculatorN"); - | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/formfact.hpp:48:24: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 48 | std::pair calculate_with_derivative(Real r) const { - | ^~~~~~~~~~~~~~~~~~~~~~~~~ +[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 -mbranch-protection=standard -fexcess-precision=fast -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; | ^ -[ 95%] 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 -mbranch-protection=standard -fexcess-precision=fast -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 -/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 = 1]': -/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/dencalc.hpp:19:54: required from 'Real gemmi::determine_cutoff_radius(Real, const ExpSum&, Real) [with int N = 1; Real = float]' - 19 | std::tie(y1, dy) = precal.calculate_with_derivative(x1); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/dencalc.hpp:136:35: required from 'gemmi::DensityCalculator::CReal gemmi::DensityCalculator::estimate_radius(const gemmi::ExpSum&, CReal) const [with int N = 1; Table = gemmi::IT92; GReal = float; CReal = float; typename Table::Coef::coef_type = float; typename Table::Coef = gemmi::GaussianCoef<4, 1, float>]' - 136 | return determine_cutoff_radius(x1, precal, (CReal)cutoff); - | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/dencalc.hpp:149:37: required from 'void gemmi::DensityCalculator::do_add_atom_density_to_grid(const gemmi::Atom&, const Coef&, float) [with Coef = gemmi::GaussianCoef<0, 1, float>; Table = gemmi::IT92; GReal = float]' - 149 | CReal radius = estimate_radius(precal, b); - | ~~~~~~~~~~~~~~~^~~~~~~~~~~ -/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/dencalc.hpp:128:32: required from 'void gemmi::DensityCalculator::add_c_contribution_to_grid(const gemmi::Atom&, float) [with Table = gemmi::IT92; GReal = float]' - 128 | do_add_atom_density_to_grid(atom, GaussianCoef<0, 1, CReal>{0}, c); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/gemmi-0.6.5+ds/python/sf.cpp:47:40: required from 'void add_dencalc(pybind11::module&, const char*) [with Table = gemmi::IT92; pybind11::module = pybind11::module_]' - 47 | .def("add_c_contribution_to_grid", &DenCalc::add_c_contribution_to_grid) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/gemmi-0.6.5+ds/python/sf.cpp:83:20: required from here - 83 | add_dencalc(m, "DensityCalculatorX"); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -/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 { - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -[ 97%] 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 -mbranch-protection=standard -fexcess-precision=fast -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 -[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 -mbranch-protection=standard -fexcess-precision=fast -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] @@ -1276,13 +1312,13 @@ | ^ [100%] Linking CXX shared module gemmi.cpython-313-aarch64-linux-gnu.so /usr/bin/cmake -E cmake_link_script CMakeFiles/gemmi_py.dir/link.txt --verbose=1 +./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 -mbranch-protection=standard -fexcess-precision=fast -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/aarch64-linux-gnu/libz.so make[3]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu' [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 { @@ -1305,59 +1341,39 @@ /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu/CMakeFiles 48 make -f CMakeFiles/Makefile2 CMakeFiles/check.dir/all make[4]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu' -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 -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/doc_example2.dir/build.make CMakeFiles/doc_example2.dir/depend make[5]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu' cd /build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu && /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-aarch64-linux-gnu /build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu /build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu/CMakeFiles/options.dir/DependInfo.cmake "--color=" -make[5]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu' -cd /build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu && /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-aarch64-linux-gnu /build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu /build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu/CMakeFiles/doc_example.dir/DependInfo.cmake "--color=" -make[5]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu' -cd /build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu && /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-aarch64-linux-gnu /build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu /build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu/CMakeFiles/cpptest.dir/DependInfo.cmake "--color=" +make -f CMakeFiles/gemmi_cpp.dir/build.make CMakeFiles/gemmi_cpp.dir/depend make[5]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu' cd /build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu && /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-aarch64-linux-gnu /build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu /build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu/CMakeFiles/gemmi_cpp.dir/DependInfo.cmake "--color=" -make[5]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu' -cd /build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu && /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-aarch64-linux-gnu /build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu /build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu/CMakeFiles/hello.dir/DependInfo.cmake "--color=" +make -f CMakeFiles/doc_example2.dir/build.make CMakeFiles/doc_example2.dir/depend make[5]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu' cd /build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu && /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-aarch64-linux-gnu /build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu /build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu/CMakeFiles/doc_example2.dir/DependInfo.cmake "--color=" -make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu' -make -f CMakeFiles/doc_example2.dir/build.make CMakeFiles/doc_example2.dir/build -make[5]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu' +make -f CMakeFiles/cpptest.dir/build.make CMakeFiles/cpptest.dir/depend Dependencies file "CMakeFiles/options.dir/prog/options.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu/CMakeFiles/options.dir/compiler_depend.internal". +make[5]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu' +Consolidate compiler generated dependencies of target options +cd /build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu && /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-aarch64-linux-gnu /build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu 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Dependencies file "CMakeFiles/gemmi_cpp.dir/src/crd.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu/CMakeFiles/gemmi_cpp.dir/compiler_depend.internal". -make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu' -make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu' -make -f CMakeFiles/cpptest.dir/build.make CMakeFiles/cpptest.dir/build -make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu' +make[5]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu' Dependencies file "CMakeFiles/gemmi_cpp.dir/src/ddl.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu/CMakeFiles/gemmi_cpp.dir/compiler_depend.internal". -make -f CMakeFiles/hello.dir/build.make CMakeFiles/hello.dir/build -make -f CMakeFiles/doc_example.dir/build.make CMakeFiles/doc_example.dir/build -Consolidate compiler generated dependencies of target options +cd /build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu && /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-aarch64-linux-gnu /build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu /build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu/CMakeFiles/hello.dir/DependInfo.cmake "--color=" Dependencies file "CMakeFiles/gemmi_cpp.dir/src/eig3.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu/CMakeFiles/gemmi_cpp.dir/compiler_depend.internal". -[ 0%] Building CXX object CMakeFiles/doc_example2.dir/docs/code/cif_cc.cpp.o Dependencies file "CMakeFiles/gemmi_cpp.dir/src/gz.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu/CMakeFiles/gemmi_cpp.dir/compiler_depend.internal". -make[5]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu' -make[5]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu' Dependencies file "CMakeFiles/gemmi_cpp.dir/src/intensit.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu/CMakeFiles/gemmi_cpp.dir/compiler_depend.internal". -make[5]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu' -/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 -mbranch-protection=standard -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/doc_example2.dir/docs/code/cif_cc.cpp.o -MF CMakeFiles/doc_example2.dir/docs/code/cif_cc.cpp.o.d -o CMakeFiles/doc_example2.dir/docs/code/cif_cc.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/docs/code/cif_cc.cpp Dependencies file "CMakeFiles/gemmi_cpp.dir/src/json.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu/CMakeFiles/gemmi_cpp.dir/compiler_depend.internal". -make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu' -make -f CMakeFiles/options.dir/build.make CMakeFiles/options.dir/build Dependencies file "CMakeFiles/gemmi_cpp.dir/src/mmcif.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu/CMakeFiles/gemmi_cpp.dir/compiler_depend.internal". 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Dependencies file "CMakeFiles/gemmi_cpp.dir/src/read_cif.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu/CMakeFiles/gemmi_cpp.dir/compiler_depend.internal". Dependencies file "CMakeFiles/gemmi_cpp.dir/src/resinfo.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu/CMakeFiles/gemmi_cpp.dir/compiler_depend.internal". @@ -1367,65 +1383,48 @@ Dependencies file "CMakeFiles/gemmi_cpp.dir/src/to_pdb.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu/CMakeFiles/gemmi_cpp.dir/compiler_depend.internal". Dependencies file "CMakeFiles/gemmi_cpp.dir/src/topo.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu/CMakeFiles/gemmi_cpp.dir/compiler_depend.internal". 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-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 -mbranch-protection=standard -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/hello.dir/examples/hello.cpp.o -MF CMakeFiles/hello.dir/examples/hello.cpp.o.d -o CMakeFiles/hello.dir/examples/hello.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/examples/hello.cpp make[5]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu' -[ 45%] 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 -mbranch-protection=standard -fexcess-precision=fast -Wdate-time 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/build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu/CMakeFiles/gemmi_prog.dir/DependInfo.cmake "--color=" +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-aarch64-linux-gnu' +cd /build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu && /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-aarch64-linux-gnu /build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu /build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu/CMakeFiles/doc_maybegz.dir/DependInfo.cmake "--color=" +make -f CMakeFiles/doc_newmtz.dir/build.make CMakeFiles/doc_newmtz.dir/depend +make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu' +make[5]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu' +cd /build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu && /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-aarch64-linux-gnu /build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu /build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu/CMakeFiles/doc_newmtz.dir/DependInfo.cmake "--color=" +make -f CMakeFiles/doc_example.dir/build.make CMakeFiles/doc_example.dir/build Dependencies file "CMakeFiles/gemmi_prog.dir/prog/align.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu/CMakeFiles/gemmi_prog.dir/compiler_depend.internal". Dependencies file "CMakeFiles/gemmi_prog.dir/prog/blobs.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu/CMakeFiles/gemmi_prog.dir/compiler_depend.internal". Dependencies file "CMakeFiles/gemmi_prog.dir/prog/cif2json.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu/CMakeFiles/gemmi_prog.dir/compiler_depend.internal". @@ -1433,6 +1432,8 @@ Dependencies file "CMakeFiles/gemmi_prog.dir/prog/cifdiff.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu/CMakeFiles/gemmi_prog.dir/compiler_depend.internal". Dependencies file "CMakeFiles/gemmi_prog.dir/prog/contact.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu/CMakeFiles/gemmi_prog.dir/compiler_depend.internal". Dependencies file "CMakeFiles/gemmi_prog.dir/prog/contents.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu/CMakeFiles/gemmi_prog.dir/compiler_depend.internal". +make[5]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu' +make -f CMakeFiles/test_disulf.dir/build.make CMakeFiles/test_disulf.dir/depend Dependencies file "CMakeFiles/gemmi_prog.dir/prog/convert.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu/CMakeFiles/gemmi_prog.dir/compiler_depend.internal". Dependencies file "CMakeFiles/gemmi_prog.dir/prog/crd.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu/CMakeFiles/gemmi_prog.dir/compiler_depend.internal". Dependencies file "CMakeFiles/gemmi_prog.dir/prog/ecalc.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu/CMakeFiles/gemmi_prog.dir/compiler_depend.internal". @@ -1442,6 +1443,7 @@ Dependencies file "CMakeFiles/gemmi_prog.dir/prog/json2cif.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu/CMakeFiles/gemmi_prog.dir/compiler_depend.internal". Dependencies file "CMakeFiles/gemmi_prog.dir/prog/main.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu/CMakeFiles/gemmi_prog.dir/compiler_depend.internal". Dependencies file "CMakeFiles/gemmi_prog.dir/prog/map.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu/CMakeFiles/gemmi_prog.dir/compiler_depend.internal". +make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu' Dependencies file "CMakeFiles/gemmi_prog.dir/prog/map2sf.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu/CMakeFiles/gemmi_prog.dir/compiler_depend.internal". Dependencies file "CMakeFiles/gemmi_prog.dir/prog/mapcoef.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu/CMakeFiles/gemmi_prog.dir/compiler_depend.internal". Dependencies file "CMakeFiles/gemmi_prog.dir/prog/mask.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu/CMakeFiles/gemmi_prog.dir/compiler_depend.internal". @@ -1462,13 +1464,47 @@ Dependencies file "CMakeFiles/gemmi_prog.dir/prog/wcn.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu/CMakeFiles/gemmi_prog.dir/compiler_depend.internal". Dependencies file "CMakeFiles/gemmi_prog.dir/prog/xds2mtz.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu/CMakeFiles/gemmi_prog.dir/compiler_depend.internal". Dependencies file "CMakeFiles/gemmi_prog.dir/link.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu/CMakeFiles/gemmi_prog.dir/compiler_depend.internal". +make[5]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu' +cd /build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu && /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-aarch64-linux-gnu /build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu /build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu/CMakeFiles/test_disulf.dir/DependInfo.cmake "--color=" +make -f CMakeFiles/doc_maybegz.dir/build.make CMakeFiles/doc_maybegz.dir/build +make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu' +[ 37%] Building CXX object CMakeFiles/doc_example.dir/docs/code/sym.cpp.o +make[5]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu' +make -f CMakeFiles/doc_newmtz.dir/build.make CMakeFiles/doc_newmtz.dir/build +/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 -mbranch-protection=standard -fexcess-precision=fast -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 +[ 39%] Building CXX object CMakeFiles/doc_example.dir/docs/code/elem.cpp.o Consolidate compiler generated dependencies of target gemmi_prog +make[5]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu' +make[5]: Leaving directory 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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 +[ 87%] Building CXX object CMakeFiles/doc_example.dir/src/resinfo.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 -mbranch-protection=standard -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -UNDEBUG -MD -MT CMakeFiles/doc_example.dir/src/resinfo.cpp.o -MF CMakeFiles/doc_example.dir/src/resinfo.cpp.o.d -o CMakeFiles/doc_example.dir/src/resinfo.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/resinfo.cpp 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-aarch64-linux-gnu' cd /build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu && /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-aarch64-linux-gnu /build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu /build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu/CMakeFiles/print-version.dir/DependInfo.cmake "--color=" @@ -1487,6 +1523,11 @@ /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; | ^ +[ 89%] 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 -mbranch-protection=standard -fexcess-precision=fast -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-aarch64-linux-gnu' +[ 89%] Built target doc_example 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: @@ -1499,31 +1540,26 @@ /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%] 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 -mbranch-protection=standard -fexcess-precision=fast -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-aarch64-linux-gnu' -[ 89%] Built target doc_example [ 91%] 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 -mbranch-protection=standard -fexcess-precision=fast -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/aarch64-linux-gnu/libz.so make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu' [ 91%] Built target doc_newmtz -[ 91%] Linking CXX executable hello +[ 93%] Linking CXX executable check_conn +/usr/bin/cmake -E cmake_link_script CMakeFiles/check_conn.dir/link.txt --verbose=1 +[ 95%] Linking CXX executable doc_example2 +/usr/bin/cmake -E cmake_link_script CMakeFiles/doc_example2.dir/link.txt --verbose=1 +[ 95%] Linking CXX executable hello /usr/bin/cmake -E cmake_link_script CMakeFiles/hello.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 -mbranch-protection=standard -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,--dependency-file=CMakeFiles/hello.dir/link.d CMakeFiles/hello.dir/examples/hello.cpp.o -o hello +/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 -mbranch-protection=standard -fexcess-precision=fast -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/aarch64-linux-gnu/libz.so make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu' -[ 91%] Built target hello -[ 93%] Linking CXX executable doc_example2 -/usr/bin/cmake -E cmake_link_script CMakeFiles/doc_example2.dir/link.txt --verbose=1 +[ 95%] Built target check_conn /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 -mbranch-protection=standard -fexcess-precision=fast -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-aarch64-linux-gnu' -[ 93%] Built target doc_example2 -[ 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 -mbranch-protection=standard -fexcess-precision=fast -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/aarch64-linux-gnu/libz.so +[ 95%] Built target doc_example2 +/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 -mbranch-protection=standard -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,--dependency-file=CMakeFiles/hello.dir/link.d CMakeFiles/hello.dir/examples/hello.cpp.o -o hello make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu' -[ 95%] Built target check_conn +[ 95%] Built target hello [ 95%] 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 -mbranch-protection=standard -fexcess-precision=fast -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 @@ -1553,7 +1589,7 @@ 100% tests passed, 0 tests failed out of 1 -Total Test time (real) = 0.01 sec +Total Test time (real) = 0.02 sec make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu' [100%] Built target check make[4]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-aarch64-linux-gnu' @@ -1582,7 +1618,7 @@ 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 0.99s +172 passed, 17 skipped, 2 deselected in 1.72s make[1]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=cmake @@ -1775,9 +1811,9 @@ dh_md5sums -O--buildsystem=cmake dh_builddeb -O--buildsystem=cmake dpkg-deb: building package 'gemmi' in '../gemmi_0.6.5+ds-3_arm64.deb'. +dpkg-deb: building package 'python3-gemmi' in '../python3-gemmi_0.6.5+ds-3_arm64.deb'. dpkg-deb: building package 'gemmi-dbgsym' in '../gemmi-dbgsym_0.6.5+ds-3_arm64.deb'. dpkg-deb: building package 'gemmi-dev' in '../gemmi-dev_0.6.5+ds-3_arm64.deb'. -dpkg-deb: building package 'python3-gemmi' in '../python3-gemmi_0.6.5+ds-3_arm64.deb'. dpkg-genbuildinfo --build=binary -O../gemmi_0.6.5+ds-3_arm64.buildinfo dpkg-genchanges --build=binary -O../gemmi_0.6.5+ds-3_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1785,12 +1821,14 @@ 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/4103583/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/4103583/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/2121061 and its subdirectories -I: Current time: Mon Mar 9 12:40:03 -12 2026 -I: pbuilder-time-stamp: 1773103203 +I: removing directory /srv/workspace/pbuilder/4103583 and its subdirectories +I: Current time: Wed Feb 5 08:24:43 +14 2025 +I: pbuilder-time-stamp: 1738693483