Diff of the two buildlogs: -- --- b1/build.log 2024-12-09 18:57:54.886723282 +0000 +++ b2/build.log 2024-12-09 19:08:09.562970350 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Dec 9 06:41:28 -12 2024 -I: pbuilder-time-stamp: 1733769688 +I: Current time: Mon Jan 12 15:20:56 +14 2026 +I: pbuilder-time-stamp: 1768180856 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -30,52 +30,84 @@ dpkg-source: info: applying tao-pegtl-3.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2147460/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3648558/tmp/hooks/D01_modify_environment starting +debug: Running on ionos15-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Jan 12 01:21 /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/3648558/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3648558/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="32" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.32(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='f2cb86ac7c6f46b9a1378daff0e683c1' - 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='2147460' - PS1='# ' - PS2='> ' + INVOCATION_ID=4c914f64f721483daf58962a3ede7e5b + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=3648558 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.UYKLhwIp/pbuilderrc_dQQe --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.UYKLhwIp/b1 --logfile b1/build.log gemmi_0.6.5+ds-2.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://46.16.76.132:3128' + 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.UYKLhwIp/pbuilderrc_8UUN --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.UYKLhwIp/b2 --logfile b2/build.log gemmi_0.6.5+ds-2.dsc' + SUDO_GID=111 + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos11-amd64 6.1.0-28-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.119-1 (2024-11-22) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.11.5+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.5-1~bpo12+1 (2024-11-11) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2147460/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/3648558/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -239,7 +271,7 @@ Get: 104 http://deb.debian.org/debian trixie/main amd64 python3-pybind11 all 2.13.6-1 [215 kB] Get: 105 http://deb.debian.org/debian trixie/main amd64 python3-pytest all 8.3.3-1 [249 kB] Get: 106 http://deb.debian.org/debian trixie/main amd64 tao-pegtl-dev all 3.2.7-1 [69.4 kB] -Fetched 64.6 MB in 11s (5809 kB/s) +Fetched 64.6 MB in 14s (4488 kB/s) debconf: delaying package configuration, since apt-utils is not installed 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 ... 19967 files and directories currently installed.) @@ -596,8 +628,8 @@ Setting up tzdata (2024b-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Mon Dec 9 18:43:22 UTC 2024. -Universal Time is now: Mon Dec 9 18:43:22 UTC 2024. +Local time is now: Mon Jan 12 01:23:45 UTC 2026. +Universal Time is now: Mon Jan 12 01:23:45 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... @@ -694,7 +726,11 @@ 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-2_source.changes +I: user script /srv/workspace/pbuilder/3648558/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/3648558/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-2_source.changes dpkg-buildpackage: info: source package gemmi dpkg-buildpackage: info: source version 0.6.5+ds-2 dpkg-buildpackage: info: source distribution unstable @@ -740,8 +776,8 @@ -- 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/python3.12 --- Configuring done (5.7s) --- Generating done (0.4s) +-- Configuring done (1.6s) +-- Generating done (0.1s) CMake Warning: Manually-specified variables were not used by the project: @@ -753,7 +789,7 @@ -- Build files have been written to: /build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu make[1]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds' dh_auto_build -O--buildsystem=cmake - cd obj-x86_64-linux-gnu && make -j20 "INSTALL=install --strip-program=true" VERBOSE=1 + cd obj-x86_64-linux-gnu && make -j42 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/gemmi-0.6.5+ds -B/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu/CMakeFiles /build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu//CMakeFiles/progress.marks @@ -766,65 +802,67 @@ make[3]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu /build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu/CMakeFiles/gemmi_cpp.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' -make -f CMakeFiles/gemmi_cpp.dir/build.make CMakeFiles/gemmi_cpp.dir/build -make[3]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' make -f CMakeFiles/options.dir/build.make CMakeFiles/options.dir/build +make -f CMakeFiles/gemmi_cpp.dir/build.make CMakeFiles/gemmi_cpp.dir/build make[3]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' -[ 0%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/gz.cpp.o -[ 4%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/eig3.cpp.o -[ 0%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/json.cpp.o -[ 4%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/mmcif.cpp.o -[ 6%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/ddl.cpp.o -[ 6%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/assembly.cpp.o -[ 6%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/mmread_gz.cpp.o -[ 8%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/intensit.cpp.o -[ 10%] Building CXX object CMakeFiles/options.dir/prog/options.cpp.o -[ 10%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/crd.cpp.o -[ 12%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/calculate.cpp.o +make[3]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' +[ 2%] 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 -fcf-protection -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 +[ 2%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/mmread_gz.cpp.o +[ 2%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/assembly.cpp.o +[ 4%] Building CXX object CMakeFiles/options.dir/prog/options.cpp.o +[ 6%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/mtz.cpp.o +[ 12%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/mtz2cif.cpp.o +[ 12%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/mmcif.cpp.o +[ 12%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/align.cpp.o +/usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection 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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 -fcf-protection -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 +[ 14%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/eig3.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 -fcf-protection -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 +[ 14%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/gz.cpp.o +[ 14%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/polyheur.cpp.o +/usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 +[ 16%] 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 -fcf-protection -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/mmcif.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/mmcif.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/mmcif.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/mmcif.cpp +[ 16%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/json.cpp.o +[ 18%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/intensit.cpp.o /usr/bin/c++ -DGEMMI_BUILD 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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 -fcf-protection -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/to_mmcif.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/to_mmcif.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/to_mmcif.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/to_mmcif.cpp +[ 29%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/monlib.cpp.o +/usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC 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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 -fcf-protection -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/monlib.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/monlib.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/monlib.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/monlib.cpp /build/reproducible-path/gemmi-0.6.5+ds/src/sprintf.cpp:30:86: note: '#pragma message: Using system stb_sprintf.h, not the bundled one. It may not work.' 30 | # pragma message("Using system stb_sprintf.h, not the bundled one. It may not work.") | ^ -In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz.hpp:23, - from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz2cif.hpp:14, - from /build/reproducible-path/gemmi-0.6.5+ds/src/mtz2cif.cpp:3: +In file included from /build/reproducible-path/gemmi-0.6.5+ds/src/gz.cpp:15: /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/src/gz.cpp:15: +In file included from /build/reproducible-path/gemmi-0.6.5+ds/prog/options.cpp:8: /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ @@ -833,16 +871,25 @@ /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; | ^ -[ 27%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/to_pdb.cpp.o -/usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/to_pdb.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/to_pdb.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/to_pdb.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/to_pdb.cpp +In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/json.hpp:10, + from /build/reproducible-path/gemmi-0.6.5+ds/src/json.cpp:3: +/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] + 37 | typedef std::unique_ptr fileptr_t; + | ^ +In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/xds_ascii.hpp:11, + from /build/reproducible-path/gemmi-0.6.5+ds/src/xds_ascii.cpp:3: +/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] + 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/intensit.hpp:14, - from /build/reproducible-path/gemmi-0.6.5+ds/src/intensit.cpp:3: + from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz2cif.hpp:14, + from /build/reproducible-path/gemmi-0.6.5+ds/src/mtz2cif.cpp:3: /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ -In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/json.hpp:10, - from /build/reproducible-path/gemmi-0.6.5+ds/src/json.cpp:3: +In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz.hpp:23, + from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/intensit.hpp:14, + from /build/reproducible-path/gemmi-0.6.5+ds/src/intensit.cpp:3: /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ @@ -851,23 +898,12 @@ /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; | ^ -[ 27%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/monlib.cpp.o -/usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/monlib.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/monlib.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/monlib.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/monlib.cpp -[ 29%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/topo.cpp.o -/usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/topo.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/topo.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/topo.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/topo.cpp -[ 29%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/xds_ascii.cpp.o -/usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/xds_ascii.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/xds_ascii.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/xds_ascii.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/xds_ascii.cpp In file included from /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/src/mmread_gz.cpp:4: /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/xds_ascii.hpp:11, - from /build/reproducible-path/gemmi-0.6.5+ds/src/xds_ascii.cpp:3: -/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] - 37 | typedef std::unique_ptr fileptr_t; - | ^ make[3]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' [ 29%] Built target options In file included from /usr/include/c++/14/bits/stl_tree.h:63, @@ -917,132 +953,148 @@ cd /build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu /build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu/CMakeFiles/gemmi_py.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' -make -f CMakeFiles/gemmi_prog.dir/build.make CMakeFiles/gemmi_prog.dir/build make -f CMakeFiles/gemmi_py.dir/build.make CMakeFiles/gemmi_py.dir/build +make -f CMakeFiles/gemmi_prog.dir/build.make CMakeFiles/gemmi_prog.dir/build make[3]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' -[ 33%] Building CXX object CMakeFiles/gemmi_py.dir/python/mol.cpp.o -[ 33%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/contact.cpp.o -[ 35%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/cifdiff.cpp.o -[ 41%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/align.cpp.o -[ 41%] Building CXX object CMakeFiles/gemmi_py.dir/python/cif.cpp.o -[ 41%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/convert.cpp.o -[ 41%] Building CXX object CMakeFiles/gemmi_py.dir/python/chemcomp.cpp.o -[ 41%] Building CXX object CMakeFiles/gemmi_py.dir/python/align.cpp.o -[ 41%] Building CXX object CMakeFiles/gemmi_py.dir/python/gemmi.cpp.o -[ 41%] Building CXX object CMakeFiles/gemmi_py.dir/python/ccp4.cpp.o -[ 43%] Building CXX object CMakeFiles/gemmi_py.dir/python/custom.cpp.o -[ 43%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/cif2json.cpp.o -[ 45%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/contents.cpp.o -/usr/bin/c++ -Dgemmi_py_EXPORTS -I/build/reproducible-path/gemmi-0.6.5+ds/include -isystem /usr/include/python3.12 -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 -fcf-protection -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/mol.cpp.o -MF CMakeFiles/gemmi_py.dir/python/mol.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/mol.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/python/mol.cpp -[ 45%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/cif2mtz.cpp.o -/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -[ 47%] Building CXX object CMakeFiles/gemmi_py.dir/python/elem.cpp.o +[ 35%] Building CXX object CMakeFiles/gemmi_py.dir/python/mol.cpp.o +[ 35%] Building CXX object CMakeFiles/gemmi_py.dir/python/gemmi.cpp.o +[ 35%] Building CXX object CMakeFiles/gemmi_py.dir/python/align.cpp.o +[ 35%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/align.cpp.o +[ 37%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/cif2mtz.cpp.o +[ 37%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/blobs.cpp.o +[ 39%] Building CXX object CMakeFiles/gemmi_py.dir/python/cif.cpp.o +[ 41%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/cif2json.cpp.o +[ 43%] Building CXX object CMakeFiles/gemmi_py.dir/python/ccp4.cpp.o +[ 43%] Building CXX object CMakeFiles/gemmi_py.dir/python/chemcomp.cpp.o /usr/bin/c++ -Dgemmi_py_EXPORTS -I/build/reproducible-path/gemmi-0.6.5+ds/include -isystem /usr/include/python3.12 -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 -fcf-protection -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/gemmi.cpp.o -MF CMakeFiles/gemmi_py.dir/python/gemmi.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/gemmi.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/python/gemmi.cpp +[ 45%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/contents.cpp.o +[ 45%] Building CXX object CMakeFiles/gemmi_py.dir/python/grid.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 -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/align.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/align.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/align.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/align.cpp +[ 47%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/cifdiff.cpp.o +/usr/bin/c++ -Dgemmi_py_EXPORTS -I/build/reproducible-path/gemmi-0.6.5+ds/include -isystem /usr/include/python3.12 -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 -fcf-protection -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/mol.cpp.o -MF CMakeFiles/gemmi_py.dir/python/mol.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/mol.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/python/mol.cpp +[ 47%] Building CXX object CMakeFiles/gemmi_py.dir/python/custom.cpp.o +[ 47%] 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 -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/blobs.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/blobs.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/blobs.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/blobs.cpp /usr/bin/c++ -Dgemmi_py_EXPORTS -I/build/reproducible-path/gemmi-0.6.5+ds/include -isystem /usr/include/python3.12 -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 -fcf-protection -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/align.cpp.o -MF CMakeFiles/gemmi_py.dir/python/align.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/align.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/python/align.cpp -/usr/bin/c++ -Dgemmi_py_EXPORTS -I/build/reproducible-path/gemmi-0.6.5+ds/include -isystem /usr/include/python3.12 -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 -fcf-protection -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/ccp4.cpp.o -MF CMakeFiles/gemmi_py.dir/python/ccp4.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/ccp4.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/python/ccp4.cpp /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 -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/cif2mtz.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/cif2mtz.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/cif2mtz.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/cif2mtz.cpp +[ 50%] Building CXX object CMakeFiles/gemmi_py.dir/python/elem.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 -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 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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 -fcf-protection -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 +/usr/bin/c++ -Dgemmi_py_EXPORTS -I/build/reproducible-path/gemmi-0.6.5+ds/include -isystem /usr/include/python3.12 -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 -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden 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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 -fcf-protection -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 +/usr/bin/c++ -Dgemmi_py_EXPORTS -I/build/reproducible-path/gemmi-0.6.5+ds/include -isystem /usr/include/python3.12 -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 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CMakeFiles/gemmi_py.dir/python/unitcell.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/python/unitcell.cpp +[ 79%] Building CXX object CMakeFiles/gemmi_py.dir/python/write.cpp.o +[ 81%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/mask.cpp.o +[ 81%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/merge.cpp.o +/usr/bin/c++ -Dgemmi_py_EXPORTS -I/build/reproducible-path/gemmi-0.6.5+ds/include -isystem /usr/include/python3.12 -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 -fcf-protection -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 +/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 -fcf-protection -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 +/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 -fcf-protection -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 +[ 83%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/mondiff.cpp.o +/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 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: + 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/prog/ecalc.cpp:5: +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; | ^ In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz.hpp:23, - from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/cif2mtz.hpp:15, - from /build/reproducible-path/gemmi-0.6.5+ds/prog/cif2mtz.cpp:10: + 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; | ^ 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_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 -fcf-protection -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 -[ 58%] 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 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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 -[ 58%] 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 -fcf-protection -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 -[ 60%] 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 -fcf-protection -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 -/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 -fcf-protection -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 -[ 62%] 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 -fcf-protection -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 -[ 62%] 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 -fcf-protection -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/python3.12 -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 -fcf-protection -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/ccp4.hpp:19, - from /build/reproducible-path/gemmi-0.6.5+ds/prog/map.cpp:6: + from /build/reproducible-path/gemmi-0.6.5+ds/prog/cif2mtz.cpp:10: /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ 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: + 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; | ^ -[ 66%] 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 -fcf-protection -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 -[ 66%] 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/python3.12 -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 -fcf-protection -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/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 -fcf-protection -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 -[ 70%] 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/python3.12 -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 -fcf-protection -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 -[ 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 -fcf-protection -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 -[ 72%] 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 -fcf-protection -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 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; | ^ -[ 75%] 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/python3.12 -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 -fcf-protection -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 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: + from /build/reproducible-path/gemmi-0.6.5+ds/python/ccp4.cpp:3: /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ 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: + 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; | ^ +[ 83%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/monlib_opt.cpp.o +/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 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: + 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; + | ^ +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; | ^ @@ -1051,75 +1103,55 @@ /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ -[ 75%] Building CXX object CMakeFiles/gemmi_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/python3.12 -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 -fcf-protection -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_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 -fcf-protection -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 +[ 85%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/mtz.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 +[ 85%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/mtz2cif.cpp.o +/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 +[ 87%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/reindex.cpp.o +/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/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 -/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 -fcf-protection -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 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; | ^ -[ 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 -fcf-protection -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 +[ 87%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/residues.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -[ 81%] 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/python3.12 -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 -fcf-protection -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 -[ 83%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/rmsz.cpp.o +[ 89%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/rmsz.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -[ 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 -fcf-protection -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 -[ 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/python3.12 -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 -fcf-protection -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 -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; - | ^ -[ 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/python3.12 -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 -fcf-protection -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 -[ 87%] 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/python3.12 -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 -fcf-protection -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 -[ 87%] 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 -fcf-protection -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 -[ 89%] Building CXX object CMakeFiles/gemmi_py.dir/python/unitcell.cpp.o -/usr/bin/c++ -Dgemmi_py_EXPORTS -I/build/reproducible-path/gemmi-0.6.5+ds/include -isystem /usr/include/python3.12 -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 -fcf-protection -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 +[ 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 -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden 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-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 -fcf-protection -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 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: + 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; | ^ -[ 91%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/sg.cpp.o -/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -[ 91%] 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 -fcf-protection -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 -[ 93%] 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 -fcf-protection -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 -[ 93%] 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 -fcf-protection -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 -[ 95%] 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/python3.12 -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 -fcf-protection -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 [ 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 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CMakeFiles/gemmi_cpp.dir/src/json.cpp.o CMakeFiles/gemmi_cpp.dir/src/mmcif.cpp.o CMakeFiles/gemmi_cpp.dir/src/mmread_gz.cpp.o CMakeFiles/gemmi_cpp.dir/src/mtz.cpp.o CMakeFiles/gemmi_cpp.dir/src/mtz2cif.cpp.o CMakeFiles/gemmi_cpp.dir/src/polyheur.cpp.o CMakeFiles/gemmi_cpp.dir/src/read_cif.cpp.o CMakeFiles/gemmi_cpp.dir/src/resinfo.cpp.o CMakeFiles/gemmi_cpp.dir/src/riding_h.cpp.o CMakeFiles/gemmi_cpp.dir/src/sprintf.cpp.o CMakeFiles/gemmi_cpp.dir/src/to_mmcif.cpp.o CMakeFiles/gemmi_cpp.dir/src/to_pdb.cpp.o CMakeFiles/gemmi_cpp.dir/src/monlib.cpp.o CMakeFiles/gemmi_cpp.dir/src/topo.cpp.o CMakeFiles/gemmi_cpp.dir/src/xds_ascii.cpp.o /usr/lib/x86_64-linux-gnu/libz.so [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 -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro 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/x86_64-linux-gnu/libz.so -lto-wrapper: warning: using serial compilation of 118 LTRANS jobs -lto-wrapper: note: see the '-flto' option documentation for more information make[3]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' [100%] Built target gemmi_prog +lto-wrapper: warning: using serial compilation of 118 LTRANS jobs +lto-wrapper: note: see the '-flto' option documentation for more information /usr/include/c++/14/bits/stl_heap.h: In function '__adjust_heap.isra': /usr/include/c++/14/bits/stl_heap.h:224: note: the ABI of passing structure with 'complex float' member has changed in GCC 4.4 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, @@ -1150,7 +1186,7 @@ debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds' dh_auto_build -- check - cd obj-x86_64-linux-gnu && make -j20 "INSTALL=install --strip-program=true" check VERBOSE=1 + cd obj-x86_64-linux-gnu && make -j42 "INSTALL=install --strip-program=true" check VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/gemmi-0.6.5+ds -B/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 check @@ -1159,36 +1195,42 @@ /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-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-x86_64-linux-gnu' -make -f CMakeFiles/options.dir/build.make CMakeFiles/options.dir/depend -make -f CMakeFiles/gemmi_cpp.dir/build.make CMakeFiles/gemmi_cpp.dir/depend make -f CMakeFiles/cpptest.dir/build.make CMakeFiles/cpptest.dir/depend -make[5]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' 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-x86_64-linux-gnu' -cd 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/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-x86_64-linux-gnu /build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu /build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu/CMakeFiles/doc_example2.dir/DependInfo.cmake "--color=" -Dependencies file "CMakeFiles/options.dir/prog/options.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu/CMakeFiles/options.dir/compiler_depend.internal". -make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' -make -f CMakeFiles/hello.dir/build.make CMakeFiles/hello.dir/build make[5]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' +cd /build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gemmi-0.6.5+ds 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'/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' +make -f CMakeFiles/cpptest.dir/build.make CMakeFiles/cpptest.dir/build +make -f CMakeFiles/hello.dir/build.make CMakeFiles/hello.dir/build Dependencies file "CMakeFiles/gemmi_cpp.dir/src/align.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu/CMakeFiles/gemmi_cpp.dir/compiler_depend.internal". -make[5]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' +Dependencies file "CMakeFiles/options.dir/prog/options.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu/CMakeFiles/options.dir/compiler_depend.internal". +make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' +make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' +make -f CMakeFiles/doc_example2.dir/build.make CMakeFiles/doc_example2.dir/build Dependencies file 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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-x86_64-linux-gnu/CMakeFiles/gemmi_cpp.dir/compiler_depend.internal". +make[5]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' +make[5]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' 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-x86_64-linux-gnu/CMakeFiles/gemmi_cpp.dir/compiler_depend.internal". 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-x86_64-linux-gnu/CMakeFiles/gemmi_cpp.dir/compiler_depend.internal". 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-x86_64-linux-gnu/CMakeFiles/gemmi_cpp.dir/compiler_depend.internal". @@ -1202,69 +1244,77 @@ 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-x86_64-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-x86_64-linux-gnu/CMakeFiles/gemmi_cpp.dir/compiler_depend.internal". 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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-x86_64-linux-gnu/CMakeFiles/gemmi_cpp.dir/compiler_depend.internal". -make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' -[ 2%] Building CXX object CMakeFiles/doc_example.dir/docs/code/elem.cpp.o Dependencies file "CMakeFiles/gemmi_cpp.dir/src/xds_ascii.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu/CMakeFiles/gemmi_cpp.dir/compiler_depend.internal". +[ 2%] Building CXX object CMakeFiles/hello.dir/examples/hello.cpp.o +[ 4%] Building CXX object CMakeFiles/cpptest.dir/tests/cif.cpp.o +[ 4%] Building CXX object CMakeFiles/doc_example2.dir/docs/code/cif_cc.cpp.o +[ 4%] Building CXX object CMakeFiles/cpptest.dir/tests/main.cpp.o +[ 6%] Building CXX object CMakeFiles/doc_example.dir/docs/code/resinfo.cpp.o +[ 6%] Building CXX object 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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-x86_64-linux-gnu/CMakeFiles/gemmi_prog.dir/compiler_depend.internal". +make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' +make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' +make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' +make -f CMakeFiles/doc_newmtz.dir/build.make CMakeFiles/doc_newmtz.dir/build 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-x86_64-linux-gnu/CMakeFiles/gemmi_prog.dir/compiler_depend.internal". +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-x86_64-linux-gnu' Dependencies file "CMakeFiles/gemmi_prog.dir/prog/cif2mtz.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu/CMakeFiles/gemmi_prog.dir/compiler_depend.internal". +make -f CMakeFiles/test_disulf.dir/build.make CMakeFiles/test_disulf.dir/build +make -f CMakeFiles/check_conn.dir/build.make CMakeFiles/check_conn.dir/build 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-x86_64-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-x86_64-linux-gnu/CMakeFiles/gemmi_prog.dir/compiler_depend.internal". +make[5]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' +make[5]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' +make[5]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' 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-x86_64-linux-gnu/CMakeFiles/gemmi_prog.dir/compiler_depend.internal". +make[5]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' 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-x86_64-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-x86_64-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-x86_64-linux-gnu/CMakeFiles/gemmi_prog.dir/compiler_depend.internal". @@ -1293,30 +1343,16 @@ Dependencies file "CMakeFiles/gemmi_prog.dir/prog/validate_mon.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu/CMakeFiles/gemmi_prog.dir/compiler_depend.internal". 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-x86_64-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-x86_64-linux-gnu/CMakeFiles/gemmi_prog.dir/compiler_depend.internal". -make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' -make -f CMakeFiles/test_disulf.dir/build.make CMakeFiles/test_disulf.dir/build -make[5]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' -make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' +[ 41%] Building CXX object CMakeFiles/doc_newmtz.dir/docs/code/newmtz.cpp.o [ 43%] Building CXX object CMakeFiles/test_disulf.dir/tests/disulf.cpp.o -/usr/bin/c++ -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 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/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu /build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu /build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu/CMakeFiles/check_conn.dir/DependInfo.cmake "--color=" -[ 45%] Building CXX object CMakeFiles/doc_newmtz.dir/docs/code/newmtz.cpp.o [ 45%] Building CXX object CMakeFiles/doc_maybegz.dir/docs/code/maybegz.cpp.o [ 45%] Building CXX object CMakeFiles/doc_maybegz.dir/docs/code/mutate.cpp.o -/usr/bin/c++ -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/doc_maybegz.dir/docs/code/maybegz.cpp.o -MF CMakeFiles/doc_maybegz.dir/docs/code/maybegz.cpp.o.d -o CMakeFiles/doc_maybegz.dir/docs/code/maybegz.cpp.o -c 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CMakeFiles/doc_maybegz.dir/docs/code/mutate.cpp.o -MF CMakeFiles/doc_maybegz.dir/docs/code/mutate.cpp.o.d -o CMakeFiles/doc_maybegz.dir/docs/code/mutate.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/docs/code/mutate.cpp -make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' -make -f CMakeFiles/check_conn.dir/build.make CMakeFiles/check_conn.dir/build -make[5]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-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 -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/doc_newmtz.dir/docs/code/newmtz.cpp.o -MF CMakeFiles/doc_newmtz.dir/docs/code/newmtz.cpp.o.d -o CMakeFiles/doc_newmtz.dir/docs/code/newmtz.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/docs/code/newmtz.cpp +/usr/bin/c++ -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 -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/test_disulf.dir/tests/disulf.cpp.o -MF CMakeFiles/test_disulf.dir/tests/disulf.cpp.o.d -o CMakeFiles/test_disulf.dir/tests/disulf.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/tests/disulf.cpp +/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 -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/doc_maybegz.dir/docs/code/maybegz.cpp.o -MF CMakeFiles/doc_maybegz.dir/docs/code/maybegz.cpp.o.d -o CMakeFiles/doc_maybegz.dir/docs/code/maybegz.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/docs/code/maybegz.cpp /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 -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/check_conn.dir/examples/check_conn.cpp.o -MF CMakeFiles/check_conn.dir/examples/check_conn.cpp.o.d -o CMakeFiles/check_conn.dir/examples/check_conn.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/examples/check_conn.cpp +/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 -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/doc_maybegz.dir/docs/code/mutate.cpp.o -MF CMakeFiles/doc_maybegz.dir/docs/code/mutate.cpp.o.d -o CMakeFiles/doc_maybegz.dir/docs/code/mutate.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/docs/code/mutate.cpp Consolidate compiler generated dependencies of target gemmi_prog make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' make -f CMakeFiles/gemmi_prog.dir/build.make CMakeFiles/gemmi_prog.dir/build @@ -1362,16 +1398,16 @@ /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 -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro CMakeFiles/doc_newmtz.dir/docs/code/newmtz.cpp.o -o doc_newmtz libgemmi_cpp.a /usr/lib/x86_64-linux-gnu/libz.so make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' [ 91%] Built target doc_newmtz +[ 91%] 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 -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro CMakeFiles/hello.dir/examples/hello.cpp.o -o hello +make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-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 /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 -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro CMakeFiles/doc_example2.dir/docs/code/cif_cc.cpp.o -o doc_example2 -[ 93%] 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 -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro CMakeFiles/hello.dir/examples/hello.cpp.o -o hello make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' [ 93%] Built target doc_example2 -make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' -[ 93%] Built target hello [ 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 -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro CMakeFiles/check_conn.dir/examples/check_conn.cpp.o -o check_conn libgemmi_cpp.a /usr/lib/x86_64-linux-gnu/libz.so @@ -1401,11 +1437,11 @@ /usr/bin/ctest -C None Test project /build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu Start 1: cpptest -1/1 Test #1: cpptest .......................... Passed 0.08 sec +1/1 Test #1: cpptest .......................... Passed 0.00 sec 100% tests passed, 0 tests failed out of 1 -Total Test time (real) = 0.08 sec +Total Test time (real) = 0.00 sec make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' [100%] Built target check make[4]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' @@ -1434,13 +1470,13 @@ SKIPPED [1] tests/test_seq.py:146: BioPython not installed. SKIPPED [1] tests/test_seq.py:105: BioPython not installed. SKIPPED [1] tests/test_seq.py:114: BioPython not installed. -172 passed, 17 skipped, 2 deselected in 5.36s +172 passed, 17 skipped, 2 deselected in 1.00s make[1]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=cmake dh_prep -O--buildsystem=cmake dh_auto_install -O--buildsystem=cmake - cd obj-x86_64-linux-gnu && make -j20 install DESTDIR=/build/reproducible-path/gemmi-0.6.5\+ds/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd obj-x86_64-linux-gnu && make -j42 install DESTDIR=/build/reproducible-path/gemmi-0.6.5\+ds/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/gemmi-0.6.5+ds -B/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -1452,110 +1488,110 @@ -- Install configuration: "None" -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/bin/gemmi -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/crd.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/span.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/bond_idx.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/chemcomp_xyz.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/seqtools.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/dirwalk.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/scaling.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/to_chemcomp.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/twin.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/seqid.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/fourier.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/smcif.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/intensit.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/pirfasta.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/fail.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/cellred.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/contact.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/fprime.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/ddl.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/dencalc.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/mmread.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/read_cif.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/riding_h.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/neighbor.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/stats.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/addends.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/third_party --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/third_party/pocketfft_hdronly.h --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/third_party/tinydir.h --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/third_party/fast_float.h --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/smcif.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/ecalc.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/floodfill.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/resinfo.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/remarks.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/gz.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/atof.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/utf.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/ccp4.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/chemcomp.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/sprintf.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/to_json.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/cif.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/qcp.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/polyheur.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/to_mmcif.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/pdb.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/eig3.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/mtz.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/fileutil.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/math.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/it92.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/assembly.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/calculate.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/chemcomp.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/neutron92.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/scaling.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/chemcomp_xyz.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/bond_idx.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/binner.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/to_pdb.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/refln.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/dencalc.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/model.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/modify.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/bessel.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/asumask.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/select.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/cellred.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/metadata.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/contact.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/cif2mtz.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/stats.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/to_chemcomp.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/mmcif.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/neutron92.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/xds_ascii.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/recgrid.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/c4322.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/fileutil.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/small.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/elem.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/mtz2cif.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/assembly.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/util.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/eig3.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/crd.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/json.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/mmdb.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/pdb_id.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/asudata.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/atof.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/sfcalc.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/symmetry.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/reciproc.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/asumask.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/ccp4.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/serialize.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/mmread_gz.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/linkhunt.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/topo.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/formfact.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/read_cif.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/monlib.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/solmask.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/mmcif_impl.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/sprintf.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/iterator.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/grid.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/addends.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/to_pdb.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/blob.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/span.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/floodfill.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/math.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/remarks.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/input.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/enumstr.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/topo.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/model.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/cif.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/json.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/numb.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/ddl.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/dirwalk.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/gz.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/metadata.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/unitcell.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/levmar.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/seqid.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/mmdb.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/atox.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/mtz2cif.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/pdb_id.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/utf.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/cifdoc.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/to_mmcif.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/intensit.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/linkhunt.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/xds_ascii.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/third_party +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/third_party/pocketfft_hdronly.h +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/third_party/fast_float.h +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/third_party/tinydir.h +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/riding_h.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/interop.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/formfact.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/small.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/to_json.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/align.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/polyheur.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/seqalign.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/calculate.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/ecalc.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/read_map.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/recgrid.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/numb.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/seqalign.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/fstream.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/version.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/elem.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/fourier.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/mmread_gz.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/sfcalc.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/serialize.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/blob.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/pirfasta.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/fail.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/modify.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/grid.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/reciproc.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/iterator.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/unitcell.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/symmetry.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/resinfo.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/twin.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/select.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/solmask.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/to_cif.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/qcp.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/util.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/cif2mtz.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/fstream.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/asudata.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/c4322.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/refln.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/atox.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/mmread.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/seqtools.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/mtz.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/align.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/mmcif_impl.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/it92.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/x86_64-linux-gnu/libgemmi_cpp.a -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/x86_64-linux-gnu/cmake/gemmi/gemmi-targets.cmake -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/x86_64-linux-gnu/cmake/gemmi/gemmi-targets-none.cmake @@ -1563,30 +1599,30 @@ -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/x86_64-linux-gnu/cmake/gemmi/gemmi-config-version.cmake -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi.cpython-312-x86_64-linux-gnu.so -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/hello.py --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/ccd_subgraph.py --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/aafreq.py --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/multiproc.py --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/rama_gather.py --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/maskdiff.py --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/from_json.py --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/rama_plot.py --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/refln-stats.py --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/merge_mtz_mmcif.py --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/patterson_slice.py -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/ccd_gi.py --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/cif_i_sigi.py +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/matthews.py -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/monomers.py --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/maskcheck.py --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/mtrix_iso.py +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/weight.py -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/mtz_i_sigi.py --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/matthews.py -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/long_geom.py --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/simple_search.py --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/weight.py --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/col_order.py --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/sub_ccd.py +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/mtrix_iso.py +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/rama_plot.py +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/rama_gather.py -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/map2mtz.py +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/sub_ccd.py +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/ccd_subgraph.py +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/refln-stats.py +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/maskdiff.py +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/merge_mtz_mmcif.py +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/from_json.py +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/multiproc.py +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/patterson_slice.py +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/col_order.py +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/aafreq.py +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/simple_search.py +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/maskcheck.py +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/cif_i_sigi.py +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/hello.py make[1]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' dh_install -O--buildsystem=cmake dh_installdocs -O--buildsystem=cmake @@ -1623,8 +1659,8 @@ dh_md5sums -O--buildsystem=cmake dh_builddeb -O--buildsystem=cmake dpkg-deb: building package 'gemmi' in '../gemmi_0.6.5+ds-2_amd64.deb'. -dpkg-deb: building package 'gemmi-dbgsym' in '../gemmi-dbgsym_0.6.5+ds-2_amd64.deb'. dpkg-deb: building package 'gemmi-dev' in '../gemmi-dev_0.6.5+ds-2_amd64.deb'. +dpkg-deb: building package 'gemmi-dbgsym' in '../gemmi-dbgsym_0.6.5+ds-2_amd64.deb'. dpkg-deb: building package 'python3-gemmi' in '../python3-gemmi_0.6.5+ds-2_amd64.deb'. dpkg-genbuildinfo --build=binary -O../gemmi_0.6.5+ds-2_amd64.buildinfo dpkg-genchanges --build=binary -O../gemmi_0.6.5+ds-2_amd64.changes @@ -1633,12 +1669,14 @@ 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/3648558/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3648558/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/2147460 and its subdirectories -I: Current time: Mon Dec 9 06:57:54 -12 2024 -I: pbuilder-time-stamp: 1733770674 +I: removing directory /srv/workspace/pbuilder/3648558 and its subdirectories +I: Current time: Mon Jan 12 15:31:07 +14 2026 +I: pbuilder-time-stamp: 1768181467