Diff of the two buildlogs: -- --- b1/build.log 2025-07-30 10:01:04.662355469 +0000 +++ b2/build.log 2025-07-30 10:04:59.874634402 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Jul 29 21:57:40 -12 2025 -I: pbuilder-time-stamp: 1753869460 +I: Current time: Wed Sep 2 06:24:29 +14 2026 +I: pbuilder-time-stamp: 1788279869 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -22,52 +22,84 @@ dpkg-source: info: unpacking libcifpp_7.0.9-1.debian.tar.xz I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/872058/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/586249/tmp/hooks/D01_modify_environment starting +debug: Running on codethink03-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Sep 1 16:24 /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/586249/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/586249/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='b169ee6cf36146598ec75b6eaea46677' - 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='872058' - PS1='# ' - PS2='> ' + INVOCATION_ID=d15323040da4443b82d87a986eee4b0c + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=586249 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.w4BMugVf/pbuilderrc_NIhR --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.w4BMugVf/b1 --logfile b1/build.log libcifpp_7.0.9-1.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.w4BMugVf/pbuilderrc_eNEp --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.w4BMugVf/b2 --logfile b2/build.log libcifpp_7.0.9-1.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink04-arm64 6.1.0-37-cloud-arm64 #1 SMP Debian 6.1.140-1 (2025-05-22) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-37-cloud-arm64 #1 SMP Debian 6.1.140-1 (2025-05-22) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 12 19:25 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/872058/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 12 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/586249/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -337,7 +369,7 @@ Get: 210 http://deb.debian.org/debian trixie/main arm64 python3-sphinxcontrib.jquery all 4.1-5 [7348 B] Get: 211 http://deb.debian.org/debian trixie/main arm64 python3-sphinx-rtd-theme all 3.0.2+dfsg-2 [29.7 kB] Get: 212 http://deb.debian.org/debian trixie/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] -Fetched 161 MB in 1s (283 MB/s) +Fetched 161 MB in 1s (203 MB/s) Preconfiguring packages ... Selecting previously unselected package fonts-lato. (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 ... 19964 files and directories currently installed.) @@ -1033,8 +1065,8 @@ Setting up tzdata (2025b-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Wed Jul 30 09:58:24 UTC 2025. -Universal Time is now: Wed Jul 30 09:58:24 UTC 2025. +Local time is now: Tue Sep 1 16:25:06 UTC 2026. +Universal Time is now: Tue Sep 1 16:25:06 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20240727.1) ... @@ -1226,7 +1258,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/libcifpp-7.0.9/ && 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 > ../libcifpp_7.0.9-1_source.changes +I: user script /srv/workspace/pbuilder/586249/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/586249/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/libcifpp-7.0.9/ && 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 > ../libcifpp_7.0.9-1_source.changes dpkg-buildpackage: info: source package libcifpp dpkg-buildpackage: info: source version 7.0.9-1 dpkg-buildpackage: info: source distribution unstable @@ -1284,7 +1320,7 @@ -- Performing Test COMPILER_HAS_DEPRECATED_ATTR - Success -- Found Doxygen: /usr/bin/doxygen (found version "1.9.8") found components: doxygen dot -- Found Sphinx: /usr/bin/sphinx-build --- Configuring done (9.3s) +-- Configuring done (9.9s) -- Generating done (0.1s) CMake Warning: Manually-specified variables were not used by the project: @@ -1312,48 +1348,48 @@ make -f docs/CMakeFiles/Doxygen-libcifpp.dir/build.make docs/CMakeFiles/Doxygen-libcifpp.dir/depend make -f docs/CMakeFiles/Sphinx-libcifpp.dir/build.make docs/CMakeFiles/Sphinx-libcifpp.dir/depend make[4]: Entering directory '/build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu' -cd /build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libcifpp-7.0.9 /build/reproducible-path/libcifpp-7.0.9/docs /build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu /build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu/docs /build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu/docs/CMakeFiles/Doxygen-libcifpp.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu' cd /build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libcifpp-7.0.9 /build/reproducible-path/libcifpp-7.0.9 /build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu /build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu /build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu/CMakeFiles/cifpp.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu' +cd /build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libcifpp-7.0.9 /build/reproducible-path/libcifpp-7.0.9/docs /build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu /build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu/docs /build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu/docs/CMakeFiles/Doxygen-libcifpp.dir/DependInfo.cmake "--color=" +make[4]: Entering directory '/build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu' cd /build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libcifpp-7.0.9 /build/reproducible-path/libcifpp-7.0.9/docs /build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu /build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu/docs /build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu/docs/CMakeFiles/Sphinx-libcifpp.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu' -make -f docs/CMakeFiles/Sphinx-libcifpp.dir/build.make docs/CMakeFiles/Sphinx-libcifpp.dir/build +make -f docs/CMakeFiles/Doxygen-libcifpp.dir/build.make docs/CMakeFiles/Doxygen-libcifpp.dir/build make[4]: Entering directory '/build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu' +make -f docs/CMakeFiles/Sphinx-libcifpp.dir/build.make docs/CMakeFiles/Sphinx-libcifpp.dir/build make[4]: Leaving directory '/build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu' make -f CMakeFiles/cifpp.dir/build.make CMakeFiles/cifpp.dir/build -make -f docs/CMakeFiles/Doxygen-libcifpp.dir/build.make docs/CMakeFiles/Doxygen-libcifpp.dir/build make[4]: Entering directory '/build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu' -[ 2%] Building CXX object CMakeFiles/cifpp.dir/src/datablock.cpp.o -[ 4%] Generating xml -[ 6%] Building CXX object CMakeFiles/cifpp.dir/src/item.cpp.o -[ 9%] Building CXX object CMakeFiles/cifpp.dir/src/category.cpp.o +[ 2%] Generating xml cd /build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu/docs && /usr/bin/cmake -E make_directory /build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu/docs/xml -/usr/bin/c++ -DBOOST_REGEX_STANDALONE=1 -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -DUSE_BOOST_REGEX=1 -Dcifpp_EXPORTS -I/build/reproducible-path/libcifpp-7.0.9/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/libcifpp-7.0.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -fPIC -MD -MT CMakeFiles/cifpp.dir/src/datablock.cpp.o -MF CMakeFiles/cifpp.dir/src/datablock.cpp.o.d -o CMakeFiles/cifpp.dir/src/datablock.cpp.o -c /build/reproducible-path/libcifpp-7.0.9/src/datablock.cpp -/usr/bin/c++ -DBOOST_REGEX_STANDALONE=1 -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -DUSE_BOOST_REGEX=1 -Dcifpp_EXPORTS -I/build/reproducible-path/libcifpp-7.0.9/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/libcifpp-7.0.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -fPIC -MD -MT CMakeFiles/cifpp.dir/src/item.cpp.o -MF CMakeFiles/cifpp.dir/src/item.cpp.o.d -o CMakeFiles/cifpp.dir/src/item.cpp.o -c /build/reproducible-path/libcifpp-7.0.9/src/item.cpp -[ 11%] Building CXX object CMakeFiles/cifpp.dir/src/condition.cpp.o -[ 13%] Building CXX object CMakeFiles/cifpp.dir/src/dictionary_parser.cpp.o -[ 15%] Generating xml +[ 4%] Building CXX object CMakeFiles/cifpp.dir/src/condition.cpp.o +[ 6%] Generating xml +[ 11%] Building CXX object CMakeFiles/cifpp.dir/src/dictionary_parser.cpp.o +[ 11%] Building CXX object CMakeFiles/cifpp.dir/src/file.cpp.o +[ 13%] Building CXX object CMakeFiles/cifpp.dir/src/datablock.cpp.o +[ 15%] Building CXX object CMakeFiles/cifpp.dir/src/category.cpp.o cd /build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu/docs && /usr/bin/cmake -E make_directory /build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu/docs/xml +[ 18%] Building CXX object CMakeFiles/cifpp.dir/src/item.cpp.o /usr/bin/c++ -DBOOST_REGEX_STANDALONE=1 -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -DUSE_BOOST_REGEX=1 -Dcifpp_EXPORTS -I/build/reproducible-path/libcifpp-7.0.9/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/libcifpp-7.0.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -fPIC -MD -MT CMakeFiles/cifpp.dir/src/category.cpp.o -MF CMakeFiles/cifpp.dir/src/category.cpp.o.d -o CMakeFiles/cifpp.dir/src/category.cpp.o -c /build/reproducible-path/libcifpp-7.0.9/src/category.cpp -[ 18%] Building CXX object CMakeFiles/cifpp.dir/src/file.cpp.o /usr/bin/c++ -DBOOST_REGEX_STANDALONE=1 -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -DUSE_BOOST_REGEX=1 -Dcifpp_EXPORTS -I/build/reproducible-path/libcifpp-7.0.9/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/libcifpp-7.0.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -fPIC -MD -MT CMakeFiles/cifpp.dir/src/condition.cpp.o -MF CMakeFiles/cifpp.dir/src/condition.cpp.o.d -o CMakeFiles/cifpp.dir/src/condition.cpp.o -c /build/reproducible-path/libcifpp-7.0.9/src/condition.cpp -[ 20%] Building CXX object CMakeFiles/cifpp.dir/src/parser.cpp.o +/usr/bin/c++ -DBOOST_REGEX_STANDALONE=1 -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -DUSE_BOOST_REGEX=1 -Dcifpp_EXPORTS -I/build/reproducible-path/libcifpp-7.0.9/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/libcifpp-7.0.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -fPIC -MD -MT CMakeFiles/cifpp.dir/src/datablock.cpp.o -MF CMakeFiles/cifpp.dir/src/datablock.cpp.o.d -o CMakeFiles/cifpp.dir/src/datablock.cpp.o -c /build/reproducible-path/libcifpp-7.0.9/src/datablock.cpp /usr/bin/c++ -DBOOST_REGEX_STANDALONE=1 -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -DUSE_BOOST_REGEX=1 -Dcifpp_EXPORTS -I/build/reproducible-path/libcifpp-7.0.9/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/libcifpp-7.0.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -fPIC -MD -MT CMakeFiles/cifpp.dir/src/dictionary_parser.cpp.o -MF CMakeFiles/cifpp.dir/src/dictionary_parser.cpp.o.d -o CMakeFiles/cifpp.dir/src/dictionary_parser.cpp.o -c /build/reproducible-path/libcifpp-7.0.9/src/dictionary_parser.cpp -[ 22%] Building CXX object CMakeFiles/cifpp.dir/src/row.cpp.o /usr/bin/c++ -DBOOST_REGEX_STANDALONE=1 -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -DUSE_BOOST_REGEX=1 -Dcifpp_EXPORTS -I/build/reproducible-path/libcifpp-7.0.9/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/libcifpp-7.0.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -fPIC -MD -MT CMakeFiles/cifpp.dir/src/file.cpp.o -MF CMakeFiles/cifpp.dir/src/file.cpp.o.d -o CMakeFiles/cifpp.dir/src/file.cpp.o -c /build/reproducible-path/libcifpp-7.0.9/src/file.cpp -[ 25%] Building CXX object CMakeFiles/cifpp.dir/src/validate.cpp.o -[ 27%] Generating docs +/usr/bin/c++ -DBOOST_REGEX_STANDALONE=1 -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -DUSE_BOOST_REGEX=1 -Dcifpp_EXPORTS -I/build/reproducible-path/libcifpp-7.0.9/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/libcifpp-7.0.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -fPIC -MD -MT CMakeFiles/cifpp.dir/src/item.cpp.o -MF CMakeFiles/cifpp.dir/src/item.cpp.o.d -o CMakeFiles/cifpp.dir/src/item.cpp.o -c /build/reproducible-path/libcifpp-7.0.9/src/item.cpp +[ 20%] Building CXX object CMakeFiles/cifpp.dir/src/parser.cpp.o /usr/bin/c++ -DBOOST_REGEX_STANDALONE=1 -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -DUSE_BOOST_REGEX=1 -Dcifpp_EXPORTS -I/build/reproducible-path/libcifpp-7.0.9/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/libcifpp-7.0.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -fPIC -MD -MT CMakeFiles/cifpp.dir/src/parser.cpp.o -MF CMakeFiles/cifpp.dir/src/parser.cpp.o.d -o CMakeFiles/cifpp.dir/src/parser.cpp.o -c /build/reproducible-path/libcifpp-7.0.9/src/parser.cpp +[ 22%] Building CXX object CMakeFiles/cifpp.dir/src/row.cpp.o /usr/bin/c++ -DBOOST_REGEX_STANDALONE=1 -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -DUSE_BOOST_REGEX=1 -Dcifpp_EXPORTS -I/build/reproducible-path/libcifpp-7.0.9/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/libcifpp-7.0.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -fPIC -MD -MT CMakeFiles/cifpp.dir/src/row.cpp.o -MF CMakeFiles/cifpp.dir/src/row.cpp.o.d -o CMakeFiles/cifpp.dir/src/row.cpp.o -c /build/reproducible-path/libcifpp-7.0.9/src/row.cpp -/usr/bin/c++ -DBOOST_REGEX_STANDALONE=1 -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -DUSE_BOOST_REGEX=1 -Dcifpp_EXPORTS -I/build/reproducible-path/libcifpp-7.0.9/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/libcifpp-7.0.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -fPIC -MD -MT CMakeFiles/cifpp.dir/src/validate.cpp.o -MF CMakeFiles/cifpp.dir/src/validate.cpp.o.d -o CMakeFiles/cifpp.dir/src/validate.cpp.o -c /build/reproducible-path/libcifpp-7.0.9/src/validate.cpp -cd /build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu/docs && /usr/bin/doxygen /build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu/docs/Doxyfile -[ 29%] Generating docs +[ 25%] Building CXX object CMakeFiles/cifpp.dir/src/validate.cpp.o +[ 27%] Generating docs cd /build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu/docs && /usr/bin/doxygen /build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu/docs/Doxyfile -[ 31%] Building CXX object CMakeFiles/cifpp.dir/src/text.cpp.o +/usr/bin/c++ -DBOOST_REGEX_STANDALONE=1 -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -DUSE_BOOST_REGEX=1 -Dcifpp_EXPORTS -I/build/reproducible-path/libcifpp-7.0.9/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/libcifpp-7.0.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -fPIC -MD -MT CMakeFiles/cifpp.dir/src/validate.cpp.o -MF CMakeFiles/cifpp.dir/src/validate.cpp.o.d -o CMakeFiles/cifpp.dir/src/validate.cpp.o -c /build/reproducible-path/libcifpp-7.0.9/src/validate.cpp +[ 29%] Building CXX object CMakeFiles/cifpp.dir/src/text.cpp.o /usr/bin/c++ -DBOOST_REGEX_STANDALONE=1 -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -DUSE_BOOST_REGEX=1 -Dcifpp_EXPORTS -I/build/reproducible-path/libcifpp-7.0.9/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/libcifpp-7.0.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -fPIC -MD -MT CMakeFiles/cifpp.dir/src/text.cpp.o -MF CMakeFiles/cifpp.dir/src/text.cpp.o.d -o CMakeFiles/cifpp.dir/src/text.cpp.o -c /build/reproducible-path/libcifpp-7.0.9/src/text.cpp +[ 31%] Generating docs +cd /build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu/docs && /usr/bin/doxygen /build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu/docs/Doxyfile Doxygen version used: 1.9.8 Searching for include files... Searching for example files... @@ -1564,7 +1600,19 @@ Generating code for file cif++/pdb/io.hpp... Generating code for file cif++/pdb/pdb2cif.hpp... Generating code for file cif++/pdb/tls.hpp... -Generating code for file c9/include/cif++/pdb/tls.hpp... +Generating code for file c/build/reproducible-path/libcifpp-7.0.9/include/cif++/validate.hpp:161: warning: Member make_error_code(validation_error e) (function) of namespace cif is not documented. +/build/reproducible-path/libcifpp-7.0.9/include/cif++/validate.hpp:166: warning: Member make_error_condition(validation_error e) (function) of namespace cif is not documented. +/build/reproducible-path/libcifpp-7.0.9/include/cif++/validate.hpp:161: warning: Member make_error_code(validation_error e) (function) of namespace cif is not documented. +/build/reproducible-path/libcifpp-7.0.9/include/cif++/validate.hpp:166: warning: Member make_error_condition(validation_error e) (function) of namespace cif is not documented. +/build/reproducible-path/libcifpp-7.0.9/include/cif++/category.hpp:975: warning: Member value_provider_type (typedef) of class cif::category is not documented. +/build/reproducible-path/libcifpp-7.0.9/include/cif++/category.hpp:153: warning: Member operator=(category rhs) (function) of class cif::category is not documented. +/build/reproducible-path/libcifpp-7.0.9/include/cif++/category.hpp:164: warning: Member swap(category &a, category &b) noexcept (friend) of class cif::category is not documented. +/build/reproducible-path/libcifpp-7.0.9/include/cif++/compound.hpp:175: warning: Member one_letter_code() const (function) of class cif::compound is not documented. +/build/reproducible-path/libcifpp-7.0.9/include/cif++/compound.hpp:273: warning: Member is_water(std::string_view res_name) const (function) of class cif::compound_factory is not documented. +/build/reproducible-path/libcifpp-7.0.9/include/cif++/compound.hpp:291: warning: Member report_missing_compound(std::string_view compound_id) (function) of class cif::compound_factory is not documented. +/build/reproducible-path/libcifpp-7.0.9/include/cif++/compound.hpp:326: warning: Member compound_source(const cif::file &file) (function) of class cif::compound_source is not documented. +/build/reproducible-path/libcifpp-7.0.9/include/cif++/datablock.hpp:77: warning: Member swap_(datablock &a, datablock &b) noexcept (friend) of class cif::datablock is not documented. +9/include/cif++/pdb/tls.hpp... Parsing file /build/reproducible-path/libcifpp-7.0.9/include/cif++/pdb/tls.hpp... Preprocessing /build/reproducible-path/libcifpp-7.0.9/include/cif++/point.hpp... Parsing file /build/reproducible-path/libcifpp-7.0.9/include/cif++/point.hpp... @@ -1660,31 +1708,9 @@ Generating code for file cif++/pdb/io.hpp... Generating code for file cif++/pdb/pdb2cif.hpp... Generating code for file cif++/pdb/tls.hpp... -Generating code for file c/build/reproducible-path/libcifpp-7.0.9/include/cif++/validate.hpp:161: warning: Member make_error_code(validation_error e) (function) of namespace cif is not documented. -/build/reproducible-path/libcifpp-7.0.9/include/cif++/validate.hpp:166: warning: Member make_error_condition(validation_error e) (function) of namespace cif is not documented. -/build/reproducible-path/libcifpp-7.0.9/include/cif++/validate.hpp:161: warning: Member make_error_code(validation_error e) (function) of namespace cif is not documented. -/build/reproducible-path/libcifpp-7.0.9/include/cif++/validate.hpp:166: warning: Member make_error_condition(validation_error e) (function) of namespace cif is not documented. -/build/reproducible-path/libcifpp-7.0.9/include/cif++/validate.hpp:161: warning: Member make_error_code(validation_error e) (function) of namespace cif is not documented. -/build/reproducible-path/libcifpp-7.0.9/include/cif++/validate.hpp:166: warning: Member make_error_condition(validation_error e) (function) of namespace cif is not documented. -/build/reproducible-path/libcifpp-7.0.9/include/cif++/category.hpp:975: warning: Member value_provider_type (typedef) of class cif::category is not documented. -/build/reproducible-path/libcifpp-7.0.9/include/cif++/category.hpp:153: warning: Member operator=(category rhs) (function) of class cif::category is not documented. -/build/reproducible-path/libcifpp-7.0.9/include/cif++/validate.hpp:161: warning: Member make_error_code(validation_error e) (function) of namespace cif is not documented. -/build/reproducible-path/libcifpp-7.0.9/include/cif++/validate.hpp:166: warning: Member make_error_condition(validation_error e) (function) of namespace cif is not documented. -/build/reproducible-path/libcifpp-7.0.9/include/cif++/category.hpp:975: warning: Member value_provider_type (typedef) of class cif::category is not documented. -/build/reproducible-path/libcifpp-7.0.9/include/cif++/category.hpp:153: warning: Member operator=(category rhs) (function) of class cif::category is not documented. -/build/reproducible-path/libcifpp-7.0.9/include/cif++/category.hpp:164: warning: Member swap(category &a, category &b) noexcept (friend) of class cif::category is not documented. -/build/reproducible-path/libcifpp-7.0.9/include/cif++/compound.hpp:175: warning: Member one_letter_code() const (function) of class cif::compound is not documented. -/build/reproducible-path/libcifpp-7.0.9/include/cif++/compound.hpp:273: warning: Member is_water(std::string_view res_name) const (function) of class cif::compound_factory is not documented. -/build/reproducible-path/libcifpp-7.0.9/include/cif++/compound.hpp:291: warning: Member report_missing_compound(std::string_view compound_id) (function) of class cif::compound_factory is not documented. -/build/reproducible-path/libcifpp-7.0.9/include/cif++/compound.hpp:326: warning: Member compound_source(const cif::file &file) (function) of class cif::compound_source is not documented. -/build/reproducible-path/libcifpp-7.0.9/include/cif++/datablock.hpp:77: warning: Member swap_(datablock &a, datablock &b) noexcept (friend) of class cif::datablock is not documented. -/build/reproducible-path/libcifpp-7.0.9/include/cif++/validate.hpp:280: warning: Member item_alias(const std::string &alias_name, const std::string &dictionary, const std::string &version) (function) of struct cif::item_alias is not documented. +Generating code for file c/build/reproducible-path/libcifpp-7.0.9/include/cif++/validate.hpp:280: warning: Member item_alias(const std::string &alias_name, const std::string &dictionary, const std::string &version) (function) of struct cif::item_alias is not documented. /build/reproducible-path/libcifpp-7.0.9/include/cif++/validate.hpp:287: warning: Member item_alias(const item_alias &)=default (function) of struct cif::item_alias is not documented. /build/reproducible-path/libcifpp-7.0.9/include/cif++/validate.hpp:288: warning: Member operator=(const item_alias &)=default (function) of struct cif::item_alias is not documented. -/build/reproducible-path/libcifpp-7.0.9/include/cif++/category.hpp:164: warning: Member swap(category &a, category &b) noexcept (friend) of class cif::category is not documented. -/build/reproducible-path/libcifpp-7.0.9/include/cif++/compound.hpp:175: warning: Member one_letter_code() const (function) of class cif::compound is not documented. -/build/reproducible-path/libcifpp-7.0.9/include/cif++/compound.hpp:273: warning: Member is_water(std::string_view res_name) const (function) of class cif::compound_factory is not documented. -/build/reproducible-path/libcifpp-7.0.9/include/cif++/compound.hpp:291: warning: Member report_missing_compound(std::string_view compound_id) (function) of class cif::compound_factory is not documented. /build/reproducible-path/libcifpp-7.0.9/include/cif++/category.hpp:87: warning: Member get_key() const noexcept (function) of class cif::missing_key_error is not documented. if++/point.hpp... Generating code for file cif++/row.hpp... @@ -1772,14 +1798,115 @@ Generating docs for compound cif::parser... Generating docs for compound cif::point_type... Generating docs for compound cif::progress_bar... -G/build/reproducible-path/libcifpp-7.0.9/include/cif++/compound.hpp:326: warning: Member compound_source(const cif::file &file) (function) of class cif::compound_source is not documented. -/build/reproducible-path/libcifpp-7.0.9/include/cif++/datablock.hpp:77: warning: Member swap_(datablock &a, datablock &b) noexcept (friend) of class cif::datablock is not documented. -/build/reproducible-path/libcifpp-7.0.9/include/cif++/validate.hpp:176: warning: Member validation_exception(validation_error err) (function) of class cif::validation_exception is not documented. +G/build/reproducible-path/libcifpp-7.0.9/include/cif++/validate.hpp:176: warning: Member validation_exception(validation_error err) (function) of class cif::validation_exception is not documented. /build/reproducible-path/libcifpp-7.0.9/include/cif++/validate.hpp:181: warning: Member validation_exception(validation_error err, std::string_view category) (function) of class cif::validation_exception is not documented. /build/reproducible-path/libcifpp-7.0.9/include/cif++/validate.hpp:186: warning: Member validation_exception(validation_error err, std::string_view category, std::string_view item) (function) of class cif::validation_exception is not documented. /build/reproducible-path/libcifpp-7.0.9/include/cif++/validate.hpp:191: warning: Member validation_exception(std::error_code ec) (function) of class cif::validation_exception is not documented. /build/reproducible-path/libcifpp-7.0.9/include/cif++/validate.hpp:193: warning: Member validation_exception(std::error_code ec, std::string_view category) (function) of class cif::validation_exception is not documented. /build/reproducible-path/libcifpp-7.0.9/include/cif++/validate.hpp:195: warning: Member validation_exception(std::error_code ec, std::string_view category, std::string_view item) (function) of class cif::validation_exception is not documented. +enerating docs for compound cif::quaternion_type... +Generating docs for compound cif::row... +Generating docs for compound cif::row_handle... +Generating docs for compound cif::row_initializer... +Generating docs for compound cif::sac_parser... +Generating docs for compound cif::space_group... +Generating docs for compound cif::spacegroup... +Generating docs for compound cif::spherical_dots... +Generating docs for compound cif::sym_op... +Generating docs for compound cif::symmetric_matrix... +Generating docs for compound cif::symmetric_matrix_fixed... +Generating docs for compound cif::symop_data... +Generating docs for compound cif::symop_datablock... +Generating docs for compound cif::transformation... +Generating docs for compound cif::type_validator... +Generating docs for compound cif::validation_category_impl... +Generating docs for compound cif::validation_exception... +Generating docs for compound cif::validator... +Generating docs for compound cif::validator_factory... +Generating docs for concept cif::Numeric... +Generating docs for compound cif::colour::detail::coloured_string_t... +Generating docs for compound cif::gzio::basic_ifstream... +Generating docs for compound cif::gzio::basic_igzip_streambuf... +Generating docs for compound cif::gzio::basic_istream... +Generating docs for compound cif::gzio::basic_ofstream... +Generating docs for compound cif::gzio::basic_ogzip_streambuf... +Generating docs for compound cif::gzio::basic_ostream... +Generating docs for compound cif::gzio::basic_streambuf... +Generating docs for compound cif::mm::atom... +Generating docs for compound cif::mm::branch... +Generating docs for compound cif::mm::monomer... +Generating docs for compound cif::mm::polymer... +Generating docs for compound cif::mm::residue... +Generating docs for compound cif::mm::structure... +Generating docs for compound cif::mm::sugar... +Generating graph info page... +Generating directory documentation... +Generating dependency graph for directory cif++/pdb +finalizing index lists... +writing tag file... +Generating XML output... +Generating XML output for class cif::mm::atom +Generating XML output for class cif::atom_type_info +Generating XML output for class cif::atom_type_traits +Generating XML output for class cif::gzio::basic_ifstream +Generating XML output for class cif::gzio::basic_igzip_streambuf +Generating XML output for class cif::gzio::basic_istream +Generating XML output for class cif::gzio::basic_ofstream +Generating XML output for class cif::gzio::basic_ogzip_streambuf +Generating XML output for class cif::gzio::basic_ostream +Generating XML output for class cif::gzio::basic_streambuf +Generating XML output for class cif::mm::branch +Generating XML output for class cif::category +Generating XML output for class cif::category_validator +Generating XML output for class cif::cell +Generating XML output for class cif::colour::detail::coloured_string_t +Generating XML output for class cif::compound +Generating XML output for class cif::compound_atom +Generating XML output for class cif::compound_bond +Generating XML output for class cif::compound_factory +Generating XML output for class cif::compound_source +Generating XML output for class cif::condition +Generating XML output for class cif::conditional_iterator_proxy +Generating XML output for class cif::crystal +Generating XML output for class cif::datablock +Generating XML output for class cif::duplicate_key_error +Generating XML output for class cif::empty_type +Generating XML output for class cif::file +Generating XML output for class cif::fill_out_streambuf +Generating XML output for class cif::identity_matrix +Generating XML output for class cif::iless +Generating XML output for class cif::item +Generating XML output for class cif::item_alias +Generating XML output for class cif::category::item_entry +Generating XML output for class cif::item_handle +Generating XML output for class cif::item_validator +Generating XML output for class cif::item_value +Generating XML output for class cif::iterator_impl +Generating XML output for class cif::iterator_impl< Category > +Generating XML output for class cif::iterator_impl< Ca/build/reproducible-path/libcifpp-7.0.9/include/cif++/validate.hpp:161: warning: Member make_error_code(validation_error e) (function) of namespace cif is not documented. +/build/reproducible-path/libcifpp-7.0.9/include/cif++/validate.hpp:166: warning: Member make_error_condition(validation_error e) (function) of namespace cif is not documented. +/build/reproducible-path/libcifpp-7.0.9/include/cif++/validate.hpp:161: warning: Member make_error_code(validation_error e) (function) of namespace cif is not documented. +/build/reproducible-path/libcifpp-7.0.9/include/cif++/validate.hpp:166: warning: Member make_error_condition(validation_error e) (function) of namespace cif is not documented. +/build/reproducible-path/libcifpp-7.0.9/include/cif++/category.hpp:975: warning: Member value_provider_type (typedef) of class cif::category is not documented. +/build/reproducible-path/libcifpp-7.0.9/include/cif++/category.hpp:153: warning: Member operator=(category rhs) (function) of class cif::category is not documented. +/build/reproducible-path/libcifpp-7.0.9/include/cif++/category.hpp:164: warning: Member swap(category &a, category &b) noexcept (friend) of class cif::category is not documented. +/build/reproducible-path/libcifpp-7.0.9/include/cif++/pdb.hpp:108: warning: argument 'file' of command @param is not found in the argument list of cif::pdb::reconstruct_pdbx(file &pdbx_file, std::string_view dictionary="mmcif_pdbx") +/build/reproducible-path/libcifpp-7.0.9/include/cif++/pdb.hpp:108: warning: The following parameter of cif::pdb::reconstruct_pdbx(file &pdbx_file, std::string_view dictionary="mmcif_pdbx") is not documented: + parameter 'pdbx_file' +/build/reproducible-path/libcifpp-7.0.9/include/cif++/pdb.hpp:120: warning: argument 'file' of command @param is not found in the argument list of cif::pdb::is_valid_pdbx_file(const file &pdbx_file, std::string_view dictionary="mmcif_pdbx") +/build/reproducible-path/libcifpp-7.0.9/include/cif++/pdb.hpp:120: warning: The following parameter of cif::pdb::is_valid_pdbx_file(const file &pdbx_file, std::string_view dictionary="mmcif_pdbx") is not documented: + parameter 'pdbx_file' +/build/reproducible-path/libcifpp-7.0.9/include/cif++/pdb.hpp:138: warning: argument 'file' of command @param is not found in the argument list of cif::pdb::is_valid_pdbx_file(const file &pdbx_file, std::error_code &ec) +/build/reproducible-path/libcifpp-7.0.9/include/cif++/pdb.hpp:138: warning: The following parameter of cif::pdb::is_valid_pdbx_file(const file &pdbx_file, std::error_code &ec) is not documented: + parameter 'pdbx_file' +/build/reproducible-path/libcifpp-7.0.9/include/cif++/pdb.hpp:157: warning: argument 'file' of command @param is not found in the argument list of cif::pdb::is_valid_pdbx_file(const file &pdbx_file, std::string_view dictionary, std::error_code &ec) +/build/reproducible-path/libcifpp-7.0.9/include/cif++/pdb.hpp:157: warning: The following parameter of cif::pdb::is_valid_pdbx_file(const file &pdbx_file, std::string_view dictionary, std::error_code &ec) is not documented: + parameter 'pdbx_file' +/build/reproducible-path/libcifpp-7.0.9/include/cif++/compound.hpp:175: warning: Member one_letter_code() const (function) of class cif::compound is not documented. +/build/reproducible-path/libcifpp-7.0.9/include/cif++/compound.hpp:273: warning: Member is_water(std::string_view res_name) const (function) of class cif::compound_factory is not documented. +/build/reproducible-path/libcifpp-7.0.9/include/cif++/compound.hpp:291: warning: Member report_missing_compound(std::string_view compound_id) (function) of class cif::compound_factory is not documented. +/build/reproducible-path/libcifpp-7.0.9/include/cif++/compound.hpp:326: warning: Member compound_source(const cif::file &file) (function) of class cif::compound_source is not documented. +/build/reproducible-path/libcifpp-7.0.9/include/cif++/datablock.hpp:77: warning: Member swap_(datablock &a, datablock &b) noexcept (friend) of class cif::datablock is not documented. /build/reproducible-path/libcifpp-7.0.9/include/cif++/validate.hpp:280: warning: Member item_alias(const std::string &alias_name, const std::string &dictionary, const std::string &version) (function) of struct cif::item_alias is not documented. /build/reproducible-path/libcifpp-7.0.9/include/cif++/validate.hpp:287: warning: Member item_alias(const item_alias &)=default (function) of struct cif::item_alias is not documented. /build/reproducible-path/libcifpp-7.0.9/include/cif++/validate.hpp:288: warning: Member operator=(const item_alias &)=default (function) of struct cif::item_alias is not documented. @@ -1876,177 +2003,7 @@ /build/reproducible-path/libcifpp-7.0.9/include/cif++/validate.hpp:191: warning: Member validation_exception(std::error_code ec) (function) of class cif::validation_exception is not documented. /build/reproducible-path/libcifpp-7.0.9/include/cif++/validate.hpp:193: warning: Member validation_exception(std::error_code ec, std::string_view category) (function) of class cif::validation_exception is not documented. /build/reproducible-path/libcifpp-7.0.9/include/cif++/validate.hpp:195: warning: Member validation_exception(std::error_code ec, std::string_view category, std::string_view item) (function) of class cif::validation_exception is not documented. -enerating docs for compound cif::quaternion_type... -Generating docs for compound cif::row... -Generating docs for compound cif::row_handle... -Generating docs for compound cif::row_initializer... -Generating docs for compound cif::sac_parser... -Generating docs for compound cif::space_group... -Generating docs for compound cif::spacegroup... -Generating docs for compound cif::spherical_dots... -Generating docs for compound cif::sym_op... -Generating docs for compound cif::symmetric_matrix... -Generating docs for compound cif::symmetric_matrix_fixed... -Generating docs for compound cif::symop_data... -Generating docs for compound cif::symop_datablock... -Generating docs for compound cif::transformation... -Generating docs for compound cif::type_validator... -Generating docs for compound cif::validation_category_impl... -Generating docs for compound cif::validation_exception... -Generating docs for compound cif::validator... -Generating docs for compound cif::validator_factory... -Generating docs for concept cif::Numeric... -Generating docs for compound cif::colour::detail::coloured_string_t... -Generating docs for compound cif::gzio::basic_ifstream... -Generating docs for compound cif::gzio::basic_igzip_streambuf... -Generating docs for compound cif::gzio::basic_istream... -Generating docs for compound cif::gzio::basic_ofstream... -Generating docs for compound cif::gzio::basic_ogzip_streambuf... -Generating docs for compound cif::gzio::basic_ostream... -Generating docs for compound cif::gzio::basic_streambuf... -Generating docs for compound cif::mm::atom... -Generating docs for compound cif::mm::branch... -Generating docs for compound cif::mm::monomer... -Generating docs for compound cif::mm::polymer... -Generating docs for compound cif::mm::residue... -Generating docs for compound cif::mm::structure... -Generating docs for compound cif::mm::sugar... -Generating graph info page... -Generating directory documentation... -Generating dependency graph for directory cif++/pdb -finalizing index lists... -writing tag file... -Generating XML output... -Generating XML output for class cif::mm::atom -Generating XML output for class cif::atom_type_info -Generating XML output for class cif::atom_type_traits -Generating XML output for class cif::gzio::basic_ifstream -Generating XML output for class cif::gzio::basic_igzip_streambuf -Generating XML output for class cif::gzio::basic_istream -Generating XML output for class cif::gzio::basic_ofstream -Generating XML output for class cif::gzio::basic_ogzip_streambuf -Generating XML output for class cif::gzio::basic_ostream -Generating XML output for class cif::gzio::basic_streambuf -Generating XML output for class cif::mm::branch -Generating XML output for class cif::category -Generating XML output for class cif::category_validator -Generating XML output for class cif::cell -Generating XML output for class cif::colour::detail::coloured_string_t -Generating XML output for class cif::compound -Generating XML output for class cif::compound_atom -Generating XML output for class cif::compound_bond -Generating XML output for class cif::compound_factory -Generating XML output for class cif::compound_source -Generating XML output for class cif::condition -Generating XML output for class cif::conditional_iterator_proxy -Generating XML output for class cif::crystal -Generating XML output for class cif::datablock -Generating XML output for class cif::duplicate_key_error -Generating XML output for class cif::empty_type -Generating XML output for class cif::file -Generating XML output for class cif::fill_out_streambuf -Generating XML output for class cif::identity_matrix -Generating XML output for class cif::iless -Generating XML output for class cif::item -Generating XML output for class cif::item_alias -Generating XML output for class cif::category::item_entry -Generating XML output for class cif::item_handle -Generating XML output for class cif::item_validator -Generating XML output for class cif::item_value -Generating XML output for class cif::iterator_impl -Generating XML output for class cif::iterator_impl< Category > -Generating XML output for class cif::iterator_impl< Ca/build/reproducible-path/libcifpp-7.0.9/include/cif++/pdb.hpp:108: warning: argument 'file' of command @param is not found in the argument list of cif::pdb::reconstruct_pdbx(file &pdbx_file, std::string_view dictionary="mmcif_pdbx") -/build/reproducible-path/libcifpp-7.0.9/include/cif++/pdb.hpp:108: warning: The following parameter of cif::pdb::reconstruct_pdbx(file &pdbx_file, std::string_view dictionary="mmcif_pdbx") is not documented: - parameter 'pdbx_file' -/build/reproducible-path/libcifpp-7.0.9/include/cif++/pdb.hpp:120: warning: argument 'file' of command @param is not found in the argument list of cif::pdb::is_valid_pdbx_file(const file &pdbx_file, std::string_view dictionary="mmcif_pdbx") -/build/reproducible-path/libcifpp-7.0.9/include/cif++/pdb.hpp:120: warning: The following parameter of cif::pdb::is_valid_pdbx_file(const file &pdbx_file, std::string_view dictionary="mmcif_pdbx") is not documented: - parameter 'pdbx_file' -/build/reproducible-path/libcifpp-7.0.9/include/cif++/pdb.hpp:138: warning: argument 'file' of command @param is not found in the argument list of cif::pdb::is_valid_pdbx_file(const file &pdbx_file, std::error_code &ec) -/build/reproducible-path/libcifpp-7.0.9/include/cif++/pdb.hpp:138: warning: The following parameter of cif::pdb::is_valid_pdbx_file(const file &pdbx_file, std::error_code &ec) is not documented: - parameter 'pdbx_file' -/build/reproducible-path/libcifpp-7.0.9/include/cif++/pdb.hpp:157: warning: argument 'file' of command @param is not found in the argument list of cif::pdb::is_valid_pdbx_file(const file &pdbx_file, std::string_view dictionary, std::error_code &ec) -/build/reproducible-path/libcifpp-7.0.9/include/cif++/pdb.hpp:157: warning: The following parameter of cif::pdb::is_valid_pdbx_file(const file &pdbx_file, std::string_view dictionary, std::error_code &ec) is not documented: - parameter 'pdbx_file' -enerating docs for compound cif::quaternion_type... -Generating docs for compound cif::row... -Generating docs for compound cif::row_handle... -Generating docs for compound cif::row_initializer... -Generating docs for compound cif::sac_parser... -Generating docs for compound cif::space_group... -Generating docs for compound cif::spacegroup... -Generating docs for compound cif::spherical_dots... -Generating docs for compound cif::sym_op... -Generating docs for compound cif::symmetric_matrix... -Generating docs for compound cif::symmetric_matrix_fixed... -Generating docs for compound cif::symop_data... -Generating docs for compound cif::symop_datablock... -Generating docs for compound cif::transformation... -Generating docs for compound cif::type_validator... -Generating docs for compound cif::validation_category_impl... -Generating docs for compound cif::validation_exception... -Generating docs for compound cif::validator... -Generating docs for compound cif::validator_factory... -Generating docs for concept cif::Numeric... -Generating docs for compound cif::colour::detail::coloured_string_t... -Generating docs for compound cif::gzio::basic_ifstream... -Generating docs for compound cif::gzio::basic_igzip_streambuf... -Generating docs for compound cif::gzio::basic_istream... -Generating docs for compound cif::gzio::basic_ofstream... -Generating docs for compound cif::gzio::basic_ogzip_streambuf... -Generating docs for compound cif::gzio::basic_ostream... -Generating docs for compound cif::gzio::basic_streambuf... -Generating docs for compound cif::mm::atom... -Generating docs for compound cif::mm::branch... -Generating docs for compound cif::mm::monomer... -Generating docs for compound cif::mm::polymer... -Generating docs for compound cif::mm::residue... -Generating docs for compound cif::mm::structure... -Generating docs for compound cif::mm::sugar... -Generating graph info page... -Generating directory documentation... -Generating dependency graph for directory cif++/pdb -finalizing index lists... -writing tag file... -Generating XML output... -Generating XML output for class cif::mm::atom -Generating XML output for class cif::atom_type_info -Generating XML output for class cif::atom_type_traits -Generating XML output for class cif::gzio::basic_ifstream -Generating XML output for class cif::gzio::basic_igzip_streambuf -Generating XML output for class cif::gzio::basic_istream -Generating XML output for class cif::gzio::basic_ofstream -Generating XML output for class cif::gzio::basic_ogzip_streambuf -Generating XML output for class cif::gzio::basic_ostream -Generating XML output for class cif::gzio::basic_streambuf -Generating XML output for class cif::mm::branch -Generating XML output for class cif::category -Generating XML output for class cif::category_validator -Generating XML output for class cif::cell -Generating XML output for class cif::colour::detail::coloured_string_t -Generating XML output for class cif::compound -Generating XML output for class cif::compound_atom -Generating XML output for class cif::compound_bond -Generating XML output for class cif::compound_factory -Generating XML output for class cif::compound_source -Generating XML output for class cif::condition -Generating XML output for class cif::conditional_iterator_proxy -Generating XML output for class cif::crystal -Generating XML output for class cif::datablock -Generating XML output for class cif::duplicate_key_error -Generating XML output for class cif::empty_type -Generating XML output for class cif::file -Generating XML output for class cif::fill_out_streambuf -Generating XML output for class cif::identity_matrix -Generating XML output for class cif::iless -Generating XML output for class cif::item -Generating XML output for class cif::item_alias -Generating XML output for class cif::category::item_entry -Generating XML output for class cif::item_handle -Generating XML output for class cif::item_validator -Generating XML output for class cif::item_value -Generating XML output for class cif::iterator_impl -Generating XML output for class cif::iterator_impl< Category > -Generating XML output for class cif::iterator_impl< Category, T > +tegory, T > Generating XML output for class cif::iterator_proxy Generating XML output for class cif::key Generating XML output for class cif::category::link @@ -2138,7 +2095,88 @@ type lookup cache used 4697/65536 hits=49311 misses=4943 symbol lookup cache used 5043/65536 hits=61869 misses=5043 finished... -/build/reproducible-path/libcifpp-7.0.9/include/cif++/pdb.hpp:108: warning: argument 'file' of command @param is not found in the argument list of cif::pdb::reconstruct_pdbx(file &pdbx_file, std::string_view dictionary="mmcif_pdbx") +[ 34%] Generating documentation with Sphinx +cd /build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu/docs && /usr/bin/sphinx-build -b html -Dbreathe_projects.libcifpp=/build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu/docs/xml /build/reproducible-path/libcifpp-7.0.9/docs /build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu/docs/sphinx +enerating docs for compound cif::quaternion_type... +Generating docs for compound cif::row... +Generating docs for compound cif::row_handle... +Generating docs for compound cif::row_initializer... +Generating docs for compound cif::sac_parser... +Generating docs for compound cif::space_group... +Generating docs for compound cif::spacegroup... +Generating docs for compound cif::spherical_dots... +Generating docs for compound cif::sym_op... +Generating docs for compound cif::symmetric_matrix... +Generating docs for compound cif::symmetric_matrix_fixed... +Generating docs for compound cif::symop_data... +Generating docs for compound cif::symop_datablock... +Generating docs for compound cif::transformation... +Generating docs for compound cif::type_validator... +Generating docs for compound cif::validation_category_impl... +Generating docs for compound cif::validation_exception... +Generating docs for compound cif::validator... +Generating docs for compound cif::validator_factory... +Generating docs for concept cif::Numeric... +Generating docs for compound cif::colour::detail::coloured_string_t... +Generating docs for compound cif::gzio::basic_ifstream... +Generating docs for compound cif::gzio::basic_igzip_streambuf... +Generating docs for compound cif::gzio::basic_istream... +Generating docs for compound cif::gzio::basic_ofstream... +Generating docs for compound cif::gzio::basic_ogzip_streambuf... +Generating docs for compound cif::gzio::basic_ostream... +Generating docs for compound cif::gzio::basic_streambuf... +Generating docs for compound cif::mm::atom... +Generating docs for compound cif::mm::branch... +Generating docs for compound cif::mm::monomer... +Generating docs for compound cif::mm::polymer... +Generating docs for compound cif::mm::residue... +Generating docs for compound cif::mm::structure... +Generating docs for compound cif::mm::sugar... +Generating graph info page... +Generating directory documentation... +Generating dependency graph for directory cif++/pdb +finalizing index lists... +writing tag file... +Generating XML output... +Generating XML output for class cif::mm::atom +Generating XML output for class cif::atom_type_info +Generating XML output for class cif::atom_type_traits +Generating XML output for class cif::gzio::basic_ifstream +Generating XML output for class cif::gzio::basic_igzip_streambuf +Generating XML output for class cif::gzio::basic_istream +Generating XML output for class cif::gzio::basic_ofstream +Generating XML output for class cif::gzio::basic_ogzip_streambuf +Generating XML output for class cif::gzio::basic_ostream +Generating XML output for class cif::gzio::basic_streambuf +Generating XML output for class cif::mm::branch +Generating XML output for class cif::category +Generating XML output for class cif::category_validator +Generating XML output for class cif::cell +Generating XML output for class cif::colour::detail::coloured_string_t +Generating XML output for class cif::compound +Generating XML output for class cif::compound_atom +Generating XML output for class cif::compound_bond +Generating XML output for class cif::compound_factory +Generating XML output for class cif::compound_source +Generating XML output for class cif::condition +Generating XML output for class cif::conditional_iterator_proxy +Generating XML output for class cif::crystal +Generating XML output for class cif::datablock +Generating XML output for class cif::duplicate_key_error +Generating XML output for class cif::empty_type +Generating XML output for class cif::file +Generating XML output for class cif::fill_out_streambuf +Generating XML output for class cif::identity_matrix +Generating XML output for class cif::iless +Generating XML output for class cif::item +Generating XML output for class cif::item_alias +Generating XML output for class cif::category::item_entry +Generating XML output for class cif::item_handle +Generating XML output for class cif::item_validator +Generating XML output for class cif::item_value +Generating XML output for class cif::iterator_impl +Generating XML output for class cif::iterator_impl< Category > +Generating XML output for class cif::iterator_impl< Ca/build/reproducible-path/libcifpp-7.0.9/include/cif++/pdb.hpp:108: warning: argument 'file' of command @param is not found in the argument list of cif::pdb::reconstruct_pdbx(file &pdbx_file, std::string_view dictionary="mmcif_pdbx") /build/reproducible-path/libcifpp-7.0.9/include/cif++/pdb.hpp:108: warning: The following parameter of cif::pdb::reconstruct_pdbx(file &pdbx_file, std::string_view dictionary="mmcif_pdbx") is not documented: parameter 'pdbx_file' /build/reproducible-path/libcifpp-7.0.9/include/cif++/pdb.hpp:120: warning: argument 'file' of command @param is not found in the argument list of cif::pdb::is_valid_pdbx_file(const file &pdbx_file, std::string_view dictionary="mmcif_pdbx") @@ -2150,8 +2188,8 @@ /build/reproducible-path/libcifpp-7.0.9/include/cif++/pdb.hpp:157: warning: argument 'file' of command @param is not found in the argument list of cif::pdb::is_valid_pdbx_file(const file &pdbx_file, std::string_view dictionary, std::error_code &ec) /build/reproducible-path/libcifpp-7.0.9/include/cif++/pdb.hpp:157: warning: The following parameter of cif::pdb::is_valid_pdbx_file(const file &pdbx_file, std::string_view dictionary, std::error_code &ec) is not documented: parameter 'pdbx_file' -[ 34%] Generating documentation with Sphinx -cd /build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu/docs && /usr/bin/sphinx-build -b html -Dbreathe_projects.libcifpp=/build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu/docs/xml /build/reproducible-path/libcifpp-7.0.9/docs /build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu/docs/sphinx +Running Sphinx v8.1.3 +loading translations [en]... done tegory, T > Generating XML output for class cif::iterator_proxy Generating XML output for class cif::key @@ -2248,13 +2286,11 @@ [ 34%] Built target Doxygen-libcifpp [ 36%] Building CXX object CMakeFiles/cifpp.dir/src/utilities.cpp.o /usr/bin/c++ -DBOOST_REGEX_STANDALONE=1 -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -DUSE_BOOST_REGEX=1 -Dcifpp_EXPORTS -I/build/reproducible-path/libcifpp-7.0.9/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/libcifpp-7.0.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -fPIC -MD -MT CMakeFiles/cifpp.dir/src/utilities.cpp.o -MF CMakeFiles/cifpp.dir/src/utilities.cpp.o.d -o CMakeFiles/cifpp.dir/src/utilities.cpp.o -c /build/reproducible-path/libcifpp-7.0.9/src/utilities.cpp -Running Sphinx v8.1.3 -loading translations [en]... done -[ 38%] Building CXX object CMakeFiles/cifpp.dir/src/atom_type.cpp.o -/usr/bin/c++ -DBOOST_REGEX_STANDALONE=1 -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -DUSE_BOOST_REGEX=1 -Dcifpp_EXPORTS -I/build/reproducible-path/libcifpp-7.0.9/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/libcifpp-7.0.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -fPIC -MD -MT CMakeFiles/cifpp.dir/src/atom_type.cpp.o -MF CMakeFiles/cifpp.dir/src/atom_type.cpp.o.d -o CMakeFiles/cifpp.dir/src/atom_type.cpp.o -c /build/reproducible-path/libcifpp-7.0.9/src/atom_type.cpp /usr/lib/python3/dist-packages/breathe/project.py:116: RemovedInSphinx90Warning: Sphinx 9 will drop support for representing paths as strings. Use "pathlib.Path" or "os.fspath" instead. self._default_build_dir = os.path.dirname(app.doctreedir.rstrip(os.sep)) making output directory... done +[ 38%] Building CXX object CMakeFiles/cifpp.dir/src/atom_type.cpp.o +/usr/bin/c++ -DBOOST_REGEX_STANDALONE=1 -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -DUSE_BOOST_REGEX=1 -Dcifpp_EXPORTS -I/build/reproducible-path/libcifpp-7.0.9/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/libcifpp-7.0.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -fPIC -MD -MT CMakeFiles/cifpp.dir/src/atom_type.cpp.o -MF CMakeFiles/cifpp.dir/src/atom_type.cpp.o.d -o CMakeFiles/cifpp.dir/src/atom_type.cpp.o -c /build/reproducible-path/libcifpp-7.0.9/src/atom_type.cpp [ 40%] Building CXX object CMakeFiles/cifpp.dir/src/compound.cpp.o /usr/bin/c++ -DBOOST_REGEX_STANDALONE=1 -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -DUSE_BOOST_REGEX=1 -Dcifpp_EXPORTS -I/build/reproducible-path/libcifpp-7.0.9/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/libcifpp-7.0.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -fPIC -MD -MT CMakeFiles/cifpp.dir/src/compound.cpp.o -MF CMakeFiles/cifpp.dir/src/compound.cpp.o.d -o CMakeFiles/cifpp.dir/src/compound.cpp.o -c /build/reproducible-path/libcifpp-7.0.9/src/compound.cpp [ 43%] Building CXX object CMakeFiles/cifpp.dir/src/point.cpp.o @@ -2265,23 +2301,23 @@ /usr/bin/c++ -DBOOST_REGEX_STANDALONE=1 -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -DUSE_BOOST_REGEX=1 -Dcifpp_EXPORTS 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[ 0%] api/classcif_1_1atom__type__traits +[ 52%] Building CXX object CMakeFiles/cifpp.dir/src/pdb/pdb2cif.cpp.o +/usr/bin/c++ -DBOOST_REGEX_STANDALONE=1 -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -DUSE_BOOST_REGEX=1 -Dcifpp_EXPORTS -I/build/reproducible-path/libcifpp-7.0.9/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/libcifpp-7.0.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -fPIC -MD -MT CMakeFiles/cifpp.dir/src/pdb/pdb2cif.cpp.o -MF CMakeFiles/cifpp.dir/src/pdb/pdb2cif.cpp.o.d -o CMakeFiles/cifpp.dir/src/pdb/pdb2cif.cpp.o -c /build/reproducible-path/libcifpp-7.0.9/src/pdb/pdb2cif.cpp +[ 54%] Building CXX object CMakeFiles/cifpp.dir/src/pdb/pdb2cif_remark_3.cpp.o +/usr/bin/c++ -DBOOST_REGEX_STANDALONE=1 -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -DUSE_BOOST_REGEX=1 -Dcifpp_EXPORTS -I/build/reproducible-path/libcifpp-7.0.9/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/libcifpp-7.0.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -fPIC -MD -MT CMakeFiles/cifpp.dir/src/pdb/pdb2cif_remark_3.cpp.o -MF CMakeFiles/cifpp.dir/src/pdb/pdb2cif_remark_3.cpp.o.d -o CMakeFiles/cifpp.dir/src/pdb/pdb2cif_remark_3.cpp.o -c /build/reproducible-path/libcifpp-7.0.9/src/pdb/pdb2cif_remark_3.cpp +[ 56%] Building CXX object CMakeFiles/cifpp.dir/src/pdb/reconstruct.cpp.o +/usr/bin/c++ -DBOOST_REGEX_STANDALONE=1 -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -DUSE_BOOST_REGEX=1 -Dcifpp_EXPORTS -I/build/reproducible-path/libcifpp-7.0.9/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/libcifpp-7.0.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -fPIC -MD -MT CMakeFiles/cifpp.dir/src/pdb/reconstruct.cpp.o -MF CMakeFiles/cifpp.dir/src/pdb/reconstruct.cpp.o.d -o CMakeFiles/cifpp.dir/src/pdb/reconstruct.cpp.o -c /build/reproducible-path/libcifpp-7.0.9/src/pdb/reconstruct.cpp [ 59%] Building CXX object CMakeFiles/cifpp.dir/src/pdb/validate-pdbx.cpp.o /usr/bin/c++ -DBOOST_REGEX_STANDALONE=1 -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -DUSE_BOOST_REGEX=1 -Dcifpp_EXPORTS -I/build/reproducible-path/libcifpp-7.0.9/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/libcifpp-7.0.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -fPIC -MD -MT CMakeFiles/cifpp.dir/src/pdb/validate-pdbx.cpp.o -MF CMakeFiles/cifpp.dir/src/pdb/validate-pdbx.cpp.o.d -o CMakeFiles/cifpp.dir/src/pdb/validate-pdbx.cpp.o -c /build/reproducible-path/libcifpp-7.0.9/src/pdb/validate-pdbx.cpp reading sources... [ 1%] api/classcif_1_1category @@ -2514,25 +2550,6 @@ reading sources... [ 69%] api/function_pdb_8hpp_1a6eb3f608312210636d8d4bd3fd69745a reading sources... [ 69%] api/function_pdb_8hpp_1a8442a8beb3ec3862b1223091ba279b3f reading sources... [ 70%] api/function_pdb_8hpp_1a965679d61a80ce38487bb63eb1759281 -In file included from /usr/include/c++/14/string:42, - from /usr/include/c++/14/stdexcept:39, - from /usr/include/c++/14/system_error:43, - from /usr/include/c++/14/bits/fs_fwd.h:35, - from /usr/include/c++/14/filesystem:51, - from /build/reproducible-path/libcifpp-7.0.9/include/cif++/utilities.hpp:31, - from /build/reproducible-path/libcifpp-7.0.9/include/cif++.hpp:29, - from /build/reproducible-path/libcifpp-7.0.9/src/pdb/reconstruct.cpp:27: -In static member function ‘static constexpr void std::char_traits::assign(char_type&, const char_type&)’, - inlined from ‘constexpr void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::push_back(_CharT) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/basic_string.h:1577:21, - inlined from ‘constexpr std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator+=(_CharT) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/basic_string.h:1399:17, - inlined from ‘void cif::pdb::createEntityPoly(cif::datablock&)’ at /build/reproducible-path/libcifpp-7.0.9/src/pdb/reconstruct.cpp:845:29: -/usr/include/c++/14/bits/char_traits.h:350:14: warning: ‘letter_can’ may be used uninitialized [-Wmaybe-uninitialized] - 350 | __c1 = __c2; - | ~~~~~^~~~~~ -/build/reproducible-path/libcifpp-7.0.9/src/pdb/reconstruct.cpp: In function ‘void cif::pdb::createEntityPoly(cif::datablock&)’: -/build/reproducible-path/libcifpp-7.0.9/src/pdb/reconstruct.cpp:780:30: note: ‘letter_can’ was declared here - 780 | char letter_can; - | ^~~~~~~~~~ reading sources... [ 70%] api/function_pdb_8hpp_1aa1addf5082e01849dc7b0af93aa0d34d reading sources... [ 70%] api/function_pdb_8hpp_1aa4bb7030a077b462d75b328a2d6ef70d reading sources... [ 70%] api/function_pdb_8hpp_1aa57fd6d1c296ee70c9784fc59382d7c1 @@ -2594,6 +2611,25 @@ reading sources... [ 87%] api/structcif_1_1key reading sources... [ 88%] api/structcif_1_1link__validator reading sources... [ 88%] api/structcif_1_1my__charconv +In file included from /usr/include/c++/14/string:42, + from /usr/include/c++/14/stdexcept:39, + from /usr/include/c++/14/system_error:43, + from /usr/include/c++/14/bits/fs_fwd.h:35, + from /usr/include/c++/14/filesystem:51, + from /build/reproducible-path/libcifpp-7.0.9/include/cif++/utilities.hpp:31, + from /build/reproducible-path/libcifpp-7.0.9/include/cif++.hpp:29, + from /build/reproducible-path/libcifpp-7.0.9/src/pdb/reconstruct.cpp:27: +In static member function ‘static constexpr void std::char_traits::assign(char_type&, const char_type&)’, + inlined from ‘constexpr void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::push_back(_CharT) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/basic_string.h:1577:21, + inlined from ‘constexpr std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator+=(_CharT) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/basic_string.h:1399:17, + inlined from ‘void cif::pdb::createEntityPoly(cif::datablock&)’ at /build/reproducible-path/libcifpp-7.0.9/src/pdb/reconstruct.cpp:845:29: +/usr/include/c++/14/bits/char_traits.h:350:14: warning: ‘letter_can’ may be used uninitialized [-Wmaybe-uninitialized] + 350 | __c1 = __c2; + | ~~~~~^~~~~~ +/build/reproducible-path/libcifpp-7.0.9/src/pdb/reconstruct.cpp: In function ‘void cif::pdb::createEntityPoly(cif::datablock&)’: +/build/reproducible-path/libcifpp-7.0.9/src/pdb/reconstruct.cpp:780:30: note: ‘letter_can’ was declared here + 780 | char letter_can; + | ^~~~~~~~~~ reading sources... [ 88%] api/structcif_1_1point__type reading sources... [ 89%] api/structcif_1_1space__group reading sources... [ 89%] api/structcif_1_1sym__op @@ -2773,6 +2809,19 @@ writing output... [ 16%] api/classcif_1_1symmetric__matrix__fixed writing output... [ 17%] api/classcif_1_1transformation writing output... [ 17%] api/classcif_1_1validation__category__impl +writing output... [ 17%] api/classcif_1_1validation__exception +writing output... [ 17%] api/classcif_1_1validator +writing output... [ 18%] api/classcif_1_1validator__factory +writing output... [ 18%] api/define_exports_8hpp_1a34c1ecdfe0e74030d387cc4e3db0f20d +writing output... [ 18%] api/define_exports_8hpp_1a42700069adcc34faeda32076bd173dc1 +writing output... [ 19%] api/define_exports_8hpp_1aab9ff10a498bf7bb72ce703e00c6551c +writing output... [ 19%] api/define_exports_8hpp_1af93831e3c71f1f7a80712cd6b3812992 +writing output... [ 19%] api/define_utilities_8hpp_1abd165ee6474b5b75bf075842fff13a04 +writing output... [ 20%] api/define_utilities_8hpp_1ae2fe1725bb5e9823d089c46b9ed5266e +writing output... [ 20%] api/dir_cif++ +writing output... [ 20%] api/dir_cif++_pdb +writing output... [ 20%] api/enum_model_8hpp_1a04742ae1684db656d2534463f850eb37 +writing output... [ 21%] api/enum_model_8hpp_1a6085af7e2c3294d3d5520e387757e8dd In file included from /usr/include/eigen3/Eigen/Core:341, from /usr/include/eigen3/Eigen/Eigenvalues:11, from /build/reproducible-path/libcifpp-7.0.9/src/symmetry.cpp:35: @@ -2801,19 +2850,6 @@ /usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h:105:24: note: by argument 5 of type ‘const float*’ to ‘static void Eigen::internal::triangular_matrix_vector_product::run(Index, Index, const LhsScalar*, Index, const RhsScalar*, Index, ResScalar*, Index, const ResScalar&) [with Index = long int; int Mode = 6; LhsScalar = float; bool ConjLhs = false; RhsScalar = float; bool ConjRhs = false; int Version = 0]’ declared here 105 | EIGEN_DONT_INLINE void triangular_matrix_vector_product | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -writing output... [ 17%] api/classcif_1_1validation__exception -writing output... [ 17%] api/classcif_1_1validator -writing output... [ 18%] api/classcif_1_1validator__factory -writing output... [ 18%] api/define_exports_8hpp_1a34c1ecdfe0e74030d387cc4e3db0f20d -writing output... [ 18%] api/define_exports_8hpp_1a42700069adcc34faeda32076bd173dc1 -writing output... [ 19%] api/define_exports_8hpp_1aab9ff10a498bf7bb72ce703e00c6551c -writing output... [ 19%] api/define_exports_8hpp_1af93831e3c71f1f7a80712cd6b3812992 -writing output... [ 19%] api/define_utilities_8hpp_1abd165ee6474b5b75bf075842fff13a04 -writing output... [ 20%] api/define_utilities_8hpp_1ae2fe1725bb5e9823d089c46b9ed5266e -writing output... [ 20%] api/dir_cif++ -writing output... [ 20%] api/dir_cif++_pdb -writing output... [ 20%] api/enum_model_8hpp_1a04742ae1684db656d2534463f850eb37 -writing output... [ 21%] api/enum_model_8hpp_1a6085af7e2c3294d3d5520e387757e8dd writing output... [ 21%] api/enum_namespacecif_1a22f8e0bb538e176ebddfe89c7ef03a6d writing output... [ 21%] api/enum_namespacecif_1a339253d4b856d267db110e2e55b6fa46 writing output... [ 22%] api/enum_namespacecif_1a636b6271c6af17a0d73dbe4557061c03 @@ -3119,65 +3155,65 @@ make -f test/CMakeFiles/format-test.dir/build.make test/CMakeFiles/format-test.dir/depend make -f test/CMakeFiles/model-test.dir/build.make test/CMakeFiles/model-test.dir/depend make -f test/CMakeFiles/rename-compound-test.dir/build.make test/CMakeFiles/rename-compound-test.dir/depend -make -f test/CMakeFiles/sugar-test.dir/build.make test/CMakeFiles/sugar-test.dir/depend make[4]: Entering directory '/build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu' +make -f test/CMakeFiles/sugar-test.dir/build.make test/CMakeFiles/sugar-test.dir/depend cd /build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libcifpp-7.0.9 /build/reproducible-path/libcifpp-7.0.9/test /build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu /build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu/test /build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu/test/CMakeFiles/unit-v2-test.dir/DependInfo.cmake "--color=" -make -f test/CMakeFiles/spinner-test.dir/build.make test/CMakeFiles/spinner-test.dir/depend make[4]: Entering directory '/build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu' cd /build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libcifpp-7.0.9 /build/reproducible-path/libcifpp-7.0.9/test /build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu /build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu/test /build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu/test/CMakeFiles/unit-3d-test.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu' -cd /build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libcifpp-7.0.9 /build/reproducible-path/libcifpp-7.0.9/test /build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu /build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu/test /build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu/test/CMakeFiles/format-test.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu' cd /build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libcifpp-7.0.9 /build/reproducible-path/libcifpp-7.0.9/test /build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu /build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu/test /build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu/test/CMakeFiles/model-test.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu' +cd /build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libcifpp-7.0.9 /build/reproducible-path/libcifpp-7.0.9/test /build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu /build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu/test /build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu/test/CMakeFiles/format-test.dir/DependInfo.cmake "--color=" +make[4]: Entering directory '/build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu' cd /build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libcifpp-7.0.9 /build/reproducible-path/libcifpp-7.0.9/test /build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu /build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu/test /build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu/test/CMakeFiles/rename-compound-test.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu' cd /build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libcifpp-7.0.9 /build/reproducible-path/libcifpp-7.0.9/test /build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu /build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu/test /build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu/test/CMakeFiles/sugar-test.dir/DependInfo.cmake "--color=" +make -f test/CMakeFiles/spinner-test.dir/build.make test/CMakeFiles/spinner-test.dir/depend make[4]: Entering directory '/build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu' -make -f test/CMakeFiles/validate-pdbx-test.dir/build.make test/CMakeFiles/validate-pdbx-test.dir/depend cd /build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libcifpp-7.0.9 /build/reproducible-path/libcifpp-7.0.9/test /build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu /build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu/test /build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu/test/CMakeFiles/spinner-test.dir/DependInfo.cmake "--color=" +make -f test/CMakeFiles/validate-pdbx-test.dir/build.make test/CMakeFiles/validate-pdbx-test.dir/depend make[4]: Entering directory '/build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu' cd /build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libcifpp-7.0.9 /build/reproducible-path/libcifpp-7.0.9/test /build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu /build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu/test /build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu/test/CMakeFiles/validate-pdbx-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu' -make -f test/CMakeFiles/unit-v2-test.dir/build.make test/CMakeFiles/unit-v2-test.dir/build +make -f test/CMakeFiles/model-test.dir/build.make test/CMakeFiles/model-test.dir/build make[4]: Entering directory '/build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu' +make -f test/CMakeFiles/unit-v2-test.dir/build.make test/CMakeFiles/unit-v2-test.dir/build make[4]: Leaving directory '/build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu' -make -f test/CMakeFiles/format-test.dir/build.make test/CMakeFiles/format-test.dir/build +make[4]: Entering directory '/build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu' make -f test/CMakeFiles/unit-3d-test.dir/build.make test/CMakeFiles/unit-3d-test.dir/build make[4]: Leaving directory '/build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu' +make -f test/CMakeFiles/format-test.dir/build.make test/CMakeFiles/format-test.dir/build +[ 65%] Building CXX object test/CMakeFiles/model-test.dir/model-test.cpp.o make[4]: Leaving directory '/build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu' +cd /build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu/test && /usr/bin/c++ -DCACHE_DIR=\"/var/cache/libcifpp\" -DCATCH22=0 -DDATA_DIR=\"/usr/share/libcifpp\" -I/usr/include/eigen3 -I/build/reproducible-path/libcifpp-7.0.9/include -g -O2 -ffile-prefix-map=/build/reproducible-path/libcifpp-7.0.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers 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Building CXX object test/CMakeFiles/model-test.dir/model-test.cpp.o -cd /build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu/test && /usr/bin/c++ -DCACHE_DIR=\"/var/cache/libcifpp\" -DCATCH22=0 -DDATA_DIR=\"/usr/share/libcifpp\" -I/usr/include/eigen3 -I/build/reproducible-path/libcifpp-7.0.9/include -g -O2 -ffile-prefix-map=/build/reproducible-path/libcifpp-7.0.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -MD -MT test/CMakeFiles/format-test.dir/format-test.cpp.o -MF CMakeFiles/format-test.dir/format-test.cpp.o.d -o CMakeFiles/format-test.dir/format-test.cpp.o -c /build/reproducible-path/libcifpp-7.0.9/test/format-test.cpp -cd /build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu/test && /usr/bin/c++ -DCACHE_DIR=\"/var/cache/libcifpp\" -DCATCH22=0 -DDATA_DIR=\"/usr/share/libcifpp\" -I/usr/include/eigen3 -I/build/reproducible-path/libcifpp-7.0.9/include -g -O2 -ffile-prefix-map=/build/reproducible-path/libcifpp-7.0.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -MD -MT test/CMakeFiles/spinner-test.dir/spinner-test.cpp.o -MF CMakeFiles/spinner-test.dir/spinner-test.cpp.o.d -o CMakeFiles/spinner-test.dir/spinner-test.cpp.o -c /build/reproducible-path/libcifpp-7.0.9/test/spinner-test.cpp -[ 79%] Building CXX object test/CMakeFiles/sugar-test.dir/sugar-test.cpp.o cd /build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu/test && /usr/bin/c++ -DCACHE_DIR=\"/var/cache/libcifpp\" -DCATCH22=0 -DDATA_DIR=\"/usr/share/libcifpp\" -I/usr/include/eigen3 -I/build/reproducible-path/libcifpp-7.0.9/include -g -O2 -ffile-prefix-map=/build/reproducible-path/libcifpp-7.0.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -MD -MT test/CMakeFiles/unit-v2-test.dir/unit-v2-test.cpp.o -MF CMakeFiles/unit-v2-test.dir/unit-v2-test.cpp.o.d -o CMakeFiles/unit-v2-test.dir/unit-v2-test.cpp.o -c /build/reproducible-path/libcifpp-7.0.9/test/unit-v2-test.cpp -cd /build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu/test && /usr/bin/c++ -DCACHE_DIR=\"/var/cache/libcifpp\" -DCATCH22=0 -DDATA_DIR=\"/usr/share/libcifpp\" -I/usr/include/eigen3 -I/build/reproducible-path/libcifpp-7.0.9/include -g -O2 -ffile-prefix-map=/build/reproducible-path/libcifpp-7.0.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -MD -MT test/CMakeFiles/unit-3d-test.dir/unit-3d-test.cpp.o -MF CMakeFiles/unit-3d-test.dir/unit-3d-test.cpp.o.d -o CMakeFiles/unit-3d-test.dir/unit-3d-test.cpp.o -c /build/reproducible-path/libcifpp-7.0.9/test/unit-3d-test.cpp -cd /build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu/test && /usr/bin/c++ -DCACHE_DIR=\"/var/cache/libcifpp\" -DCATCH22=0 -DDATA_DIR=\"/usr/share/libcifpp\" -I/usr/include/eigen3 -I/build/reproducible-path/libcifpp-7.0.9/include -g -O2 -ffile-prefix-map=/build/reproducible-path/libcifpp-7.0.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -MD -MT test/CMakeFiles/rename-compound-test.dir/rename-compound-test.cpp.o -MF CMakeFiles/rename-compound-test.dir/rename-compound-test.cpp.o.d -o CMakeFiles/rename-compound-test.dir/rename-compound-test.cpp.o -c /build/reproducible-path/libcifpp-7.0.9/test/rename-compound-test.cpp +[ 77%] Building CXX object test/CMakeFiles/format-test.dir/format-test.cpp.o +[ 77%] Building CXX object test/CMakeFiles/sugar-test.dir/sugar-test.cpp.o cd /build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu/test && /usr/bin/c++ -DCACHE_DIR=\"/var/cache/libcifpp\" -DCATCH22=0 -DDATA_DIR=\"/usr/share/libcifpp\" -I/usr/include/eigen3 -I/build/reproducible-path/libcifpp-7.0.9/include -g -O2 -ffile-prefix-map=/build/reproducible-path/libcifpp-7.0.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -MD -MT test/CMakeFiles/sugar-test.dir/sugar-test.cpp.o -MF CMakeFiles/sugar-test.dir/sugar-test.cpp.o.d -o CMakeFiles/sugar-test.dir/sugar-test.cpp.o -c /build/reproducible-path/libcifpp-7.0.9/test/sugar-test.cpp -cd /build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu/test && /usr/bin/c++ -DCACHE_DIR=\"/var/cache/libcifpp\" -DCATCH22=0 -DDATA_DIR=\"/usr/share/libcifpp\" -I/usr/include/eigen3 -I/build/reproducible-path/libcifpp-7.0.9/include -g -O2 -ffile-prefix-map=/build/reproducible-path/libcifpp-7.0.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -MD -MT test/CMakeFiles/model-test.dir/model-test.cpp.o -MF CMakeFiles/model-test.dir/model-test.cpp.o.d -o CMakeFiles/model-test.dir/model-test.cpp.o -c /build/reproducible-path/libcifpp-7.0.9/test/model-test.cpp -[ 81%] Building CXX object test/CMakeFiles/validate-pdbx-test.dir/validate-pdbx-test.cpp.o +cd /build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu/test && /usr/bin/c++ -DCACHE_DIR=\"/var/cache/libcifpp\" -DCATCH22=0 -DDATA_DIR=\"/usr/share/libcifpp\" -I/usr/include/eigen3 -I/build/reproducible-path/libcifpp-7.0.9/include -g -O2 -ffile-prefix-map=/build/reproducible-path/libcifpp-7.0.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -MD -MT test/CMakeFiles/format-test.dir/format-test.cpp.o -MF CMakeFiles/format-test.dir/format-test.cpp.o.d -o CMakeFiles/format-test.dir/format-test.cpp.o -c /build/reproducible-path/libcifpp-7.0.9/test/format-test.cpp +[ 79%] Building CXX object test/CMakeFiles/validate-pdbx-test.dir/validate-pdbx-test.cpp.o cd /build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu/test && /usr/bin/c++ -DCACHE_DIR=\"/var/cache/libcifpp\" -DCATCH22=0 -DDATA_DIR=\"/usr/share/libcifpp\" -I/usr/include/eigen3 -I/build/reproducible-path/libcifpp-7.0.9/include -g -O2 -ffile-prefix-map=/build/reproducible-path/libcifpp-7.0.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -MD -MT test/CMakeFiles/validate-pdbx-test.dir/validate-pdbx-test.cpp.o -MF CMakeFiles/validate-pdbx-test.dir/validate-pdbx-test.cpp.o.d -o CMakeFiles/validate-pdbx-test.dir/validate-pdbx-test.cpp.o -c /build/reproducible-path/libcifpp-7.0.9/test/validate-pdbx-test.cpp +[ 81%] Building CXX object test/CMakeFiles/spinner-test.dir/spinner-test.cpp.o +cd /build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu/test && /usr/bin/c++ -DCACHE_DIR=\"/var/cache/libcifpp\" -DCATCH22=0 -DDATA_DIR=\"/usr/share/libcifpp\" -I/usr/include/eigen3 -I/build/reproducible-path/libcifpp-7.0.9/include -g -O2 -ffile-prefix-map=/build/reproducible-path/libcifpp-7.0.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -MD -MT test/CMakeFiles/spinner-test.dir/spinner-test.cpp.o -MF CMakeFiles/spinner-test.dir/spinner-test.cpp.o.d -o CMakeFiles/spinner-test.dir/spinner-test.cpp.o -c /build/reproducible-path/libcifpp-7.0.9/test/spinner-test.cpp [ 84%] Linking CXX executable spinner-test cd /build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/spinner-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libcifpp-7.0.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/spinner-test.dir/link.d "CMakeFiles/spinner-test.dir/spinner-test.cpp.o" "CMakeFiles/test-main.dir/test-main.cpp.o" -o spinner-test -Wl,-rpath,/build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu ../libcifpp.so.7.0.9 /usr/lib/libCatch2.a /usr/lib/aarch64-linux-gnu/libz.so @@ -3195,11 +3231,11 @@ [ 88%] Built target rename-compound-test [ 90%] Linking CXX executable sugar-test cd /build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/sugar-test.dir/link.txt --verbose=1 -[ 93%] Linking CXX executable validate-pdbx-test -cd /build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/validate-pdbx-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libcifpp-7.0.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/sugar-test.dir/link.d "CMakeFiles/sugar-test.dir/sugar-test.cpp.o" "CMakeFiles/test-main.dir/test-main.cpp.o" -o sugar-test -Wl,-rpath,/build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu ../libcifpp.so.7.0.9 /usr/lib/libCatch2.a /usr/lib/aarch64-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu' -[ 93%] Built target sugar-test +[ 90%] Built target sugar-test +[ 93%] Linking CXX executable validate-pdbx-test +cd /build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/validate-pdbx-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libcifpp-7.0.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/validate-pdbx-test.dir/link.d "CMakeFiles/validate-pdbx-test.dir/validate-pdbx-test.cpp.o" "CMakeFiles/test-main.dir/test-main.cpp.o" -o validate-pdbx-test -Wl,-rpath,/build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu ../libcifpp.so.7.0.9 /usr/lib/libCatch2.a /usr/lib/aarch64-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu' [ 93%] Built target validate-pdbx-test @@ -3315,7 +3351,7 @@ 8: Test command: /build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu/test/validate-pdbx-test "--data-dir" "/build/reproducible-path/libcifpp-7.0.9/test" 8: Working Directory: /build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu/test 8: Test timeout computed to be: 1500 -3: Randomness seeded to: 1082654537 +3: Randomness seeded to: 3792472311 3: Hello, world! 3: Hello, world! 3: Hello, world! @@ -3326,21 +3362,28 @@ 3: =============================================================================== 3: All tests passed (2 assertions in 2 test cases) 3: -1/8 Test #3: format-test ...................... Passed 0.04 sec -5: Randomness seeded to: 1584908264 +1/8 Test #3: format-test ...................... Passed 0.02 sec +5: Randomness seeded to: 1794161154 5: inconsistent mandatory value for _diffrn_refln.standard_code in dictionary 5: choosing N -1: Randomness seeded to: 2132715892 +1: Randomness seeded to: 1280388059 1: warning: no child to parent links were found for child cat_1 and parent cat_3 1: Error parsing mmCIF: This file does not seem to be an mmCIF file -4: Randomness seeded to: 3944033910 +4: Randomness seeded to: 1534645777 +4: Warning: no atoms loaded 4: Warning: no atoms loaded 5: inconsistent mandatory value for _diffrn_refln.frame_id in dictionary 5: choosing N -4: Warning: no atoms loaded 5: Creating component index ... done 5: Loading component RXA... done 5: Will not rename in child category since there are already rows that link to the parent +4: =============================================================================== +4: All tests passed (8500 assertions in 6 test cases) +4: +8: Randomness seeded to: 3527933869 +8: =============================================================================== +8: All tests passed (15 assertions in 1 test case) +8: 5: data_1CBS 5: # 5: _entry.id 1CBS @@ -4630,6 +4673,7 @@ 5: ATOM 452 C CB . VAL A 1 58 ? 26.602 31.287 19.155 1.00 9.96 ? 58 VAL A CB 1 5: ATOM 453 C CG1 . VAL A 1 58 ? 27.976 31.161 18.454 1.00 11.08 ? 58 VAL A CG1 1 5: ATOM 454 C CG2 . VAL A 1 58 ? 26.010 29.890 19.404 1.00 9.41 ? 58 VAL A CG2 1 +2/8 Test #4: model-test ....................... Passed 0.20 sec 5: ATOM 455 N N . ARG A 1 59 ? 25.100 31.620 22.266 1.00 8.88 ? 59 ARG A N 1 5: ATOM 456 C CA . ARG A 1 59 ? 23.783 31.655 22.882 1.00 9.95 ? 59 ARG A CA 1 5: ATOM 457 C C . ARG A 1 59 ? 23.843 31.140 24.303 1.00 10.14 ? 59 ARG A C 1 @@ -5657,6 +5701,7 @@ 5: _pdbx_struct_sheet_hbond.range_2_auth_seq_id 5: A 1 2 O PHE A 65 ? O PHE A 65 N PHE A 50 ? N PHE A 50 5: A 2 3 N SER A 55 ? N SER A 55 O ALA A 40 ? O ALA A 40 +3/8 Test #8: validate-pdbx-test ............... Passed 0.19 sec 5: A 3 4 N ILE A 43 ? N ILE A 43 O GLY A 5 ? O GLY A 5 5: A 4 5 N GLU A 13 ? N GLU A 13 O THR A 131 ? O THR A 131 5: A 5 6 N TYR A 134 ? N TYR A 134 O LEU A 119 ? O LEU A 119 @@ -5666,58 +5711,6 @@ 5: A 9 10 N SER A 83 ? N SER A 83 O PHE A 71 ? O PHE A 71 5: # 5: Skipping validation of empty category pdbx_branch_scheme -8: Randomness seeded to: 1089814905 -8: =============================================================================== -8: All tests passed (15 assertions in 1 test case) -8: -2/8 Test #8: validate-pdbx-test ............... Passed 0.23 sec -1: Adding mandatory item conn_type_id to category struct_conn -1: Adding mandatory item ptnr1_label_asym_id to category struct_conn -1: Adding mandatory item ptnr1_label_comp_id to category struct_conn -1: Adding mandatory item ptnr1_label_seq_id to category struct_conn -1: Adding mandatory item ptnr2_label_asym_id to category struct_conn -1: Adding mandatory item ptnr2_label_comp_id to category struct_conn -1: Adding mandatory item ptnr2_label_seq_id to category struct_conn -1: The asym ID's of ndb_poly_seq_scheme and pdbx_poly_seq_scheme are not equal, dropping ndb_poly_seq_scheme -1: -1: Configuration error: -1: -1: The attempt to retrieve compound information for "&&&" failed. -1: -1: This information is searched for in a CCD file called components.cif or -1: components.cif.gz which should be located in one of the following directories: -1: -1: -1: (Note that you can add a directory to the search paths by setting the -1: LIBCIFPP_DATA_DIR environmental variable) -1: -1: On Linux an optional cron script might have been installed that automatically updates -1: components.cif and mmCIF dictionary files. This script only works when the file -1: libcifpp.conf contains an uncommented line with the text: -1: -1: update=true -1: -1: If you do not have a working cron script, you can manually update the files -1: in /var/cache/libcifpp using the following commands: -1: -1: curl -o /var/cache/libcifpp/components.cif https://files.wwpdb.org/pub/pdb/data/monomers/components.cif -1: curl -o /var/cache/libcifpp/mmcif_pdbx.dic https://mmcif.wwpdb.org/dictionaries/ascii/mmcif_pdbx_v50.dic -1: curl -o /var/cache/libcifpp/mmcif_ma.dic https://github.com/ihmwg/ModelCIF/raw/master/dist/mmcif_ma.dic -1: -1: The current order of compound factory objects is: -1: -1: CCD components file: "/build/reproducible-path/libcifpp-7.0.9/test/REA_v2.cif" -1: CCD components file: "/build/reproducible-path/libcifpp-7.0.9/test/HEM.cif" -1: CCD components.cif resource -1: -1: The following named resources were loaded: -1: components.cif -> "/build/reproducible-path/libcifpp-7.0.9/test/../rsrc/ccd-subset.cif" -1: mmcif_pdbx.dic -> "/build/reproducible-path/libcifpp-7.0.9/test/../rsrc/mmcif_pdbx.dic" -4: =============================================================================== -4: All tests passed (8500 assertions in 6 test cases) -4: -3/8 Test #4: model-test ....................... Passed 0.25 sec -1: Choosing X-PLOR version '' as refinement program. Score = 1 5: data_1CBS 5: # 5: _entry.id 1CBS @@ -8051,7 +8044,50 @@ 5: test cases: 1 | 1 passed 5: assertions: - none - 5: -4/8 Test #5: rename-compound-test ............. Passed 0.28 sec +1: Adding mandatory item conn_type_id to category struct_conn +1: Adding mandatory item ptnr1_label_asym_id to category struct_conn +1: Adding mandatory item ptnr1_label_comp_id to category struct_conn +1: Adding mandatory item ptnr1_label_seq_id to category struct_conn +1: Adding mandatory item ptnr2_label_asym_id to category struct_conn +1: Adding mandatory item ptnr2_label_comp_id to category struct_conn +1: Adding mandatory item ptnr2_label_seq_id to category struct_conn +1: The asym ID's of ndb_poly_seq_scheme and pdbx_poly_seq_scheme are not equal, dropping ndb_poly_seq_scheme +4/8 Test #5: rename-compound-test ............. Passed 0.23 sec +1: +1: Configuration error: +1: +1: The attempt to retrieve compound information for "&&&" failed. +1: +1: This information is searched for in a CCD file called components.cif or +1: components.cif.gz which should be located in one of the following directories: +1: +1: +1: (Note that you can add a directory to the search paths by setting the +1: LIBCIFPP_DATA_DIR environmental variable) +1: +1: On Linux an optional cron script might have been installed that automatically updates +1: components.cif and mmCIF dictionary files. This script only works when the file +1: libcifpp.conf contains an uncommented line with the text: +1: +1: update=true +1: +1: If you do not have a working cron script, you can manually update the files +1: in /var/cache/libcifpp using the following commands: +1: +1: curl -o /var/cache/libcifpp/components.cif https://files.wwpdb.org/pub/pdb/data/monomers/components.cif +1: curl -o /var/cache/libcifpp/mmcif_pdbx.dic https://mmcif.wwpdb.org/dictionaries/ascii/mmcif_pdbx_v50.dic +1: curl -o /var/cache/libcifpp/mmcif_ma.dic https://github.com/ihmwg/ModelCIF/raw/master/dist/mmcif_ma.dic +1: +1: The current order of compound factory objects is: +1: +1: CCD components file: "/build/reproducible-path/libcifpp-7.0.9/test/REA_v2.cif" +1: CCD components file: "/build/reproducible-path/libcifpp-7.0.9/test/HEM.cif" +1: CCD components.cif resource +1: +1: The following named resources were loaded: +1: components.cif -> "/build/reproducible-path/libcifpp-7.0.9/test/../rsrc/ccd-subset.cif" +1: mmcif_pdbx.dic -> "/build/reproducible-path/libcifpp-7.0.9/test/../rsrc/mmcif_pdbx.dic" +1: Choosing X-PLOR version '' as refinement program. Score = 1 1: Adding mandatory item value to category pdbx_struct_assembly_prop 1: Adding mandatory item conn_type_id to category struct_conn 1: Adding mandatory item ptnr1_label_asym_id to category struct_conn @@ -8064,30 +8100,30 @@ 1: =============================================================================== 1: All tests passed (100465 assertions in 51 test cases) 1: -5/8 Test #1: unit-v2-test ..................... Passed 0.35 sec -2: Randomness seeded to: 1547239619 +5/8 Test #1: unit-v2-test ..................... Passed 0.39 sec +2: Randomness seeded to: 1152345042 2: (1.70711,1.70711,0) 2: =============================================================================== 2: All tests passed (5099624 assertions in 15 test cases) 2: -6/8 Test #2: unit-3d-test ..................... Passed 1.18 sec -6: Randomness seeded to: 2161448627 +6/8 Test #2: unit-3d-test ..................... Passed 1.16 sec +6: Randomness seeded to: 1730558393 6: =============================================================================== 6: All tests passed (10 assertions in 2 test cases) 6: -7/8 Test #6: sugar-test ....................... Passed 3.35 sec -7: Randomness seeded to: 1602120368 +7/8 Test #6: sugar-test ....................... Passed 3.30 sec +7: Randomness seeded to: 9031770 7: =============================================================================== 7: test cases: 3 | 3 passed 7: assertions: - none - 7: -8/8 Test #7: spinner-test ..................... Passed 6.03 sec +8/8 Test #7: spinner-test ..................... Passed 6.57 sec 100% tests passed, 0 tests failed out of 8 -Total Test time (real) = 6.06 sec +Total Test time (real) = 6.59 sec make[1]: Leaving directory '/build/reproducible-path/libcifpp-7.0.9/obj-aarch64-linux-gnu' - rm -fr -- /tmp/dh-xdg-rundir-40h250CF + rm -fr -- /tmp/dh-xdg-rundir-e0KHDY42 create-stamp debian/debhelper-build-stamp dh_prep rm -f -- debian/libcifpp-dev.substvars debian/libcifpp-doc.substvars debian/libcifpp7.substvars debian/libcifpp-data.substvars @@ -8885,18 +8921,18 @@ install -m0755 -d debian/libcifpp-data/usr/share/doc/libcifpp-data install -p -m0644 debian/copyright debian/libcifpp-data/usr/share/doc/libcifpp-data/copyright dh_installchangelogs + install -m0755 -d debian/libcifpp-data/usr/share/doc/libcifpp-data + install -p -m0644 debian/.debhelper/generated/libcifpp-data/dh_installchangelogs.dch.trimmed debian/libcifpp-data/usr/share/doc/libcifpp-data/changelog.Debian + install -p -m0644 ./changelog debian/libcifpp-data/usr/share/doc/libcifpp-data/changelog install -m0755 -d debian/libcifpp-doc/usr/share/doc/libcifpp-doc install -p -m0644 debian/.debhelper/generated/libcifpp-doc/dh_installchangelogs.dch.trimmed debian/libcifpp-doc/usr/share/doc/libcifpp-doc/changelog.Debian install -p -m0644 ./changelog debian/libcifpp-doc/usr/share/doc/libcifpp-doc/changelog - install -m0755 -d debian/libcifpp-dev/usr/share/doc/libcifpp-dev - install -p -m0644 debian/.debhelper/generated/libcifpp-dev/dh_installchangelogs.dch.trimmed debian/libcifpp-dev/usr/share/doc/libcifpp-dev/changelog.Debian - install -p -m0644 ./changelog debian/libcifpp-dev/usr/share/doc/libcifpp-dev/changelog install -m0755 -d debian/libcifpp7/usr/share/doc/libcifpp7 install -p -m0644 debian/.debhelper/generated/libcifpp7/dh_installchangelogs.dch.trimmed debian/libcifpp7/usr/share/doc/libcifpp7/changelog.Debian install -p -m0644 ./changelog debian/libcifpp7/usr/share/doc/libcifpp7/changelog - install -m0755 -d debian/libcifpp-data/usr/share/doc/libcifpp-data - install -p -m0644 debian/.debhelper/generated/libcifpp-data/dh_installchangelogs.dch.trimmed debian/libcifpp-data/usr/share/doc/libcifpp-data/changelog.Debian - install -p -m0644 ./changelog debian/libcifpp-data/usr/share/doc/libcifpp-data/changelog + install -m0755 -d debian/libcifpp-dev/usr/share/doc/libcifpp-dev + install -p -m0644 debian/.debhelper/generated/libcifpp-dev/dh_installchangelogs.dch.trimmed debian/libcifpp-dev/usr/share/doc/libcifpp-dev/changelog.Debian + install -p -m0644 ./changelog debian/libcifpp-dev/usr/share/doc/libcifpp-dev/changelog dh_installexamples install -m0755 -d debian/libcifpp-dev/usr/share/doc/libcifpp-dev/examples cp --reflink=auto -a ./examples/1cbs.cif.gz debian/libcifpp-dev/usr/share/doc/libcifpp-dev/examples @@ -8924,45 +8960,45 @@ Normalizing debian/libcifpp-dev/usr/share/doc/libcifpp-dev/examples/1cbs.cif.gz using File::StripNondeterminism::handlers::gzip Using 1738076869 as canonical time Normalizing debian/libcifpp-doc/usr/share/doc/libcifpp/_static/plus.png using File::StripNondeterminism::handlers::png - Normalizing debian/libcifpp-doc/usr/share/doc/libcifpp/_static/file.png using File::StripNondeterminism::handlers::png Normalizing debian/libcifpp-doc/usr/share/doc/libcifpp/_static/minus.png using File::StripNondeterminism::handlers::png + Normalizing debian/libcifpp-doc/usr/share/doc/libcifpp/_static/file.png using File::StripNondeterminism::handlers::png dh_compress cd debian/libcifpp-dev + cd debian/libcifpp-doc cd debian/libcifpp7 cd debian/libcifpp-data - cd debian/libcifpp-doc - chmod a-x usr/share/doc/libcifpp-dev/changelog usr/share/doc/libcifpp-dev/changelog.Debian chmod a-x usr/share/doc/libcifpp7/README.md usr/share/doc/libcifpp7/changelog usr/share/doc/libcifpp7/changelog.Debian + chmod a-x usr/share/doc/libcifpp-dev/changelog usr/share/doc/libcifpp-dev/changelog.Debian chmod a-x usr/share/doc/libcifpp-data/changelog usr/share/doc/libcifpp-data/changelog.Debian - gzip -9nf usr/share/doc/libcifpp-dev/changelog usr/share/doc/libcifpp-dev/changelog.Debian - gzip -9nf usr/share/doc/libcifpp7/README.md usr/share/doc/libcifpp7/changelog usr/share/doc/libcifpp7/changelog.Debian gzip -9nf usr/share/doc/libcifpp-data/changelog usr/share/doc/libcifpp-data/changelog.Debian + gzip -9nf usr/share/doc/libcifpp7/README.md usr/share/doc/libcifpp7/changelog usr/share/doc/libcifpp7/changelog.Debian + gzip -9nf usr/share/doc/libcifpp-dev/changelog usr/share/doc/libcifpp-dev/changelog.Debian + chmod a-x usr/share/doc/libcifpp-doc/changelog usr/share/doc/libcifpp-doc/changelog.Debian usr/share/doc/libcifpp/_static/fonts/Lato-Bold.ttf usr/share/doc/libcifpp/_static/fonts/Lato-BoldItalic.ttf usr/share/doc/libcifpp/_static/fonts/Lato-Italic.ttf usr/share/doc/libcifpp/_static/fonts/Lato-Regular.ttf usr/share/doc/libcifpp/_static/fonts/fontawesome-webfont.eot usr/share/doc/libcifpp/_static/fonts/fontawesome-webfont.ttf + gzip -9nf usr/share/doc/libcifpp-doc/changelog usr/share/doc/libcifpp-doc/changelog.Debian usr/share/doc/libcifpp/_static/fonts/Lato-Bold.ttf usr/share/doc/libcifpp/_static/fonts/Lato-BoldItalic.ttf usr/share/doc/libcifpp/_static/fonts/Lato-Italic.ttf usr/share/doc/libcifpp/_static/fonts/Lato-Regular.ttf usr/share/doc/libcifpp/_static/fonts/fontawesome-webfont.eot usr/share/doc/libcifpp/_static/fonts/fontawesome-webfont.ttf cd '/build/reproducible-path/libcifpp-7.0.9' cd '/build/reproducible-path/libcifpp-7.0.9' cd '/build/reproducible-path/libcifpp-7.0.9' - chmod a-x usr/share/doc/libcifpp-doc/changelog usr/share/doc/libcifpp-doc/changelog.Debian usr/share/doc/libcifpp/_static/fonts/Lato-Bold.ttf usr/share/doc/libcifpp/_static/fonts/Lato-BoldItalic.ttf usr/share/doc/libcifpp/_static/fonts/Lato-Italic.ttf usr/share/doc/libcifpp/_static/fonts/Lato-Regular.ttf usr/share/doc/libcifpp/_static/fonts/fontawesome-webfont.eot usr/share/doc/libcifpp/_static/fonts/fontawesome-webfont.ttf - gzip -9nf usr/share/doc/libcifpp-doc/changelog usr/share/doc/libcifpp-doc/changelog.Debian usr/share/doc/libcifpp/_static/fonts/Lato-Bold.ttf usr/share/doc/libcifpp/_static/fonts/Lato-BoldItalic.ttf usr/share/doc/libcifpp/_static/fonts/Lato-Italic.ttf usr/share/doc/libcifpp/_static/fonts/Lato-Regular.ttf usr/share/doc/libcifpp/_static/fonts/fontawesome-webfont.eot usr/share/doc/libcifpp/_static/fonts/fontawesome-webfont.ttf cd '/build/reproducible-path/libcifpp-7.0.9' dh_fixperms find debian/libcifpp-dev ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/libcifpp-doc ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/libcifpp7 ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/libcifpp-data ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s - find debian/libcifpp7/usr/share/doc -type f -a -true -a ! -regex 'debian/libcifpp7/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 - find debian/libcifpp-dev/usr/share/doc -type f -a -true -a ! -regex 'debian/libcifpp-dev/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libcifpp-data/usr/share/doc -type f -a -true -a ! -regex 'debian/libcifpp-data/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 + find debian/libcifpp-dev/usr/share/doc -type f -a -true -a ! -regex 'debian/libcifpp-dev/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 + find debian/libcifpp7/usr/share/doc -type f -a -true -a ! -regex 'debian/libcifpp7/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libcifpp-doc/usr/share/doc -type f -a -true -a ! -regex 'debian/libcifpp-doc/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 - find debian/libcifpp7/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 - find debian/libcifpp-dev/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/libcifpp-data/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 - find debian/libcifpp7 -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 - find debian/libcifpp-dev/usr/include -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 + find debian/libcifpp-dev/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 + find debian/libcifpp7/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/libcifpp-data -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 - find debian/libcifpp7/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w - find debian/libcifpp-dev -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 + find debian/libcifpp-dev/usr/include -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 + find debian/libcifpp7 -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libcifpp-doc/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 - find debian/libcifpp-dev/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w + find debian/libcifpp-dev -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 + find debian/libcifpp7/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w find debian/libcifpp-doc -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 + find debian/libcifpp-dev/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w dh_missing dh_dwz -a dwz -- debian/libcifpp7/usr/lib/aarch64-linux-gnu/libcifpp.so.7.0.9 @@ -9014,18 +9050,18 @@ echo misc:Pre-Depends= >> debian/libcifpp7.substvars install -m0755 -d debian/.debhelper/libcifpp7/dbgsym-root/DEBIAN dpkg-gencontrol -plibcifpp7 -ldebian/changelog -Tdebian/libcifpp7.substvars -cdebian/control -Pdebian/.debhelper/libcifpp7/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -UProtected -UBuilt-Using -UStatic-Built-Using -DPackage=libcifpp7-dbgsym "-DDepends=libcifpp7 (= \${binary:Version})" "-DDescription=debug symbols for libcifpp7" -DBuild-Ids=2073f13690ea1640bce5d17f0f98524f69ad4465 -DSection=debug -UReplaces -UBreaks - install -m0755 -d debian/libcifpp-data/DEBIAN - echo misc:Pre-Depends= >> debian/libcifpp-data.substvars - dpkg-gencontrol -plibcifpp-data -ldebian/changelog -Tdebian/libcifpp-data.substvars -cdebian/control -Pdebian/libcifpp-data install -m0755 -d debian/libcifpp-doc/DEBIAN echo misc:Depends= >> debian/libcifpp-doc.substvars echo misc:Pre-Depends= >> debian/libcifpp-doc.substvars dpkg-gencontrol -plibcifpp-doc -ldebian/changelog -Tdebian/libcifpp-doc.substvars -cdebian/control -Pdebian/libcifpp-doc - chmod 0644 -- debian/libcifpp-dev/DEBIAN/control + install -m0755 -d debian/libcifpp-data/DEBIAN + echo misc:Pre-Depends= >> debian/libcifpp-data.substvars + dpkg-gencontrol -plibcifpp-data -ldebian/changelog -Tdebian/libcifpp-data.substvars -cdebian/control -Pdebian/libcifpp-data chmod 0644 -- debian/.debhelper/libcifpp7/dbgsym-root/DEBIAN/control dpkg-gencontrol -plibcifpp7 -ldebian/changelog -Tdebian/libcifpp7.substvars -cdebian/control -Pdebian/libcifpp7 - chmod 0644 -- debian/libcifpp-data/DEBIAN/control chmod 0644 -- debian/libcifpp-doc/DEBIAN/control + chmod 0644 -- debian/libcifpp-dev/DEBIAN/control + chmod 0644 -- debian/libcifpp-data/DEBIAN/control chmod 0644 -- debian/libcifpp7/DEBIAN/control dh_md5sums install -m0755 -d debian/libcifpp-dev/DEBIAN @@ -9046,12 +9082,12 @@ dh_builddeb dpkg-deb --root-owner-group --build debian/libcifpp-dev .. dpkg-deb --root-owner-group --build debian/libcifpp-doc .. - dpkg-deb --root-owner-group --build debian/libcifpp7 .. dpkg-deb --root-owner-group --build debian/.debhelper/libcifpp7/dbgsym-root .. + dpkg-deb --root-owner-group --build debian/libcifpp7 .. dpkg-deb --root-owner-group --build debian/libcifpp-data .. dpkg-deb: building package 'libcifpp7' in '../libcifpp7_7.0.9-1_arm64.deb'. -dpkg-deb: building package 'libcifpp-dev' in '../libcifpp-dev_7.0.9-1_arm64.deb'. dpkg-deb: building package 'libcifpp-doc' in '../libcifpp-doc_7.0.9-1_all.deb'. +dpkg-deb: building package 'libcifpp-dev' in '../libcifpp-dev_7.0.9-1_arm64.deb'. dpkg-deb: building package 'libcifpp7-dbgsym' in '../libcifpp7-dbgsym_7.0.9-1_arm64.deb'. dpkg-deb: building package 'libcifpp-data' in '../libcifpp-data_7.0.9-1_all.deb'. dpkg-genbuildinfo --build=binary -O../libcifpp_7.0.9-1_arm64.buildinfo @@ -9061,12 +9097,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/586249/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/586249/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/872058 and its subdirectories -I: Current time: Tue Jul 29 22:01:00 -12 2025 -I: pbuilder-time-stamp: 1753869660 +I: removing directory /srv/workspace/pbuilder/586249 and its subdirectories +I: Current time: Wed Sep 2 06:27:57 +14 2026 +I: pbuilder-time-stamp: 1788280077