Diff of the two buildlogs: -- --- b1/build.log 2025-07-30 06:21:28.418731601 +0000 +++ b2/build.log 2025-07-30 06:26:31.655112790 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Sep 1 00:42:52 -12 2026 -I: pbuilder-time-stamp: 1788266572 +I: Current time: Wed Jul 30 20:21:30 +14 2025 +I: pbuilder-time-stamp: 1753856490 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/experimental-reproducible-base.tgz] I: copying local configuration @@ -22,52 +22,84 @@ dpkg-source: info: unpacking libpdb-redo_3.3.0-1.debian.tar.xz I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2229785/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1207063/tmp/hooks/D01_modify_environment starting +debug: Running on ionos1-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Jul 30 06:21 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/1207063/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1207063/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' - DISTRIBUTION='experimental' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-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=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=40 ' + DIRSTACK=() + DISTRIBUTION=experimental + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='d482874c82d049ebb4d610256092cbe6' - 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='2229785' - PS1='# ' - PS2='> ' + INVOCATION_ID=383e12fcda1c4985bf8aefe65828e79f + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=1207063 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.HveMhxHg/pbuilderrc_MdX5 --distribution experimental --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/experimental-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.HveMhxHg/b1 --logfile b1/build.log libpdb-redo_3.3.0-1.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://213.165.73.152:3128' + 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.HveMhxHg/pbuilderrc_qhYE --distribution experimental --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/experimental-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.HveMhxHg/b2 --logfile b2/build.log libpdb-redo_3.3.0-1.dsc' + SUDO_GID=110 + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://46.16.76.132:3128 I: uname -a - Linux ionos15-amd64 6.12.33+deb12-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.33-1~bpo12+1 (2025-07-09) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-37-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.140-1 (2025-05-22) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 12 2025 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2229785/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 12 19:25 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1207063/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -252,7 +284,7 @@ Get: 127 http://deb.debian.org/debian unstable/main amd64 libgslcblas0 amd64 2.8+dfsg-5 [116 kB] Get: 128 http://deb.debian.org/debian unstable/main amd64 libgsl28 amd64 2.8+dfsg-5 [994 kB] Get: 129 http://deb.debian.org/debian unstable/main amd64 libgsl-dev amd64 2.8+dfsg-5 [1222 kB] -Fetched 137 MB in 1s (125 MB/s) +Fetched 137 MB in 5s (25.8 MB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1:amd64. (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 ... 19849 files and directories currently installed.) @@ -783,7 +815,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/libpdb-redo-3.3.0/ && 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 > ../libpdb-redo_3.3.0-1_source.changes +I: user script /srv/workspace/pbuilder/1207063/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for experimental +I: user script /srv/workspace/pbuilder/1207063/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/libpdb-redo-3.3.0/ && 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 > ../libpdb-redo_3.3.0-1_source.changes dpkg-buildpackage: info: source package libpdb-redo dpkg-buildpackage: info: source version 3.3.0-1 dpkg-buildpackage: info: source distribution experimental @@ -839,8 +875,8 @@ -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY - Success -- Performing Test COMPILER_HAS_DEPRECATED_ATTR -- Performing Test COMPILER_HAS_DEPRECATED_ATTR - Success --- Configuring done (2.2s) --- Generating done (0.0s) +-- Configuring done (10.1s) +-- Generating done (0.1s) CMake Warning: Manually-specified variables were not used by the project: @@ -853,7 +889,7 @@ -- Build files have been written to: /build/reproducible-path/libpdb-redo-3.3.0/obj-x86_64-linux-gnu make[1]: Leaving directory '/build/reproducible-path/libpdb-redo-3.3.0' dh_auto_build - cd obj-x86_64-linux-gnu && make -j42 "INSTALL=install --strip-program=true" VERBOSE=1 + cd obj-x86_64-linux-gnu && make -j40 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/libpdb-redo-3.3.0/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/libpdb-redo-3.3.0 -B/build/reproducible-path/libpdb-redo-3.3.0/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/libpdb-redo-3.3.0/obj-x86_64-linux-gnu/CMakeFiles /build/reproducible-path/libpdb-redo-3.3.0/obj-x86_64-linux-gnu//CMakeFiles/progress.marks @@ -865,29 +901,29 @@ make[3]: Leaving directory '/build/reproducible-path/libpdb-redo-3.3.0/obj-x86_64-linux-gnu' make -f CMakeFiles/pdb-redo.dir/build.make CMakeFiles/pdb-redo.dir/build make[3]: Entering directory '/build/reproducible-path/libpdb-redo-3.3.0/obj-x86_64-linux-gnu' -[ 23%] Building CXX object CMakeFiles/pdb-redo.dir/src/AtomShape.cpp.o -[ 23%] Building CXX object CMakeFiles/pdb-redo.dir/src/ClipperWrapper.cpp.o -[ 23%] Building CXX object CMakeFiles/pdb-redo.dir/src/BondMap.cpp.o -[ 23%] Building CXX object CMakeFiles/pdb-redo.dir/src/Compound.cpp.o -[ 29%] Building CXX object CMakeFiles/pdb-redo.dir/src/DistanceMap.cpp.o -[ 35%] Building CXX object CMakeFiles/pdb-redo.dir/src/MapMaker.cpp.o -[ 41%] Building CXX object CMakeFiles/pdb-redo.dir/src/Ramachandran.cpp.o -[ 47%] Building CXX object CMakeFiles/pdb-redo.dir/src/ResolutionCalculator.cpp.o -[ 52%] Building CXX object CMakeFiles/pdb-redo.dir/src/SkipList.cpp.o -/usr/bin/c++ -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -Dpdb_redo_EXPORTS -I/build/reproducible-path/libpdb-redo-3.3.0/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.3.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -fPIC -MD -MT CMakeFiles/pdb-redo.dir/src/ClipperWrapper.cpp.o -MF CMakeFiles/pdb-redo.dir/src/ClipperWrapper.cpp.o.d -o CMakeFiles/pdb-redo.dir/src/ClipperWrapper.cpp.o -c /build/reproducible-path/libpdb-redo-3.3.0/src/ClipperWrapper.cpp +[ 5%] Building CXX object CMakeFiles/pdb-redo.dir/src/AtomShape.cpp.o /usr/bin/c++ -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -Dpdb_redo_EXPORTS -I/build/reproducible-path/libpdb-redo-3.3.0/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.3.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -fPIC -MD -MT CMakeFiles/pdb-redo.dir/src/AtomShape.cpp.o -MF CMakeFiles/pdb-redo.dir/src/AtomShape.cpp.o.d -o CMakeFiles/pdb-redo.dir/src/AtomShape.cpp.o -c /build/reproducible-path/libpdb-redo-3.3.0/src/AtomShape.cpp -[ 58%] Building CXX object CMakeFiles/pdb-redo.dir/src/Statistics.cpp.o +[ 11%] Building CXX object CMakeFiles/pdb-redo.dir/src/BondMap.cpp.o +[ 17%] Building CXX object CMakeFiles/pdb-redo.dir/src/ClipperWrapper.cpp.o /usr/bin/c++ -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -Dpdb_redo_EXPORTS -I/build/reproducible-path/libpdb-redo-3.3.0/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.3.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -fPIC -MD -MT CMakeFiles/pdb-redo.dir/src/BondMap.cpp.o -MF CMakeFiles/pdb-redo.dir/src/BondMap.cpp.o.d -o CMakeFiles/pdb-redo.dir/src/BondMap.cpp.o -c /build/reproducible-path/libpdb-redo-3.3.0/src/BondMap.cpp -[ 64%] Building CXX object CMakeFiles/pdb-redo.dir/src/TLS.cpp.o +/usr/bin/c++ -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -Dpdb_redo_EXPORTS -I/build/reproducible-path/libpdb-redo-3.3.0/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.3.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -fPIC -MD -MT CMakeFiles/pdb-redo.dir/src/ClipperWrapper.cpp.o -MF CMakeFiles/pdb-redo.dir/src/ClipperWrapper.cpp.o.d -o CMakeFiles/pdb-redo.dir/src/ClipperWrapper.cpp.o -c /build/reproducible-path/libpdb-redo-3.3.0/src/ClipperWrapper.cpp +[ 23%] Building CXX object CMakeFiles/pdb-redo.dir/src/Compound.cpp.o /usr/bin/c++ -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -Dpdb_redo_EXPORTS -I/build/reproducible-path/libpdb-redo-3.3.0/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.3.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -fPIC -MD -MT CMakeFiles/pdb-redo.dir/src/Compound.cpp.o -MF CMakeFiles/pdb-redo.dir/src/Compound.cpp.o.d -o CMakeFiles/pdb-redo.dir/src/Compound.cpp.o -c /build/reproducible-path/libpdb-redo-3.3.0/src/Compound.cpp -[ 70%] Building CXX object CMakeFiles/pdb-redo.dir/src/Version.cpp.o +[ 29%] Building CXX object CMakeFiles/pdb-redo.dir/src/DistanceMap.cpp.o /usr/bin/c++ -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -Dpdb_redo_EXPORTS -I/build/reproducible-path/libpdb-redo-3.3.0/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.3.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -fPIC -MD -MT CMakeFiles/pdb-redo.dir/src/DistanceMap.cpp.o -MF CMakeFiles/pdb-redo.dir/src/DistanceMap.cpp.o.d -o CMakeFiles/pdb-redo.dir/src/DistanceMap.cpp.o -c /build/reproducible-path/libpdb-redo-3.3.0/src/DistanceMap.cpp +[ 35%] Building CXX object CMakeFiles/pdb-redo.dir/src/MapMaker.cpp.o /usr/bin/c++ -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -Dpdb_redo_EXPORTS -I/build/reproducible-path/libpdb-redo-3.3.0/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.3.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -fPIC -MD -MT CMakeFiles/pdb-redo.dir/src/MapMaker.cpp.o -MF CMakeFiles/pdb-redo.dir/src/MapMaker.cpp.o.d -o CMakeFiles/pdb-redo.dir/src/MapMaker.cpp.o -c /build/reproducible-path/libpdb-redo-3.3.0/src/MapMaker.cpp +[ 41%] Building CXX object CMakeFiles/pdb-redo.dir/src/Ramachandran.cpp.o /usr/bin/c++ -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -Dpdb_redo_EXPORTS -I/build/reproducible-path/libpdb-redo-3.3.0/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.3.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -fPIC -MD -MT CMakeFiles/pdb-redo.dir/src/Ramachandran.cpp.o -MF CMakeFiles/pdb-redo.dir/src/Ramachandran.cpp.o.d -o CMakeFiles/pdb-redo.dir/src/Ramachandran.cpp.o -c /build/reproducible-path/libpdb-redo-3.3.0/src/Ramachandran.cpp +[ 47%] Building CXX object CMakeFiles/pdb-redo.dir/src/ResolutionCalculator.cpp.o /usr/bin/c++ -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -Dpdb_redo_EXPORTS -I/build/reproducible-path/libpdb-redo-3.3.0/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.3.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -fPIC -MD -MT CMakeFiles/pdb-redo.dir/src/ResolutionCalculator.cpp.o -MF CMakeFiles/pdb-redo.dir/src/ResolutionCalculator.cpp.o.d -o CMakeFiles/pdb-redo.dir/src/ResolutionCalculator.cpp.o -c /build/reproducible-path/libpdb-redo-3.3.0/src/ResolutionCalculator.cpp +[ 52%] Building CXX object CMakeFiles/pdb-redo.dir/src/SkipList.cpp.o /usr/bin/c++ -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -Dpdb_redo_EXPORTS -I/build/reproducible-path/libpdb-redo-3.3.0/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.3.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -fPIC -MD -MT CMakeFiles/pdb-redo.dir/src/SkipList.cpp.o -MF CMakeFiles/pdb-redo.dir/src/SkipList.cpp.o.d -o CMakeFiles/pdb-redo.dir/src/SkipList.cpp.o -c /build/reproducible-path/libpdb-redo-3.3.0/src/SkipList.cpp +[ 58%] Building CXX object CMakeFiles/pdb-redo.dir/src/Statistics.cpp.o /usr/bin/c++ -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -Dpdb_redo_EXPORTS -I/build/reproducible-path/libpdb-redo-3.3.0/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.3.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -fPIC -MD -MT CMakeFiles/pdb-redo.dir/src/Statistics.cpp.o -MF CMakeFiles/pdb-redo.dir/src/Statistics.cpp.o.d -o CMakeFiles/pdb-redo.dir/src/Statistics.cpp.o -c /build/reproducible-path/libpdb-redo-3.3.0/src/Statistics.cpp +[ 64%] Building CXX object CMakeFiles/pdb-redo.dir/src/TLS.cpp.o /usr/bin/c++ -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -Dpdb_redo_EXPORTS -I/build/reproducible-path/libpdb-redo-3.3.0/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.3.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -fPIC -MD -MT CMakeFiles/pdb-redo.dir/src/TLS.cpp.o -MF CMakeFiles/pdb-redo.dir/src/TLS.cpp.o.d -o CMakeFiles/pdb-redo.dir/src/TLS.cpp.o -c /build/reproducible-path/libpdb-redo-3.3.0/src/TLS.cpp +[ 70%] Building CXX object CMakeFiles/pdb-redo.dir/src/Version.cpp.o /usr/bin/c++ -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -Dpdb_redo_EXPORTS -I/build/reproducible-path/libpdb-redo-3.3.0/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.3.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -fPIC -MD -MT CMakeFiles/pdb-redo.dir/src/Version.cpp.o -MF CMakeFiles/pdb-redo.dir/src/Version.cpp.o.d -o CMakeFiles/pdb-redo.dir/src/Version.cpp.o -c /build/reproducible-path/libpdb-redo-3.3.0/src/Version.cpp [ 76%] Linking CXX shared library libpdb-redo.so /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb-redo.dir/link.txt --verbose=1 @@ -896,21 +932,21 @@ make[3]: Leaving directory '/build/reproducible-path/libpdb-redo-3.3.0/obj-x86_64-linux-gnu' [ 76%] Built target pdb-redo make -f test/CMakeFiles/pdb-redo-unit-test.dir/build.make test/CMakeFiles/pdb-redo-unit-test.dir/depend -make -f test/CMakeFiles/restr2ccd-test.dir/build.make test/CMakeFiles/restr2ccd-test.dir/depend make[3]: Entering directory '/build/reproducible-path/libpdb-redo-3.3.0/obj-x86_64-linux-gnu' +make -f test/CMakeFiles/restr2ccd-test.dir/build.make test/CMakeFiles/restr2ccd-test.dir/depend cd /build/reproducible-path/libpdb-redo-3.3.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libpdb-redo-3.3.0 /build/reproducible-path/libpdb-redo-3.3.0/test /build/reproducible-path/libpdb-redo-3.3.0/obj-x86_64-linux-gnu /build/reproducible-path/libpdb-redo-3.3.0/obj-x86_64-linux-gnu/test /build/reproducible-path/libpdb-redo-3.3.0/obj-x86_64-linux-gnu/test/CMakeFiles/pdb-redo-unit-test.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/libpdb-redo-3.3.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/libpdb-redo-3.3.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libpdb-redo-3.3.0 /build/reproducible-path/libpdb-redo-3.3.0/test /build/reproducible-path/libpdb-redo-3.3.0/obj-x86_64-linux-gnu /build/reproducible-path/libpdb-redo-3.3.0/obj-x86_64-linux-gnu/test /build/reproducible-path/libpdb-redo-3.3.0/obj-x86_64-linux-gnu/test/CMakeFiles/restr2ccd-test.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/libpdb-redo-3.3.0/obj-x86_64-linux-gnu' -make[3]: Leaving directory '/build/reproducible-path/libpdb-redo-3.3.0/obj-x86_64-linux-gnu' make -f test/CMakeFiles/pdb-redo-unit-test.dir/build.make test/CMakeFiles/pdb-redo-unit-test.dir/build -make -f test/CMakeFiles/restr2ccd-test.dir/build.make test/CMakeFiles/restr2ccd-test.dir/build +make[3]: Leaving directory '/build/reproducible-path/libpdb-redo-3.3.0/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/libpdb-redo-3.3.0/obj-x86_64-linux-gnu' +make -f test/CMakeFiles/restr2ccd-test.dir/build.make test/CMakeFiles/restr2ccd-test.dir/build make[3]: Entering directory '/build/reproducible-path/libpdb-redo-3.3.0/obj-x86_64-linux-gnu' -[ 82%] Building CXX object test/CMakeFiles/pdb-redo-unit-test.dir/pdb-redo-unit-test.cpp.o -[ 88%] Building CXX object test/CMakeFiles/restr2ccd-test.dir/restr2ccd-test.cpp.o -cd /build/reproducible-path/libpdb-redo-3.3.0/obj-x86_64-linux-gnu/test && /usr/bin/c++ -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -I/build/reproducible-path/libpdb-redo-3.3.0/include -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.3.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -MD -MT test/CMakeFiles/pdb-redo-unit-test.dir/pdb-redo-unit-test.cpp.o -MF CMakeFiles/pdb-redo-unit-test.dir/pdb-redo-unit-test.cpp.o.d -o CMakeFiles/pdb-redo-unit-test.dir/pdb-redo-unit-test.cpp.o -c /build/reproducible-path/libpdb-redo-3.3.0/test/pdb-redo-unit-test.cpp +[ 82%] Building CXX object test/CMakeFiles/restr2ccd-test.dir/restr2ccd-test.cpp.o +[ 88%] Building CXX object test/CMakeFiles/pdb-redo-unit-test.dir/pdb-redo-unit-test.cpp.o cd /build/reproducible-path/libpdb-redo-3.3.0/obj-x86_64-linux-gnu/test && /usr/bin/c++ -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -I/build/reproducible-path/libpdb-redo-3.3.0/include -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.3.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -MD -MT test/CMakeFiles/restr2ccd-test.dir/restr2ccd-test.cpp.o -MF CMakeFiles/restr2ccd-test.dir/restr2ccd-test.cpp.o.d -o CMakeFiles/restr2ccd-test.dir/restr2ccd-test.cpp.o -c /build/reproducible-path/libpdb-redo-3.3.0/test/restr2ccd-test.cpp +cd /build/reproducible-path/libpdb-redo-3.3.0/obj-x86_64-linux-gnu/test && /usr/bin/c++ -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -I/build/reproducible-path/libpdb-redo-3.3.0/include -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.3.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -MD -MT test/CMakeFiles/pdb-redo-unit-test.dir/pdb-redo-unit-test.cpp.o -MF CMakeFiles/pdb-redo-unit-test.dir/pdb-redo-unit-test.cpp.o.d -o CMakeFiles/pdb-redo-unit-test.dir/pdb-redo-unit-test.cpp.o -c /build/reproducible-path/libpdb-redo-3.3.0/test/pdb-redo-unit-test.cpp [ 94%] Linking CXX executable restr2ccd-test cd /build/reproducible-path/libpdb-redo-3.3.0/obj-x86_64-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/restr2ccd-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.3.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/restr2ccd-test.dir/link.d "CMakeFiles/restr2ccd-test.dir/restr2ccd-test.cpp.o" -o restr2ccd-test -Wl,-rpath,/build/reproducible-path/libpdb-redo-3.3.0/obj-x86_64-linux-gnu ../libpdb-redo.so.3.3.0 /usr/lib/libCatch2.a /usr/lib/x86_64-linux-gnu/libcifpp.so.7.0.9 /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libgsl.so /usr/lib/x86_64-linux-gnu/libgslcblas.so /usr/lib/x86_64-linux-gnu/libclipper-ccp4.so /usr/lib/x86_64-linux-gnu/libclipper-contrib.so /usr/lib/x86_64-linux-gnu/libclipper-core.so /usr/lib/x86_64-linux-gnu/libccp4c.so @@ -925,10 +961,10 @@ /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/libpdb-redo-3.3.0/obj-x86_64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/reproducible-path/libpdb-redo-3.3.0/obj-x86_64-linux-gnu' dh_auto_test - cd obj-x86_64-linux-gnu && make -j42 test ARGS\+=--verbose ARGS\+=-j42 + cd obj-x86_64-linux-gnu && make -j40 test ARGS\+=--verbose ARGS\+=-j40 make[1]: Entering directory '/build/reproducible-path/libpdb-redo-3.3.0/obj-x86_64-linux-gnu' Running tests... -/usr/bin/ctest --force-new-ctest-process --verbose -j42 +/usr/bin/ctest --force-new-ctest-process --verbose -j40 UpdateCTestConfiguration from :/build/reproducible-path/libpdb-redo-3.3.0/obj-x86_64-linux-gnu/DartConfiguration.tcl Parse Config file:/build/reproducible-path/libpdb-redo-3.3.0/obj-x86_64-linux-gnu/DartConfiguration.tcl UpdateCTestConfiguration from :/build/reproducible-path/libpdb-redo-3.3.0/obj-x86_64-linux-gnu/DartConfiguration.tcl @@ -954,12 +990,12 @@ 2: Working Directory: /build/reproducible-path/libpdb-redo-3.3.0/obj-x86_64-linux-gnu/test 2: Test timeout computed to be: 1500 2: CCD components.cif resource was not found -2: Randomness seeded to: 4083270069 +2: Randomness seeded to: 1725771743 2: Could not load the mon_lib_list.cif file from CCP4, please make sure you have installed CCP4 and sourced the environment. 2: 2: Configuration error: 2: -2: The attempt to retrieve compound information for "Z57-a" failed. +2: The attempt to retrieve compound information for "U8U" failed. 2: 2: This information is searched for in a CCD file called components.cif or 2: components.cif.gz which should be located in one of the following directories: @@ -989,8 +1025,8 @@ 2: =============================================================================== 2: All tests passed (12 assertions in 1 test case) 2: -1/2 Test #2: restr2ccd-test ................... Passed 0.01 sec -1: Randomness seeded to: 2972724397 +1/2 Test #2: restr2ccd-test ................... Passed 0.05 sec +1: Randomness seeded to: 2802047958 1: Reading map from "/build/reproducible-path/libpdb-redo-3.3.0/test/../examples/1cbs_map.mtz" 1: with labels: FB: FWT,PHWT 1: with labels: FD: DELFWT,PHDELWT @@ -1129,16 +1165,16 @@ 1: =============================================================================== 1: All tests passed (738136 assertions in 7 test cases) 1: -2/2 Test #1: pdb-redo-unit-test ............... Passed 2.45 sec +2/2 Test #1: pdb-redo-unit-test ............... Passed 9.91 sec 100% tests passed, 0 tests failed out of 2 -Total Test time (real) = 2.46 sec +Total Test time (real) = 9.92 sec make[1]: Leaving directory '/build/reproducible-path/libpdb-redo-3.3.0/obj-x86_64-linux-gnu' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install - cd obj-x86_64-linux-gnu && make -j42 install DESTDIR=/build/reproducible-path/libpdb-redo-3.3.0/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd obj-x86_64-linux-gnu && make -j40 install DESTDIR=/build/reproducible-path/libpdb-redo-3.3.0/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/libpdb-redo-3.3.0/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/libpdb-redo-3.3.0 -B/build/reproducible-path/libpdb-redo-3.3.0/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -1154,21 +1190,21 @@ -- Installing: /build/reproducible-path/libpdb-redo-3.3.0/debian/tmp/usr/lib/x86_64-linux-gnu/cmake/pdb-redo/pdb-redoTargets.cmake -- Installing: /build/reproducible-path/libpdb-redo-3.3.0/debian/tmp/usr/lib/x86_64-linux-gnu/cmake/pdb-redo/pdb-redoTargets-none.cmake -- Installing: /build/reproducible-path/libpdb-redo-3.3.0/debian/tmp/usr/include/pdb-redo --- Installing: /build/reproducible-path/libpdb-redo-3.3.0/debian/tmp/usr/include/pdb-redo/Restraints.hpp --- Installing: /build/reproducible-path/libpdb-redo-3.3.0/debian/tmp/usr/include/pdb-redo/Version.hpp --- Installing: /build/reproducible-path/libpdb-redo-3.3.0/debian/tmp/usr/include/pdb-redo/MapMaker.hpp --- Installing: /build/reproducible-path/libpdb-redo-3.3.0/debian/tmp/usr/include/pdb-redo/Statistics.hpp +-- Installing: /build/reproducible-path/libpdb-redo-3.3.0/debian/tmp/usr/include/pdb-redo/exports.hpp +-- Installing: /build/reproducible-path/libpdb-redo-3.3.0/debian/tmp/usr/include/pdb-redo/Compound.hpp -- Installing: /build/reproducible-path/libpdb-redo-3.3.0/debian/tmp/usr/include/pdb-redo/DistanceMap.hpp --- Installing: /build/reproducible-path/libpdb-redo-3.3.0/debian/tmp/usr/include/pdb-redo/Ramachandran.hpp --- Installing: /build/reproducible-path/libpdb-redo-3.3.0/debian/tmp/usr/include/pdb-redo/ClipperWrapper.hpp +-- Installing: /build/reproducible-path/libpdb-redo-3.3.0/debian/tmp/usr/include/pdb-redo/Minimizer.hpp +-- Installing: /build/reproducible-path/libpdb-redo-3.3.0/debian/tmp/usr/include/pdb-redo/MapMaker.hpp -- Installing: /build/reproducible-path/libpdb-redo-3.3.0/debian/tmp/usr/include/pdb-redo/TLS.hpp --- Installing: /build/reproducible-path/libpdb-redo-3.3.0/debian/tmp/usr/include/pdb-redo/exports.hpp +-- Installing: /build/reproducible-path/libpdb-redo-3.3.0/debian/tmp/usr/include/pdb-redo/Version.hpp +-- Installing: /build/reproducible-path/libpdb-redo-3.3.0/debian/tmp/usr/include/pdb-redo/ClipperWrapper.hpp +-- Installing: /build/reproducible-path/libpdb-redo-3.3.0/debian/tmp/usr/include/pdb-redo/BondMap.hpp -- Installing: /build/reproducible-path/libpdb-redo-3.3.0/debian/tmp/usr/include/pdb-redo/ResolutionCalculator.hpp --- Installing: /build/reproducible-path/libpdb-redo-3.3.0/debian/tmp/usr/include/pdb-redo/Minimizer.hpp --- Installing: /build/reproducible-path/libpdb-redo-3.3.0/debian/tmp/usr/include/pdb-redo/Compound.hpp -- Installing: /build/reproducible-path/libpdb-redo-3.3.0/debian/tmp/usr/include/pdb-redo/AtomShape.hpp --- Installing: /build/reproducible-path/libpdb-redo-3.3.0/debian/tmp/usr/include/pdb-redo/BondMap.hpp -- Installing: /build/reproducible-path/libpdb-redo-3.3.0/debian/tmp/usr/include/pdb-redo/SkipList.hpp +-- Installing: /build/reproducible-path/libpdb-redo-3.3.0/debian/tmp/usr/include/pdb-redo/Statistics.hpp +-- Installing: /build/reproducible-path/libpdb-redo-3.3.0/debian/tmp/usr/include/pdb-redo/Ramachandran.hpp +-- Installing: /build/reproducible-path/libpdb-redo-3.3.0/debian/tmp/usr/include/pdb-redo/Restraints.hpp -- Installing: /build/reproducible-path/libpdb-redo-3.3.0/debian/tmp/usr/lib/x86_64-linux-gnu/cmake/pdb-redo/pdb-redoConfig.cmake -- Installing: /build/reproducible-path/libpdb-redo-3.3.0/debian/tmp/usr/lib/x86_64-linux-gnu/cmake/pdb-redo/pdb-redoConfigVersion.cmake -- Installing: /build/reproducible-path/libpdb-redo-3.3.0/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig/libpdb-redo.pc @@ -1191,8 +1227,8 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'libpdb-redo-dev' in '../libpdb-redo-dev_3.3.0-1_amd64.deb'. dpkg-deb: building package 'libpdb-redo3.3-dbgsym' in '../libpdb-redo3.3-dbgsym_3.3.0-1_amd64.deb'. +dpkg-deb: building package 'libpdb-redo-dev' in '../libpdb-redo-dev_3.3.0-1_amd64.deb'. dpkg-deb: building package 'libpdb-redo3.3' in '../libpdb-redo3.3_3.3.0-1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../libpdb-redo_3.3.0-1_amd64.buildinfo dpkg-genchanges --build=binary -O../libpdb-redo_3.3.0-1_amd64.changes @@ -1201,12 +1237,14 @@ 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/1207063/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1207063/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/2229785 and its subdirectories -I: Current time: Tue Sep 1 00:44:26 -12 2026 -I: pbuilder-time-stamp: 1788266666 +I: removing directory /srv/workspace/pbuilder/1207063 and its subdirectories +I: Current time: Wed Jul 30 20:26:30 +14 2025 +I: pbuilder-time-stamp: 1753856790