Diff of the two buildlogs: -- --- b1/build.log 2024-11-07 04:38:18.730614865 +0000 +++ b2/build.log 2024-11-07 04:41:43.047376403 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Nov 6 16:35:55 -12 2024 -I: pbuilder-time-stamp: 1730954155 +I: Current time: Thu Dec 11 01:01:21 +14 2025 +I: pbuilder-time-stamp: 1765364481 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -26,51 +26,83 @@ dpkg-source: info: unpacking libpdb-redo_3.1.5-5.debian.tar.xz I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1951647/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1849306/tmp/hooks/D01_modify_environment starting +debug: Running on infom02-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 Dec 10 11:01 /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/1849306/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1849306/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' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="32" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.32(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='amd64' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='731d23550e804a998038b67ef0ae29dd' - 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='1951647' - PS1='# ' - PS2='> ' + INVOCATION_ID=971b6e59098741e183a717e813a9c74e + 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=1849306 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.kDIEd9rj/pbuilderrc_cExJ --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.kDIEd9rj/b1 --logfile b1/build.log libpdb-redo_3.1.5-5.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' + 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.kDIEd9rj/pbuilderrc_uJfv --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.kDIEd9rj/b2 --logfile b2/build.log libpdb-redo_3.1.5-5.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' I: uname -a - Linux infom01-amd64 6.1.0-26-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.112-1 (2024-09-30) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.10.11+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.10.11-1~bpo12+1 (2024-10-03) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1951647/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1849306/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: 122 http://deb.debian.org/debian trixie/main amd64 libgsl-dev amd64 2.8+dfsg-4 [1224 kB] Get: 123 http://deb.debian.org/debian trixie/main amd64 libnewuoa0 amd64 0.1.2-1 [18.6 kB] Get: 124 http://deb.debian.org/debian trixie/main amd64 libnewuoa-dev amd64 0.1.2-1 [7508 B] -Fetched 131 MB in 2s (71.5 MB/s) +Fetched 131 MB in 2s (75.2 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libproc2-0: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 ... 19970 files and directories currently installed.) @@ -764,7 +796,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/libpdb-redo-3.1.5/ && 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_3.1.5-5_source.changes +I: user script /srv/workspace/pbuilder/1849306/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/1849306/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/libpdb-redo-3.1.5/ && 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_3.1.5-5_source.changes dpkg-buildpackage: info: source package libpdb-redo dpkg-buildpackage: info: source version 3.1.5-5 dpkg-buildpackage: info: source distribution unstable @@ -831,8 +867,8 @@ -- Looking for clipper/clipper-contrib.h - /usr/include -- Found CCP4: /usr/lib/x86_64-linux-gnu/libclipper-contrib.so -- CCP4 include directory: /usr/include --- Configuring done (1.7s) --- Generating done (0.0s) +-- Configuring done (3.4s) +-- Generating done (0.1s) CMake Warning: Manually-specified variables were not used by the project: @@ -858,29 +894,29 @@ make -f CMakeFiles/pdb-redo.dir/build.make CMakeFiles/pdb-redo.dir/build make[3]: Entering directory '/build/reproducible-path/libpdb-redo-3.1.5/obj-x86_64-linux-gnu' [ 5%] Building CXX object CMakeFiles/pdb-redo.dir/src/AtomShape.cpp.o -[ 35%] Building CXX object CMakeFiles/pdb-redo.dir/src/ResolutionCalculator.cpp.o -[ 35%] Building CXX object CMakeFiles/pdb-redo.dir/src/DistanceMap.cpp.o -[ 35%] Building CXX object CMakeFiles/pdb-redo.dir/src/BondMap.cpp.o -[ 35%] Building CXX object CMakeFiles/pdb-redo.dir/src/MapMaker.cpp.o -[ 35%] Building CXX object CMakeFiles/pdb-redo.dir/src/Compound.cpp.o -[ 47%] Building CXX object CMakeFiles/pdb-redo.dir/src/Statistics.cpp.o -[ 47%] Building CXX object CMakeFiles/pdb-redo.dir/src/SkipList.cpp.o +[ 11%] Building CXX object CMakeFiles/pdb-redo.dir/src/BondMap.cpp.o /usr/bin/c++ -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -Dpdb_redo_EXPORTS -I/build/reproducible-path/libpdb-redo-3.1.5/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.1.5=. -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-3.1.5/src/AtomShape.cpp /usr/bin/c++ -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -Dpdb_redo_EXPORTS -I/build/reproducible-path/libpdb-redo-3.1.5/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.1.5=. -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-3.1.5/src/BondMap.cpp +[ 17%] Building CXX object CMakeFiles/pdb-redo.dir/src/ClipperWrapper.cpp.o +[ 23%] Building CXX object CMakeFiles/pdb-redo.dir/src/DistanceMap.cpp.o +[ 29%] 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-3.1.5/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.1.5=. -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-3.1.5/src/ClipperWrapper.cpp /usr/bin/c++ -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -Dpdb_redo_EXPORTS -I/build/reproducible-path/libpdb-redo-3.1.5/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.1.5=. -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-3.1.5/src/Compound.cpp +[ 35%] 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-3.1.5/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.1.5=. -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-3.1.5/src/DistanceMap.cpp +[ 41%] 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-3.1.5/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.1.5=. -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-3.1.5/src/MapMaker.cpp -[ 52%] 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-3.1.5/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.1.5=. -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-3.1.5/src/Ramachandran.cpp +[ 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-3.1.5/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.1.5=. -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-3.1.5/src/ResolutionCalculator.cpp /usr/bin/c++ -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -Dpdb_redo_EXPORTS -I/build/reproducible-path/libpdb-redo-3.1.5/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.1.5=. -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-3.1.5/src/SkipList.cpp -[ 58%] 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-3.1.5/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.1.5=. -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-3.1.5/src/Ramachandran.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-3.1.5/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.1.5=. -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-3.1.5/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-3.1.5/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.1.5=. -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-3.1.5/src/ClipperWrapper.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-3.1.5/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.1.5=. -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-3.1.5/src/TLS.cpp +[ 64%] 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-3.1.5/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.1.5=. -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-3.1.5/src/Version.cpp +[ 70%] 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-3.1.5/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.1.5=. -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-3.1.5/src/TLS.cpp [ 76%] Linking CXX shared library libpdb-redo.so /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb-redo.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.1.5=. -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 -shared -Wl,-soname,libpdb-redo.so.3.1 -o libpdb-redo.so.3.1.5 "CMakeFiles/pdb-redo.dir/src/AtomShape.cpp.o" "CMakeFiles/pdb-redo.dir/src/BondMap.cpp.o" "CMakeFiles/pdb-redo.dir/src/ClipperWrapper.cpp.o" "CMakeFiles/pdb-redo.dir/src/Compound.cpp.o" "CMakeFiles/pdb-redo.dir/src/DistanceMap.cpp.o" "CMakeFiles/pdb-redo.dir/src/MapMaker.cpp.o" "CMakeFiles/pdb-redo.dir/src/Ramachandran.cpp.o" "CMakeFiles/pdb-redo.dir/src/ResolutionCalculator.cpp.o" "CMakeFiles/pdb-redo.dir/src/SkipList.cpp.o" "CMakeFiles/pdb-redo.dir/src/Statistics.cpp.o" "CMakeFiles/pdb-redo.dir/src/TLS.cpp.o" "CMakeFiles/pdb-redo.dir/src/Version.cpp.o" /usr/lib/x86_64-linux-gnu/libcifpp.so.7.0.7 /usr/lib/x86_64-linux-gnu/libnewuoa.so.0.1.2 /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 /usr/lib/x86_64-linux-gnu/libz.so @@ -890,19 +926,19 @@ make -f CMakeFiles/pdb-redo-unit-test.dir/build.make CMakeFiles/pdb-redo-unit-test.dir/depend make -f examples/CMakeFiles/pdb-redo-example.dir/build.make examples/CMakeFiles/pdb-redo-example.dir/depend make[3]: Entering directory '/build/reproducible-path/libpdb-redo-3.1.5/obj-x86_64-linux-gnu' -cd /build/reproducible-path/libpdb-redo-3.1.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libpdb-redo-3.1.5 /build/reproducible-path/libpdb-redo-3.1.5/examples /build/reproducible-path/libpdb-redo-3.1.5/obj-x86_64-linux-gnu /build/reproducible-path/libpdb-redo-3.1.5/obj-x86_64-linux-gnu/examples /build/reproducible-path/libpdb-redo-3.1.5/obj-x86_64-linux-gnu/examples/CMakeFiles/pdb-redo-example.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/libpdb-redo-3.1.5/obj-x86_64-linux-gnu' +cd /build/reproducible-path/libpdb-redo-3.1.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libpdb-redo-3.1.5 /build/reproducible-path/libpdb-redo-3.1.5/examples /build/reproducible-path/libpdb-redo-3.1.5/obj-x86_64-linux-gnu /build/reproducible-path/libpdb-redo-3.1.5/obj-x86_64-linux-gnu/examples /build/reproducible-path/libpdb-redo-3.1.5/obj-x86_64-linux-gnu/examples/CMakeFiles/pdb-redo-example.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/libpdb-redo-3.1.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libpdb-redo-3.1.5 /build/reproducible-path/libpdb-redo-3.1.5 /build/reproducible-path/libpdb-redo-3.1.5/obj-x86_64-linux-gnu /build/reproducible-path/libpdb-redo-3.1.5/obj-x86_64-linux-gnu /build/reproducible-path/libpdb-redo-3.1.5/obj-x86_64-linux-gnu/CMakeFiles/pdb-redo-unit-test.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/libpdb-redo-3.1.5/obj-x86_64-linux-gnu' -make[3]: Leaving directory '/build/reproducible-path/libpdb-redo-3.1.5/obj-x86_64-linux-gnu' -make -f examples/CMakeFiles/pdb-redo-example.dir/build.make examples/CMakeFiles/pdb-redo-example.dir/build make -f CMakeFiles/pdb-redo-unit-test.dir/build.make CMakeFiles/pdb-redo-unit-test.dir/build +make[3]: Leaving directory '/build/reproducible-path/libpdb-redo-3.1.5/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/libpdb-redo-3.1.5/obj-x86_64-linux-gnu' +make -f examples/CMakeFiles/pdb-redo-example.dir/build.make examples/CMakeFiles/pdb-redo-example.dir/build make[3]: Entering directory '/build/reproducible-path/libpdb-redo-3.1.5/obj-x86_64-linux-gnu' +[ 82%] Building CXX object CMakeFiles/pdb-redo-unit-test.dir/test/pdb-redo-unit-test.cpp.o [ 88%] Building CXX object examples/CMakeFiles/pdb-redo-example.dir/example.cpp.o -[ 88%] Building CXX object CMakeFiles/pdb-redo-unit-test.dir/test/pdb-redo-unit-test.cpp.o -cd /build/reproducible-path/libpdb-redo-3.1.5/obj-x86_64-linux-gnu/examples && /usr/bin/c++ -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -I/build/reproducible-path/libpdb-redo-3.1.5/include -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.1.5=. -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 examples/CMakeFiles/pdb-redo-example.dir/example.cpp.o -MF CMakeFiles/pdb-redo-example.dir/example.cpp.o.d -o CMakeFiles/pdb-redo-example.dir/example.cpp.o -c /build/reproducible-path/libpdb-redo-3.1.5/examples/example.cpp /usr/bin/c++ -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -I/build/reproducible-path/libpdb-redo-3.1.5/include -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.1.5=. -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 CMakeFiles/pdb-redo-unit-test.dir/test/pdb-redo-unit-test.cpp.o -MF CMakeFiles/pdb-redo-unit-test.dir/test/pdb-redo-unit-test.cpp.o.d -o CMakeFiles/pdb-redo-unit-test.dir/test/pdb-redo-unit-test.cpp.o -c /build/reproducible-path/libpdb-redo-3.1.5/test/pdb-redo-unit-test.cpp +cd /build/reproducible-path/libpdb-redo-3.1.5/obj-x86_64-linux-gnu/examples && /usr/bin/c++ -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -I/build/reproducible-path/libpdb-redo-3.1.5/include -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.1.5=. -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 examples/CMakeFiles/pdb-redo-example.dir/example.cpp.o -MF CMakeFiles/pdb-redo-example.dir/example.cpp.o.d -o CMakeFiles/pdb-redo-example.dir/example.cpp.o -c /build/reproducible-path/libpdb-redo-3.1.5/examples/example.cpp [ 94%] Linking CXX executable pdb-redo-example cd /build/reproducible-path/libpdb-redo-3.1.5/obj-x86_64-linux-gnu/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb-redo-example.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.1.5=. -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 "CMakeFiles/pdb-redo-example.dir/example.cpp.o" -o pdb-redo-example -Wl,-rpath,/build/reproducible-path/libpdb-redo-3.1.5/obj-x86_64-linux-gnu ../libpdb-redo.so.3.1.5 /usr/lib/x86_64-linux-gnu/libcifpp.so.7.0.7 /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libnewuoa.so.0.1.2 /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 @@ -1270,7 +1306,7 @@ 2: 0.329081 2: 1.18026 2: 0.943706 -1/2 Test #2: pdb-redo-example ................. Passed 0.29 sec +1/2 Test #2: pdb-redo-example ................. Passed 0.72 sec 1: Running 7 test cases... 1: Reading map from "/build/reproducible-path/libpdb-redo-3.1.5/test/../examples/1cbs_map.mtz" 1: with labels: FB: FWT,PHWT @@ -1416,11 +1452,11 @@ 1: 1: *** No errors detected 1:  -2/2 Test #1: pdb-redo-unit-test ............... Passed 1.60 sec +2/2 Test #1: pdb-redo-unit-test ............... Passed 3.78 sec 100% tests passed, 0 tests failed out of 2 -Total Test time (real) = 1.60 sec +Total Test time (real) = 3.79 sec make[1]: Leaving directory '/build/reproducible-path/libpdb-redo-3.1.5/obj-x86_64-linux-gnu' create-stamp debian/debhelper-build-stamp dh_prep @@ -1441,21 +1477,21 @@ -- Installing: /build/reproducible-path/libpdb-redo-3.1.5/debian/tmp/usr/lib/x86_64-linux-gnu/cmake/pdb-redo/pdb-redoTargets.cmake -- Installing: /build/reproducible-path/libpdb-redo-3.1.5/debian/tmp/usr/lib/x86_64-linux-gnu/cmake/pdb-redo/pdb-redoTargets-none.cmake -- Installing: /build/reproducible-path/libpdb-redo-3.1.5/debian/tmp/usr/include/pdb-redo --- Installing: /build/reproducible-path/libpdb-redo-3.1.5/debian/tmp/usr/include/pdb-redo/TLS.hpp --- Installing: /build/reproducible-path/libpdb-redo-3.1.5/debian/tmp/usr/include/pdb-redo/SkipList.hpp -- Installing: /build/reproducible-path/libpdb-redo-3.1.5/debian/tmp/usr/include/pdb-redo/MapMaker.hpp --- Installing: /build/reproducible-path/libpdb-redo-3.1.5/debian/tmp/usr/include/pdb-redo/exports.hpp -- Installing: /build/reproducible-path/libpdb-redo-3.1.5/debian/tmp/usr/include/pdb-redo/Version.hpp +-- Installing: /build/reproducible-path/libpdb-redo-3.1.5/debian/tmp/usr/include/pdb-redo/Restraints.hpp -- Installing: /build/reproducible-path/libpdb-redo-3.1.5/debian/tmp/usr/include/pdb-redo/ClipperWrapper.hpp --- Installing: /build/reproducible-path/libpdb-redo-3.1.5/debian/tmp/usr/include/pdb-redo/BondMap.hpp -- Installing: /build/reproducible-path/libpdb-redo-3.1.5/debian/tmp/usr/include/pdb-redo/Compound.hpp +-- Installing: /build/reproducible-path/libpdb-redo-3.1.5/debian/tmp/usr/include/pdb-redo/DistanceMap.hpp -- Installing: /build/reproducible-path/libpdb-redo-3.1.5/debian/tmp/usr/include/pdb-redo/AtomShape.hpp --- Installing: /build/reproducible-path/libpdb-redo-3.1.5/debian/tmp/usr/include/pdb-redo/Restraints.hpp --- Installing: /build/reproducible-path/libpdb-redo-3.1.5/debian/tmp/usr/include/pdb-redo/Statistics.hpp +-- Installing: /build/reproducible-path/libpdb-redo-3.1.5/debian/tmp/usr/include/pdb-redo/SkipList.hpp +-- Installing: /build/reproducible-path/libpdb-redo-3.1.5/debian/tmp/usr/include/pdb-redo/BondMap.hpp -- Installing: /build/reproducible-path/libpdb-redo-3.1.5/debian/tmp/usr/include/pdb-redo/Ramachandran.hpp +-- Installing: /build/reproducible-path/libpdb-redo-3.1.5/debian/tmp/usr/include/pdb-redo/TLS.hpp +-- Installing: /build/reproducible-path/libpdb-redo-3.1.5/debian/tmp/usr/include/pdb-redo/exports.hpp -- Installing: /build/reproducible-path/libpdb-redo-3.1.5/debian/tmp/usr/include/pdb-redo/Minimizer.hpp --- Installing: /build/reproducible-path/libpdb-redo-3.1.5/debian/tmp/usr/include/pdb-redo/DistanceMap.hpp -- Installing: /build/reproducible-path/libpdb-redo-3.1.5/debian/tmp/usr/include/pdb-redo/ResolutionCalculator.hpp +-- Installing: /build/reproducible-path/libpdb-redo-3.1.5/debian/tmp/usr/include/pdb-redo/Statistics.hpp -- Installing: /build/reproducible-path/libpdb-redo-3.1.5/debian/tmp/usr/lib/x86_64-linux-gnu/cmake/pdb-redo/pdb-redoConfig.cmake -- Installing: /build/reproducible-path/libpdb-redo-3.1.5/debian/tmp/usr/lib/x86_64-linux-gnu/cmake/pdb-redo/pdb-redoConfigVersion.cmake -- Installing: /build/reproducible-path/libpdb-redo-3.1.5/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig/libpdb-redo.pc @@ -1478,9 +1514,9 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'libpdb-redo-dev' in '../libpdb-redo-dev_3.1.5-5_amd64.deb'. -dpkg-deb: building package 'libpdb-redo3-dbgsym' in '../libpdb-redo3-dbgsym_3.1.5-5_amd64.deb'. dpkg-deb: building package 'libpdb-redo3' in '../libpdb-redo3_3.1.5-5_amd64.deb'. +dpkg-deb: building package 'libpdb-redo3-dbgsym' in '../libpdb-redo3-dbgsym_3.1.5-5_amd64.deb'. +dpkg-deb: building package 'libpdb-redo-dev' in '../libpdb-redo-dev_3.1.5-5_amd64.deb'. dpkg-genbuildinfo --build=binary -O../libpdb-redo_3.1.5-5_amd64.buildinfo dpkg-genchanges --build=binary -O../libpdb-redo_3.1.5-5_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1488,12 +1524,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/1849306/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1849306/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/1951647 and its subdirectories -I: Current time: Wed Nov 6 16:38:17 -12 2024 -I: pbuilder-time-stamp: 1730954297 +I: removing directory /srv/workspace/pbuilder/1849306 and its subdirectories +I: Current time: Thu Dec 11 01:04:35 +14 2025 +I: pbuilder-time-stamp: 1765364675