Diff of the two buildlogs: -- --- b1/build.log 2025-10-19 22:14:08.140500976 +0000 +++ b2/build.log 2025-10-19 22:22:34.913188703 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Oct 19 10:07:06 -12 2025 -I: pbuilder-time-stamp: 1760911626 +I: Current time: Sun Nov 22 18:37:09 +14 2026 +I: pbuilder-time-stamp: 1795322229 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration @@ -26,53 +26,85 @@ dpkg-source: info: applying build-python-bindings.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/3699318/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1073153/tmp/hooks/D01_modify_environment starting +debug: Running on ionos15-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Nov 22 04:37 /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/1073153/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1073153/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=40 ' - DISTRIBUTION='forky' - 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]="3" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.3.3(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' + DIRSTACK=() + DISTRIBUTION=forky + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='88de77bdaf5f45b7bbd6e06534b7be73' - 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='3699318' - PS1='# ' - PS2='> ' + INVOCATION_ID=f6a96c6bd1cb4af39e6de4d8c8b15b22 + 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=1073153 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.hYY87XdC/pbuilderrc_L0EW --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.hYY87XdC/b1 --logfile b1/build.log voronota_1.29.4415+ds-1.dsc' - SUDO_GID='111' - SUDO_HOME='/var/lib/jenkins' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://46.16.76.132:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.hYY87XdC/pbuilderrc_pnU7 --distribution forky --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.hYY87XdC/b2 --logfile b2/build.log voronota_1.29.4415+ds-1.dsc' + SUDO_GID=111 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos11-amd64 6.12.48+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.48-1 (2025-09-20) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.48+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.48-1 (2025-09-20) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/3699318/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1073153/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -200,7 +232,7 @@ Get: 80 http://deb.debian.org/debian forky/main amd64 libpython3.13-dev amd64 3.13.8-1 [5308 kB] Get: 81 http://deb.debian.org/debian forky/main amd64 libpython3-dev amd64 3.13.7-1 [10.5 kB] Get: 82 http://deb.debian.org/debian forky/main amd64 swig amd64 4.3.0-2 [1508 kB] -Fetched 48.8 MB in 2s (24.3 MB/s) +Fetched 48.8 MB in 1s (56.3 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 ... 19898 files and directories currently installed.) @@ -482,8 +514,8 @@ Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' -Local time is now: Sun Oct 19 22:08:46 UTC 2025. -Universal Time is now: Sun Oct 19 22:08:46 UTC 2025. +Local time is now: Sun Nov 22 04:40:07 UTC 2026. +Universal Time is now: Sun Nov 22 04:40:07 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20240727.1) ... @@ -555,7 +587,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/voronota-1.29.4415+ds/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../voronota_1.29.4415+ds-1_source.changes +I: user script /srv/workspace/pbuilder/1073153/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for forky +I: user script /srv/workspace/pbuilder/1073153/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/voronota-1.29.4415+ds/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../voronota_1.29.4415+ds-1_source.changes dpkg-buildpackage: info: source package voronota dpkg-buildpackage: info: source version 1.29.4415+ds-1 dpkg-buildpackage: info: source distribution unstable @@ -634,7 +670,7 @@ expansion_lt/swig/CMakeLists.txt:11 (swig_add_library) This warning is for project developers. Use -Wno-dev to suppress it. --- Configuring done (2.0s) +-- Configuring done (1.4s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: @@ -651,7 +687,7 @@ -- Build files have been written to: /build/reproducible-path/voronota-1.29.4415+ds/obj-x86_64-linux-gnu make[1]: Leaving directory '/build/reproducible-path/voronota-1.29.4415+ds' dh_auto_build - cd obj-x86_64-linux-gnu && make -j40 INSTALL="install --strip-program=true" VERBOSE=1 + cd obj-x86_64-linux-gnu && make -j42 INSTALL="install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/voronota-1.29.4415+ds/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/voronota-1.29.4415+ds -B/build/reproducible-path/voronota-1.29.4415+ds/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/voronota-1.29.4415+ds/obj-x86_64-linux-gnu/CMakeFiles /build/reproducible-path/voronota-1.29.4415+ds/obj-x86_64-linux-gnu//CMakeFiles/progress.marks @@ -670,120 +706,134 @@ Dependee "/build/reproducible-path/voronota-1.29.4415+ds/obj-x86_64-linux-gnu/expansion_lt/swig/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/voronota-1.29.4415+ds/obj-x86_64-linux-gnu/expansion_lt/swig/CMakeFiles/voronotalt_swig_compilation.dir/depend.internal". make[3]: Leaving directory '/build/reproducible-path/voronota-1.29.4415+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/voronota-1.29.4415+ds/obj-x86_64-linux-gnu' -make -f expansion_lt/CMakeFiles/voronota-lt.dir/build.make expansion_lt/CMakeFiles/voronota-lt.dir/build make -f CMakeFiles/voronota.dir/build.make CMakeFiles/voronota.dir/build +make -f expansion_lt/CMakeFiles/voronota-lt.dir/build.make expansion_lt/CMakeFiles/voronota-lt.dir/build Scanning dependencies of target voronotalt_swig_compilation -make[3]: Entering directory '/build/reproducible-path/voronota-1.29.4415+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/voronota-1.29.4415+ds/obj-x86_64-linux-gnu' +make[3]: Entering directory '/build/reproducible-path/voronota-1.29.4415+ds/obj-x86_64-linux-gnu' make -f expansion_lt/swig/CMakeFiles/voronotalt_swig_compilation.dir/build.make expansion_lt/swig/CMakeFiles/voronotalt_swig_compilation.dir/build make[3]: Entering directory '/build/reproducible-path/voronota-1.29.4415+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/voronota-1.29.4415+ds/obj-x86_64-linux-gnu' -[ 3%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_calculate_contacts.cpp.o -[ 3%] Building CXX object expansion_lt/CMakeFiles/voronota-lt.dir/src/voronota_lt.cpp.o -[ 5%] Swig compile voronotalt_python.i for python -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/voronota-1.29.4415+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/voronota.dir/src/modes/mode_calculate_contacts.cpp.o -MF CMakeFiles/voronota.dir/src/modes/mode_calculate_contacts.cpp.o.d -o CMakeFiles/voronota.dir/src/modes/mode_calculate_contacts.cpp.o -c /build/reproducible-path/voronota-1.29.4415+ds/src/modes/mode_calculate_contacts.cpp [ 7%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_calculate_mock_solvent.cpp.o -[ 9%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_compare_contacts.cpp.o -cd /build/reproducible-path/voronota-1.29.4415+ds/obj-x86_64-linux-gnu/expansion_lt && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/voronota-1.29.4415+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++14 -fopenmp -MD -MT expansion_lt/CMakeFiles/voronota-lt.dir/src/voronota_lt.cpp.o -MF CMakeFiles/voronota-lt.dir/src/voronota_lt.cpp.o.d -o CMakeFiles/voronota-lt.dir/src/voronota_lt.cpp.o -c /build/reproducible-path/voronota-1.29.4415+ds/expansion_lt/src/voronota_lt.cpp +[ 11%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_calculate_vertices_in_parallel.cpp.o +[ 21%] Swig compile voronotalt_python.i for python +[ 23%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_compare_contacts.cpp.o +[ 25%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_demo_hypercut.cpp.o +[ 27%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_draw_contacts.cpp.o +[ 29%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_draw_values_bitmap.cpp.o +[ 33%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_expand_descriptors.cpp.o +[ 35%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_demo_ses.cpp.o +[ 39%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_place_membrane.cpp.o +[ 47%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_query_contacts_simulating_unfolding.cpp.o +[ 58%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_score_contacts_global_energy_by_cuts.cpp.o cd /build/reproducible-path/voronota-1.29.4415+ds/obj-x86_64-linux-gnu/expansion_lt/swig && /usr/bin/cmake -E make_directory /build/reproducible-path/voronota-1.29.4415+ds/obj-x86_64-linux-gnu/expansion_lt/swig/CMakeFiles/_voronotalt.dir /build/reproducible-path/voronota-1.29.4415+ds/obj-x86_64-linux-gnu/expansion_lt/swig /build/reproducible-path/voronota-1.29.4415+ds/obj-x86_64-linux-gnu/expansion_lt/swig/CMakeFiles/_voronotalt.dir -[ 11%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_calculate_vertices.cpp.o +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/voronota-1.29.4415+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/voronota.dir/src/modes/mode_demo_hypercut.cpp.o -MF CMakeFiles/voronota.dir/src/modes/mode_demo_hypercut.cpp.o.d -o CMakeFiles/voronota.dir/src/modes/mode_demo_hypercut.cpp.o -c /build/reproducible-path/voronota-1.29.4415+ds/src/modes/mode_demo_hypercut.cpp +[ 66%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_query_contacts_interface_exposure_values.cpp.o +[ 66%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_score_contacts_energy_stats.cpp.o +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/voronota-1.29.4415+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/voronota.dir/src/modes/mode_calculate_vertices_in_parallel.cpp.o -MF CMakeFiles/voronota.dir/src/modes/mode_calculate_vertices_in_parallel.cpp.o.d -o CMakeFiles/voronota.dir/src/modes/mode_calculate_vertices_in_parallel.cpp.o -c /build/reproducible-path/voronota-1.29.4415+ds/src/modes/mode_calculate_vertices_in_parallel.cpp +[ 76%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_vectorize_contact_environments.cpp.o +[ 76%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_score_contacts_energy.cpp.o /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/voronota-1.29.4415+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/voronota.dir/src/modes/mode_compare_contacts.cpp.o -MF CMakeFiles/voronota.dir/src/modes/mode_compare_contacts.cpp.o.d -o CMakeFiles/voronota.dir/src/modes/mode_compare_contacts.cpp.o -c /build/reproducible-path/voronota-1.29.4415+ds/src/modes/mode_compare_contacts.cpp -[ 13%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_calculate_vertices_in_parallel.cpp.o -[ 15%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_compare_files_as_sets.cpp.o -[ 17%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_calculate_path_centralities.cpp.o +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/voronota-1.29.4415+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/voronota.dir/src/modes/mode_demo_ses.cpp.o -MF CMakeFiles/voronota.dir/src/modes/mode_demo_ses.cpp.o.d -o CMakeFiles/voronota.dir/src/modes/mode_demo_ses.cpp.o -c /build/reproducible-path/voronota-1.29.4415+ds/src/modes/mode_demo_ses.cpp /usr/bin/c++ -g -O2 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/build/reproducible-path/voronota-1.29.4415+ds/src/modes/mode_simulate_potential_for_membrane_proteins.cpp -make[3]: Leaving directory '/build/reproducible-path/voronota-1.29.4415+ds/obj-x86_64-linux-gnu' -[ 78%] Built target voronotalt_swig_compilation -[ 80%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_split_atoms_file.cpp.o /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/voronota-1.29.4415+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/voronota.dir/src/modes/mode_split_atoms_file.cpp.o -MF CMakeFiles/voronota.dir/src/modes/mode_split_atoms_file.cpp.o.d -o CMakeFiles/voronota.dir/src/modes/mode_split_atoms_file.cpp.o -c /build/reproducible-path/voronota-1.29.4415+ds/src/modes/mode_split_atoms_file.cpp +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/voronota-1.29.4415+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/voronota.dir/src/modes/mode_vectorize_contact_environments.cpp.o -MF CMakeFiles/voronota.dir/src/modes/mode_vectorize_contact_environments.cpp.o.d -o CMakeFiles/voronota.dir/src/modes/mode_vectorize_contact_environments.cpp.o -c /build/reproducible-path/voronota-1.29.4415+ds/src/modes/mode_vectorize_contact_environments.cpp +cd /build/reproducible-path/voronota-1.29.4415+ds/obj-x86_64-linux-gnu/expansion_lt/swig && /usr/bin/cmake -E env SWIG_LIB=/usr/share/swig/4.3.0 /usr/bin/swig -python -outdir /build/reproducible-path/voronota-1.29.4415+ds/obj-x86_64-linux-gnu/expansion_lt/swig -c++ -interface _voronotalt -I/usr/include/python3.13 -I/build/reproducible-path/voronota-1.29.4415+ds/expansion_lt/swig -I/build/reproducible-path/voronota-1.29.4415+ds/expansion_lt/swig/../src -o /build/reproducible-path/voronota-1.29.4415+ds/obj-x86_64-linux-gnu/expansion_lt/swig/CMakeFiles/_voronotalt.dir/voronotalt_pythonPYTHON_wrap.cxx /build/reproducible-path/voronota-1.29.4415+ds/expansion_lt/swig/voronotalt_python.i +[ 84%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_vectorize_contacts.cpp.o +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/voronota-1.29.4415+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/voronota.dir/src/modes/mode_vectorize_contacts.cpp.o -MF CMakeFiles/voronota.dir/src/modes/mode_vectorize_contacts.cpp.o.d -o CMakeFiles/voronota.dir/src/modes/mode_vectorize_contacts.cpp.o -c /build/reproducible-path/voronota-1.29.4415+ds/src/modes/mode_vectorize_contacts.cpp +make[3]: Leaving directory '/build/reproducible-path/voronota-1.29.4415+ds/obj-x86_64-linux-gnu' +[ 84%] Built target voronotalt_swig_compilation +[ 86%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_vectorize_points.cpp.o +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/voronota-1.29.4415+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/voronota.dir/src/modes/mode_vectorize_points.cpp.o -MF CMakeFiles/voronota.dir/src/modes/mode_vectorize_points.cpp.o.d -o CMakeFiles/voronota.dir/src/modes/mode_vectorize_points.cpp.o -c /build/reproducible-path/voronota-1.29.4415+ds/src/modes/mode_vectorize_points.cpp +[ 88%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_write_balls_to_atoms_file.cpp.o +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/voronota-1.29.4415+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/voronota.dir/src/modes/mode_write_balls_to_atoms_file.cpp.o -MF CMakeFiles/voronota.dir/src/modes/mode_write_balls_to_atoms_file.cpp.o.d -o CMakeFiles/voronota.dir/src/modes/mode_write_balls_to_atoms_file.cpp.o -c /build/reproducible-path/voronota-1.29.4415+ds/src/modes/mode_write_balls_to_atoms_file.cpp make -f expansion_lt/swig/CMakeFiles/_voronotalt.dir/build.make expansion_lt/swig/CMakeFiles/_voronotalt.dir/depend make[3]: Entering directory '/build/reproducible-path/voronota-1.29.4415+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/voronota-1.29.4415+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/voronota-1.29.4415+ds /build/reproducible-path/voronota-1.29.4415+ds/expansion_lt/swig /build/reproducible-path/voronota-1.29.4415+ds/obj-x86_64-linux-gnu /build/reproducible-path/voronota-1.29.4415+ds/obj-x86_64-linux-gnu/expansion_lt/swig /build/reproducible-path/voronota-1.29.4415+ds/obj-x86_64-linux-gnu/expansion_lt/swig/CMakeFiles/_voronotalt.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/voronota-1.29.4415+ds/obj-x86_64-linux-gnu' make -f expansion_lt/swig/CMakeFiles/_voronotalt.dir/build.make expansion_lt/swig/CMakeFiles/_voronotalt.dir/build make[3]: Entering directory '/build/reproducible-path/voronota-1.29.4415+ds/obj-x86_64-linux-gnu' -[ 82%] Building CXX object expansion_lt/swig/CMakeFiles/_voronotalt.dir/CMakeFiles/_voronotalt.dir/voronotalt_pythonPYTHON_wrap.cxx.o +[ 90%] Building CXX object expansion_lt/swig/CMakeFiles/_voronotalt.dir/CMakeFiles/_voronotalt.dir/voronotalt_pythonPYTHON_wrap.cxx.o cd /build/reproducible-path/voronota-1.29.4415+ds/obj-x86_64-linux-gnu/expansion_lt/swig && /usr/bin/c++ -D_voronotalt_EXPORTS -I/usr/include/python3.13 -I/build/reproducible-path/voronota-1.29.4415+ds/expansion_lt/swig -I/build/reproducible-path/voronota-1.29.4415+ds/expansion_lt/swig/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/voronota-1.29.4415+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++14 -fPIC -MD -MT expansion_lt/swig/CMakeFiles/_voronotalt.dir/CMakeFiles/_voronotalt.dir/voronotalt_pythonPYTHON_wrap.cxx.o -MF CMakeFiles/_voronotalt.dir/CMakeFiles/_voronotalt.dir/voronotalt_pythonPYTHON_wrap.cxx.o.d -o CMakeFiles/_voronotalt.dir/CMakeFiles/_voronotalt.dir/voronotalt_pythonPYTHON_wrap.cxx.o -c /build/reproducible-path/voronota-1.29.4415+ds/obj-x86_64-linux-gnu/expansion_lt/swig/CMakeFiles/_voronotalt.dir/voronotalt_pythonPYTHON_wrap.cxx -[ 84%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_vectorize_contact_environments.cpp.o -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/voronota-1.29.4415+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/voronota.dir/src/modes/mode_vectorize_contact_environments.cpp.o -MF CMakeFiles/voronota.dir/src/modes/mode_vectorize_contact_environments.cpp.o.d -o CMakeFiles/voronota.dir/src/modes/mode_vectorize_contact_environments.cpp.o -c /build/reproducible-path/voronota-1.29.4415+ds/src/modes/mode_vectorize_contact_environments.cpp -[ 86%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_vectorize_contacts.cpp.o -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/voronota-1.29.4415+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/voronota.dir/src/modes/mode_vectorize_contacts.cpp.o -MF CMakeFiles/voronota.dir/src/modes/mode_vectorize_contacts.cpp.o.d -o CMakeFiles/voronota.dir/src/modes/mode_vectorize_contacts.cpp.o -c /build/reproducible-path/voronota-1.29.4415+ds/src/modes/mode_vectorize_contacts.cpp -[ 88%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_vectorize_points.cpp.o -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/voronota-1.29.4415+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/voronota.dir/src/modes/mode_vectorize_points.cpp.o -MF CMakeFiles/voronota.dir/src/modes/mode_vectorize_points.cpp.o.d -o CMakeFiles/voronota.dir/src/modes/mode_vectorize_points.cpp.o -c /build/reproducible-path/voronota-1.29.4415+ds/src/modes/mode_vectorize_points.cpp -[ 90%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_write_balls_to_atoms_file.cpp.o -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/voronota-1.29.4415+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/voronota.dir/src/modes/mode_write_balls_to_atoms_file.cpp.o -MF CMakeFiles/voronota.dir/src/modes/mode_write_balls_to_atoms_file.cpp.o.d -o CMakeFiles/voronota.dir/src/modes/mode_write_balls_to_atoms_file.cpp.o -c /build/reproducible-path/voronota-1.29.4415+ds/src/modes/mode_write_balls_to_atoms_file.cpp [ 92%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_write_qa_scores_in_casp_format.cpp.o /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/voronota-1.29.4415+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/voronota.dir/src/modes/mode_write_qa_scores_in_casp_format.cpp.o -MF CMakeFiles/voronota.dir/src/modes/mode_write_qa_scores_in_casp_format.cpp.o.d -o CMakeFiles/voronota.dir/src/modes/mode_write_qa_scores_in_casp_format.cpp.o -c /build/reproducible-path/voronota-1.29.4415+ds/src/modes/mode_write_qa_scores_in_casp_format.cpp [ 94%] Building CXX object CMakeFiles/voronota.dir/src/voronota.cpp.o /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/voronota-1.29.4415+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/voronota.dir/src/voronota.cpp.o -MF CMakeFiles/voronota.dir/src/voronota.cpp.o.d -o CMakeFiles/voronota.dir/src/voronota.cpp.o -c /build/reproducible-path/voronota-1.29.4415+ds/src/voronota.cpp +/build/reproducible-path/voronota-1.29.4415+ds/src/voronota.cpp:59:22: warning: 'template class std::pointer_to_unary_function' is deprecated [-Wdeprecated-declarations] + 59 | typedef std::pointer_to_unary_function FunctionPtr; + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/15/string:51, + from /usr/include/c++/15/bits/locale_classes.h:42, + from /usr/include/c++/15/bits/ios_base.h:43, + from /usr/include/c++/15/ios:46, + from /usr/include/c++/15/bits/ostream.h:43, + from /usr/include/c++/15/ostream:42, + from /usr/include/c++/15/iostream:43, + from /build/reproducible-path/voronota-1.29.4415+ds/src/voronota.cpp:1: +/usr/include/c++/15/bits/stl_function.h:1102:11: note: declared here + 1102 | class pointer_to_unary_function : public unary_function<_Arg, _Result> + | ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/voronota-1.29.4415+ds/src/modes/../scripting/operators/vcblocks.h:5, from /build/reproducible-path/voronota-1.29.4415+ds/src/modes/../scripting/script_execution_manager.h:173, from /build/reproducible-path/voronota-1.29.4415+ds/src/modes/../scripting/script_execution_manager_with_variant_output.h:4, @@ -804,20 +854,6 @@ /usr/include/c++/15/bits/stl_vector.h:1261:7: note: declared here 1261 | operator[](size_type __n) _GLIBCXX_NOEXCEPT | ^~~~~~~~ -/build/reproducible-path/voronota-1.29.4415+ds/src/voronota.cpp:59:22: warning: 'template class std::pointer_to_unary_function' is deprecated [-Wdeprecated-declarations] - 59 | typedef std::pointer_to_unary_function FunctionPtr; - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/15/string:51, - from /usr/include/c++/15/bits/locale_classes.h:42, - from /usr/include/c++/15/bits/ios_base.h:43, - from /usr/include/c++/15/ios:46, - from /usr/include/c++/15/bits/ostream.h:43, - from /usr/include/c++/15/ostream:42, - from /usr/include/c++/15/iostream:43, - from /build/reproducible-path/voronota-1.29.4415+ds/src/voronota.cpp:1: -/usr/include/c++/15/bits/stl_function.h:1102:11: note: declared here - 1102 | class pointer_to_unary_function : public unary_function<_Arg, _Result> - | ^~~~~~~~~~~~~~~~~~~~~~~~~ [ 96%] Linking CXX shared module _voronotalt.so cd /build/reproducible-path/voronota-1.29.4415+ds/obj-x86_64-linux-gnu/expansion_lt/swig && /usr/bin/cmake -E cmake_link_script CMakeFiles/_voronotalt.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/voronota-1.29.4415+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,--dependency-file=CMakeFiles/_voronotalt.dir/link.d -specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z,relro -shared -o _voronotalt.so CMakeFiles/_voronotalt.dir/CMakeFiles/_voronotalt.dir/voronotalt_pythonPYTHON_wrap.cxx.o @@ -840,7 +876,7 @@ create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install - cd obj-x86_64-linux-gnu && make -j40 install DESTDIR=/build/reproducible-path/voronota-1.29.4415\+ds/debian/tmp AM_UPDATE_INFO_DIR=no INSTALL="install --strip-program=true" + cd obj-x86_64-linux-gnu && make -j42 install DESTDIR=/build/reproducible-path/voronota-1.29.4415\+ds/debian/tmp AM_UPDATE_INFO_DIR=no INSTALL="install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/voronota-1.29.4415+ds/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/voronota-1.29.4415+ds -B/build/reproducible-path/voronota-1.29.4415+ds/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -887,10 +923,10 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'voronota' in '../voronota_1.29.4415+ds-1_amd64.deb'. -dpkg-deb: building package 'python3-voronotalt' in '../python3-voronotalt_1.29.4415+ds-1_amd64.deb'. -dpkg-deb: building package 'python3-voronotalt-dbgsym' in '../python3-voronotalt-dbgsym_1.29.4415+ds-1_amd64.deb'. dpkg-deb: building package 'voronota-dbgsym' in '../voronota-dbgsym_1.29.4415+ds-1_amd64.deb'. +dpkg-deb: building package 'python3-voronotalt-dbgsym' in '../python3-voronotalt-dbgsym_1.29.4415+ds-1_amd64.deb'. +dpkg-deb: building package 'python3-voronotalt' in '../python3-voronotalt_1.29.4415+ds-1_amd64.deb'. +dpkg-deb: building package 'voronota' in '../voronota_1.29.4415+ds-1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../voronota_1.29.4415+ds-1_amd64.buildinfo dpkg-genchanges --build=binary -O../voronota_1.29.4415+ds-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -898,12 +934,14 @@ 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/1073153/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1073153/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/3699318 and its subdirectories -I: Current time: Sun Oct 19 10:14:07 -12 2025 -I: pbuilder-time-stamp: 1760912047 +I: removing directory /srv/workspace/pbuilder/1073153 and its subdirectories +I: Current time: Sun Nov 22 18:45:33 +14 2026 +I: pbuilder-time-stamp: 1795322733