Diff of the two buildlogs: -- --- b1/build.log 2025-02-18 20:20:14.346094711 +0000 +++ b2/build.log 2025-02-18 20:25:44.927114100 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Feb 18 08:12:43 -12 2025 -I: pbuilder-time-stamp: 1739909563 +I: Current time: Tue Mar 24 16:43:25 +14 2026 +I: pbuilder-time-stamp: 1774320205 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -25,54 +25,86 @@ dpkg-source: info: applying use-system-packages.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/28699/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/109783/tmp/hooks/D01_modify_environment starting +debug: Running on ionos6-i386. +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 Mar 24 02:43 /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/109783/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/109783/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='i386' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=11 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='i386' + 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]="i686-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=i386 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=21 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - INVOCATION_ID='21f10a79c896439eaa8020daa7ef3c80' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - LD_LIBRARY_PATH='/usr/lib/libeatmydata' - LD_PRELOAD='libeatmydata.so' - 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='28699' - PS1='# ' - PS2='> ' + INVOCATION_ID=d31914781d494c38bf89f07face68ea1 + LANG=C + LANGUAGE=de_CH:de + LC_ALL=C + LD_LIBRARY_PATH=/usr/lib/libeatmydata + LD_PRELOAD=libeatmydata.so + MACHTYPE=i686-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=109783 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.rwuOlkrz/pbuilderrc_PdJv --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.rwuOlkrz/b1 --logfile b1/build.log voronota_1.29.4307+ds-1.dsc' - SUDO_GID='112' - SUDO_UID='107' - 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.rwuOlkrz/pbuilderrc_Q3yv --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.rwuOlkrz/b2 --logfile b2/build.log voronota_1.29.4307+ds-1.dsc' + SUDO_GID=112 + SUDO_UID=107 + 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 ionos12-i386 6.1.0-31-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-31-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/28699/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/109783/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -174,7 +206,7 @@ Get: 60 http://deb.debian.org/debian unstable/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 61 http://deb.debian.org/debian unstable/main i386 debhelper all 13.24.1 [920 kB] Get: 62 http://deb.debian.org/debian unstable/main i386 help2man i386 1.49.3 [198 kB] -Fetched 42.6 MB in 1s (83.3 MB/s) +Fetched 42.6 MB in 1s (70.4 MB/s) Preconfiguring packages ... Selecting previously unselected package liblocale-gettext-perl. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19784 files and directories currently installed.) @@ -437,7 +469,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/voronota-1.29.4307+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_1.29.4307+ds-1_source.changes +I: user script /srv/workspace/pbuilder/109783/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/109783/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/voronota-1.29.4307+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_1.29.4307+ds-1_source.changes dpkg-buildpackage: info: source package voronota dpkg-buildpackage: info: source version 1.29.4307+ds-1 dpkg-buildpackage: info: source distribution unstable @@ -474,7 +510,7 @@ -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done --- Configuring done (1.1s) +-- Configuring done (0.5s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: @@ -491,7 +527,7 @@ -- Build files have been written to: /build/reproducible-path/voronota-1.29.4307+ds/obj-i686-linux-gnu dh_auto_build - cd obj-i686-linux-gnu && make -j11 "INSTALL=install --strip-program=true" VERBOSE=1 + cd obj-i686-linux-gnu && make -j21 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/voronota-1.29.4307+ds/obj-i686-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/voronota-1.29.4307+ds -B/build/reproducible-path/voronota-1.29.4307+ds/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/voronota-1.29.4307+ds/obj-i686-linux-gnu/CMakeFiles /build/reproducible-path/voronota-1.29.4307+ds/obj-i686-linux-gnu//CMakeFiles/progress.marks @@ -503,44 +539,143 @@ make[3]: Leaving directory '/build/reproducible-path/voronota-1.29.4307+ds/obj-i686-linux-gnu' make -f CMakeFiles/voronota.dir/build.make CMakeFiles/voronota.dir/build make[3]: Entering directory '/build/reproducible-path/voronota-1.29.4307+ds/obj-i686-linux-gnu' -[ 2%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_calculate_contacts.cpp.o -[ 4%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_demo_blank.cpp.o +[ 4%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_demo_ses.cpp.o +[ 4%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_calculate_contacts.cpp.o [ 6%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_calculate_mock_solvent.cpp.o -[ 8%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_calculate_vertices_in_parallel.cpp.o -[ 13%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_calculate_vertices.cpp.o -[ 13%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_compare_contacts.cpp.o -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/voronota-1.29.4307+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/voronota.dir/src/modes/mode_demo_blank.cpp.o -MF CMakeFiles/voronota.dir/src/modes/mode_demo_blank.cpp.o.d -o CMakeFiles/voronota.dir/src/modes/mode_demo_blank.cpp.o -c /build/reproducible-path/voronota-1.29.4307+ds/src/modes/mode_demo_blank.cpp -[ 15%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_calculate_path_centralities.cpp.o -[ 17%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_compare_files_as_sets.cpp.o +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/voronota-1.29.4307+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -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-1.29.4307+ds/src/modes/mode_demo_ses.cpp +[ 8%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_calculate_path_centralities.cpp.o +[ 10%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_calculate_vertices_in_parallel.cpp.o /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/voronota-1.29.4307+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -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-1.29.4307+ds/src/modes/mode_calculate_contacts.cpp +[ 15%] 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-1.29.4307+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/voronota.dir/src/modes/mode_calculate_mock_solvent.cpp.o -MF CMakeFiles/voronota.dir/src/modes/mode_calculate_mock_solvent.cpp.o.d -o CMakeFiles/voronota.dir/src/modes/mode_calculate_mock_solvent.cpp.o -c /build/reproducible-path/voronota-1.29.4307+ds/src/modes/mode_calculate_mock_solvent.cpp -[ 19%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_demo_ses.cpp.o -[ 23%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_demo_hypercut.cpp.o -[ 23%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_demo_polygon_triangulation.cpp.o -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/voronota-1.29.4307+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/voronota.dir/src/modes/mode_calculate_vertices.cpp.o -MF CMakeFiles/voronota.dir/src/modes/mode_calculate_vertices.cpp.o.d -o CMakeFiles/voronota.dir/src/modes/mode_calculate_vertices.cpp.o -c /build/reproducible-path/voronota-1.29.4307+ds/src/modes/mode_calculate_vertices.cpp +[ 17%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_demo_blank.cpp.o +[ 17%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_compare_files_as_sets.cpp.o /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/voronota-1.29.4307+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/voronota.dir/src/modes/mode_calculate_path_centralities.cpp.o -MF CMakeFiles/voronota.dir/src/modes/mode_calculate_path_centralities.cpp.o.d -o CMakeFiles/voronota.dir/src/modes/mode_calculate_path_centralities.cpp.o -c /build/reproducible-path/voronota-1.29.4307+ds/src/modes/mode_calculate_path_centralities.cpp +[ 19%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_demo_polygon_triangulation.cpp.o +[ 21%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_demo_hypercut.cpp.o /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/voronota-1.29.4307+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -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-1.29.4307+ds/src/modes/mode_calculate_vertices_in_parallel.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/voronota-1.29.4307+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -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-1.29.4307+ds/src/modes/mode_compare_contacts.cpp +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/voronota-1.29.4307+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/voronota.dir/src/modes/mode_calculate_vertices.cpp.o -MF CMakeFiles/voronota.dir/src/modes/mode_calculate_vertices.cpp.o.d -o CMakeFiles/voronota.dir/src/modes/mode_calculate_vertices.cpp.o -c /build/reproducible-path/voronota-1.29.4307+ds/src/modes/mode_calculate_vertices.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/voronota-1.29.4307+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/voronota.dir/src/modes/mode_compare_files_as_sets.cpp.o -MF CMakeFiles/voronota.dir/src/modes/mode_compare_files_as_sets.cpp.o.d -o CMakeFiles/voronota.dir/src/modes/mode_compare_files_as_sets.cpp.o -c /build/reproducible-path/voronota-1.29.4307+ds/src/modes/mode_compare_files_as_sets.cpp +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/voronota-1.29.4307+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 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-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/voronota.dir/src/modes/mode_demo_polygon_triangulation.cpp.o -MF CMakeFiles/voronota.dir/src/modes/mode_demo_polygon_triangulation.cpp.o.d -o CMakeFiles/voronota.dir/src/modes/mode_demo_polygon_triangulation.cpp.o -c /build/reproducible-path/voronota-1.29.4307+ds/src/modes/mode_demo_polygon_triangulation.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/voronota-1.29.4307+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -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-1.29.4307+ds/src/modes/mode_demo_ses.cpp -[ 26%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_draw_balls.cpp.o +[ 23%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_draw_balls.cpp.o +[ 26%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_draw_contacts.cpp.o +[ 28%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_draw_values_bitmap.cpp.o /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/voronota-1.29.4307+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/voronota.dir/src/modes/mode_draw_balls.cpp.o -MF CMakeFiles/voronota.dir/src/modes/mode_draw_balls.cpp.o.d -o CMakeFiles/voronota.dir/src/modes/mode_draw_balls.cpp.o -c /build/reproducible-path/voronota-1.29.4307+ds/src/modes/mode_draw_balls.cpp -[ 28%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_draw_contacts.cpp.o +[ 30%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_expand_descriptors.cpp.o +[ 32%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_get_balls_from_atoms_file.cpp.o /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/voronota-1.29.4307+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/voronota.dir/src/modes/mode_draw_contacts.cpp.o -MF CMakeFiles/voronota.dir/src/modes/mode_draw_contacts.cpp.o.d -o CMakeFiles/voronota.dir/src/modes/mode_draw_contacts.cpp.o -c /build/reproducible-path/voronota-1.29.4307+ds/src/modes/mode_draw_contacts.cpp -[ 30%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_draw_values_bitmap.cpp.o +[ 34%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_plot_contacts.cpp.o +[ 36%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_query_balls.cpp.o +[ 39%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_place_membrane.cpp.o +[ 41%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_query_balls_distances.cpp.o +[ 43%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_query_balls_clashes.cpp.o /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/voronota-1.29.4307+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/voronota.dir/src/modes/mode_draw_values_bitmap.cpp.o -MF CMakeFiles/voronota.dir/src/modes/mode_draw_values_bitmap.cpp.o.d -o CMakeFiles/voronota.dir/src/modes/mode_draw_values_bitmap.cpp.o -c /build/reproducible-path/voronota-1.29.4307+ds/src/modes/mode_draw_values_bitmap.cpp -[ 32%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_expand_descriptors.cpp.o /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/voronota-1.29.4307+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time 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/build/reproducible-path/voronota-1.29.4307+ds/src/modes/mode_get_balls_from_atoms_file.cpp -[ 36%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_place_membrane.cpp.o /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/voronota-1.29.4307+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/voronota.dir/src/modes/mode_place_membrane.cpp.o -MF CMakeFiles/voronota.dir/src/modes/mode_place_membrane.cpp.o.d -o CMakeFiles/voronota.dir/src/modes/mode_place_membrane.cpp.o -c /build/reproducible-path/voronota-1.29.4307+ds/src/modes/mode_place_membrane.cpp -[ 39%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_plot_contacts.cpp.o /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/voronota-1.29.4307+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time 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-ffile-prefix-map=/build/reproducible-path/voronota-1.29.4307+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/voronota.dir/src/modes/mode_query_balls_clashes.cpp.o -MF CMakeFiles/voronota.dir/src/modes/mode_query_balls_clashes.cpp.o.d -o CMakeFiles/voronota.dir/src/modes/mode_query_balls_clashes.cpp.o -c /build/reproducible-path/voronota-1.29.4307+ds/src/modes/mode_query_balls_clashes.cpp +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/voronota-1.29.4307+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/voronota.dir/src/modes/mode_query_balls_distances.cpp.o -MF CMakeFiles/voronota.dir/src/modes/mode_query_balls_distances.cpp.o.d -o CMakeFiles/voronota.dir/src/modes/mode_query_balls_distances.cpp.o -c /build/reproducible-path/voronota-1.29.4307+ds/src/modes/mode_query_balls_distances.cpp +[ 45%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_compare_contacts.cpp.o +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/voronota-1.29.4307+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -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-1.29.4307+ds/src/modes/mode_compare_contacts.cpp +[ 47%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_query_balls_sequences_pairings_stats.cpp.o +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/voronota-1.29.4307+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/voronota.dir/src/modes/mode_query_balls_sequences_pairings_stats.cpp.o -MF CMakeFiles/voronota.dir/src/modes/mode_query_balls_sequences_pairings_stats.cpp.o.d -o CMakeFiles/voronota.dir/src/modes/mode_query_balls_sequences_pairings_stats.cpp.o -c /build/reproducible-path/voronota-1.29.4307+ds/src/modes/mode_query_balls_sequences_pairings_stats.cpp +[ 50%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_query_contacts.cpp.o +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/voronota-1.29.4307+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/voronota.dir/src/modes/mode_query_contacts.cpp.o -MF CMakeFiles/voronota.dir/src/modes/mode_query_contacts.cpp.o.d -o CMakeFiles/voronota.dir/src/modes/mode_query_contacts.cpp.o -c /build/reproducible-path/voronota-1.29.4307+ds/src/modes/mode_query_contacts.cpp +[ 52%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_query_contacts_depth_values.cpp.o +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/voronota-1.29.4307+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/voronota.dir/src/modes/mode_query_contacts_depth_values.cpp.o -MF CMakeFiles/voronota.dir/src/modes/mode_query_contacts_depth_values.cpp.o.d -o CMakeFiles/voronota.dir/src/modes/mode_query_contacts_depth_values.cpp.o -c /build/reproducible-path/voronota-1.29.4307+ds/src/modes/mode_query_contacts_depth_values.cpp +[ 54%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_query_contacts_interface_exposure_values.cpp.o +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/voronota-1.29.4307+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/voronota.dir/src/modes/mode_query_contacts_interface_exposure_values.cpp.o -MF CMakeFiles/voronota.dir/src/modes/mode_query_contacts_interface_exposure_values.cpp.o.d -o CMakeFiles/voronota.dir/src/modes/mode_query_contacts_interface_exposure_values.cpp.o -c /build/reproducible-path/voronota-1.29.4307+ds/src/modes/mode_query_contacts_interface_exposure_values.cpp +In file included from /usr/include/c++/14/bits/stl_tree.h:63, + from /usr/include/c++/14/set:62, + from /build/reproducible-path/voronota-1.29.4307+ds/src/modes/../apollota/search_for_spherical_collisions.h:4, + from /build/reproducible-path/voronota-1.29.4307+ds/src/modes/mode_query_balls_clashes.cpp:1: +In static member function 'static _Up* std::__copy_move<_IsMove, true, std::random_access_iterator_tag>::__copy_m(_Tp*, _Tp*, _Up*) [with _Tp = const unsigned int; _Up = unsigned int; bool _IsMove = false]', + inlined from '_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = const unsigned int*; _OI = unsigned int*]' at /usr/include/c++/14/bits/stl_algobase.h:521:30, + inlined from '_OI std::__copy_move_a1(_II, _II, _OI) [with bool _IsMove = false; _II = const unsigned int*; _OI = unsigned int*]' at /usr/include/c++/14/bits/stl_algobase.h:548:42, + inlined from '_OI std::__copy_move_a(_II, _II, _OI) [with bool _IsMove = false; _II = __gnu_cxx::__normal_iterator >; _OI = unsigned int*]' at /usr/include/c++/14/bits/stl_algobase.h:555:31, + inlined from '_OI std::copy(_II, _II, _OI) [with _II = __gnu_cxx::__normal_iterator >; _OI = unsigned int*]' at /usr/include/c++/14/bits/stl_algobase.h:651:7, + inlined from 'static _ForwardIterator std::__uninitialized_copy::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = unsigned int*]' at /usr/include/c++/14/bits/stl_uninitialized.h:147:27, + inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = unsigned int*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, + inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = unsigned int*; _Tp = unsigned int]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, + inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = unsigned int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:606:31, + inlined from 'static std::vector voronota::apollota::SplittingOfSpheres::order_for_median(const std::vector&, const std::vector&, unsigned int) [with PointType = voronota::apollota::BoundingSpheresHierarchy::Cluster]' at /build/reproducible-path/voronota-1.29.4307+ds/src/modes/../apollota/splitting_of_spheres.h:69:11, + inlined from 'static std::vector > voronota::apollota::SplittingOfSpheres::split_by_median(const std::vector&, const std::vector&, unsigned int) [with PointType = voronota::apollota::BoundingSpheresHierarchy::Cluster]' at /build/reproducible-path/voronota-1.29.4307+ds/src/modes/../apollota/splitting_of_spheres.h:61:42, + inlined from 'static std::vector > voronota::apollota::SplittingOfSpheres::binary_split(const std::vector&, unsigned int) [with PointType = voronota::apollota::BoundingSpheresHierarchy::Cluster]' at /build/reproducible-path/voronota-1.29.4307+ds/src/modes/../apollota/splitting_of_spheres.h:43:51: +/usr/include/c++/14/bits/stl_algobase.h:452:30: warning: 'void* __builtin_memmove(void*, const void*, unsigned int)' writing between 5 and 2147483647 bytes into a region of size 4 overflows the destination [-Wstringop-overflow=] + 452 | __builtin_memmove(__result, __first, sizeof(_Tp) * _Num); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/i386-linux-gnu/c++/14/bits/c++allocator.h:33, + from /usr/include/c++/14/bits/allocator.h:46, + from /usr/include/c++/14/bits/stl_tree.h:64: +In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = unsigned int]', + inlined from 'static _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = unsigned int]' at /usr/include/c++/14/bits/alloc_traits.h:515:28, + inlined from 'std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = unsigned int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:380:33, + inlined from 'void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = unsigned int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:398:44, + inlined from 'std::_Vector_base<_Tp, _Alloc>::_Vector_base(std::size_t, const allocator_type&) [with _Tp = unsigned int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:334:26, + inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = unsigned int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:603:61, + inlined from 'static std::vector voronota::apollota::SplittingOfSpheres::order_for_median(const std::vector&, const std::vector&, unsigned int) [with PointType = voronota::apollota::BoundingSpheresHierarchy::Cluster]' at /build/reproducible-path/voronota-1.29.4307+ds/src/modes/../apollota/splitting_of_spheres.h:69:11, + inlined from 'static std::vector > voronota::apollota::SplittingOfSpheres::split_by_median(const std::vector&, const std::vector&, unsigned int) [with PointType = voronota::apollota::BoundingSpheresHierarchy::Cluster]' at /build/reproducible-path/voronota-1.29.4307+ds/src/modes/../apollota/splitting_of_spheres.h:61:42, + inlined from 'static std::vector > voronota::apollota::SplittingOfSpheres::binary_split(const std::vector&, unsigned int) [with PointType = voronota::apollota::BoundingSpheresHierarchy::Cluster]' at /build/reproducible-path/voronota-1.29.4307+ds/src/modes/../apollota/splitting_of_spheres.h:43:51: +/usr/include/c++/14/bits/new_allocator.h:151:55: note: destination object of size 4 allocated by 'operator new' + 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); + | ^ +[ 56%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_query_contacts_simulating_unfolding.cpp.o +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/voronota-1.29.4307+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/voronota.dir/src/modes/mode_query_contacts_simulating_unfolding.cpp.o -MF CMakeFiles/voronota.dir/src/modes/mode_query_contacts_simulating_unfolding.cpp.o.d -o CMakeFiles/voronota.dir/src/modes/mode_query_contacts_simulating_unfolding.cpp.o -c /build/reproducible-path/voronota-1.29.4307+ds/src/modes/mode_query_contacts_simulating_unfolding.cpp +In static member function 'static _Up* std::__copy_move<_IsMove, true, std::random_access_iterator_tag>::__copy_m(_Tp*, _Tp*, _Up*) [with _Tp = const unsigned int; _Up = unsigned int; bool _IsMove = false]', + inlined from '_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = const unsigned int*; _OI = unsigned int*]' at /usr/include/c++/14/bits/stl_algobase.h:521:30, + inlined from '_OI std::__copy_move_a1(_II, _II, _OI) [with bool _IsMove = false; _II = const unsigned int*; _OI = unsigned int*]' at /usr/include/c++/14/bits/stl_algobase.h:548:42, + inlined from '_OI std::__copy_move_a(_II, _II, _OI) [with bool _IsMove = false; _II = __gnu_cxx::__normal_iterator >; _OI = unsigned int*]' at /usr/include/c++/14/bits/stl_algobase.h:555:31, + inlined from '_OI std::copy(_II, _II, _OI) [with _II = __gnu_cxx::__normal_iterator >; _OI = unsigned int*]' at /usr/include/c++/14/bits/stl_algobase.h:651:7, + inlined from 'static _ForwardIterator std::__uninitialized_copy::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = unsigned int*]' at /usr/include/c++/14/bits/stl_uninitialized.h:147:27, + inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = unsigned int*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, + inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = unsigned int*; _Tp = unsigned int]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, + inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = unsigned int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:606:31, + inlined from 'static std::vector voronota::apollota::SplittingOfSpheres::order_for_median(const std::vector&, const std::vector&, unsigned int) [with PointType = voronota::apollota::SimpleSphere]' at /build/reproducible-path/voronota-1.29.4307+ds/src/modes/../apollota/splitting_of_spheres.h:69:11, + inlined from 'static std::vector > voronota::apollota::SplittingOfSpheres::split_by_median(const std::vector&, const std::vector&, unsigned int) [with PointType = voronota::apollota::SimpleSphere]' at /build/reproducible-path/voronota-1.29.4307+ds/src/modes/../apollota/splitting_of_spheres.h:61:42, + inlined from 'static std::vector > voronota::apollota::SplittingOfSpheres::binary_split(const std::vector&, unsigned int) [with PointType = voronota::apollota::SimpleSphere]' at /build/reproducible-path/voronota-1.29.4307+ds/src/modes/../apollota/splitting_of_spheres.h:43:51: +/usr/include/c++/14/bits/stl_algobase.h:452:30: warning: 'void* __builtin_memmove(void*, const void*, unsigned int)' writing between 5 and 2147483647 bytes into a region of size 4 overflows the destination [-Wstringop-overflow=] + 452 | __builtin_memmove(__result, __first, sizeof(_Tp) * _Num); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = unsigned int]', + inlined from 'static _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = unsigned int]' at /usr/include/c++/14/bits/alloc_traits.h:515:28, + inlined from 'std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = unsigned int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:380:33, + inlined from 'void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = unsigned int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:398:44, + inlined from 'std::_Vector_base<_Tp, _Alloc>::_Vector_base(std::size_t, const allocator_type&) [with _Tp = unsigned int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:334:26, + inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = unsigned int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:603:61, + inlined from 'static std::vector voronota::apollota::SplittingOfSpheres::order_for_median(const std::vector&, const std::vector&, unsigned int) [with PointType = voronota::apollota::SimpleSphere]' at /build/reproducible-path/voronota-1.29.4307+ds/src/modes/../apollota/splitting_of_spheres.h:69:11, + inlined from 'static std::vector > voronota::apollota::SplittingOfSpheres::split_by_median(const std::vector&, const std::vector&, unsigned int) [with PointType = voronota::apollota::SimpleSphere]' at /build/reproducible-path/voronota-1.29.4307+ds/src/modes/../apollota/splitting_of_spheres.h:61:42, + inlined from 'static std::vector > voronota::apollota::SplittingOfSpheres::binary_split(const std::vector&, unsigned int) [with PointType = voronota::apollota::SimpleSphere]' at /build/reproducible-path/voronota-1.29.4307+ds/src/modes/../apollota/splitting_of_spheres.h:43:51: +/usr/include/c++/14/bits/new_allocator.h:151:55: note: destination object of size 4 allocated by 'operator new' + 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); + | ^ +[ 58%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_query_contacts_solvation_values.cpp.o +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/voronota-1.29.4307+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/voronota.dir/src/modes/mode_query_contacts_solvation_values.cpp.o -MF CMakeFiles/voronota.dir/src/modes/mode_query_contacts_solvation_values.cpp.o.d -o CMakeFiles/voronota.dir/src/modes/mode_query_contacts_solvation_values.cpp.o -c /build/reproducible-path/voronota-1.29.4307+ds/src/modes/mode_query_contacts_solvation_values.cpp +[ 60%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_reprint_hbp.cpp.o +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/voronota-1.29.4307+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/voronota.dir/src/modes/mode_reprint_hbp.cpp.o -MF CMakeFiles/voronota.dir/src/modes/mode_reprint_hbp.cpp.o.d -o CMakeFiles/voronota.dir/src/modes/mode_reprint_hbp.cpp.o -c /build/reproducible-path/voronota-1.29.4307+ds/src/modes/mode_reprint_hbp.cpp +[ 63%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_rotational_optimization_demo.cpp.o +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/voronota-1.29.4307+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/voronota.dir/src/modes/mode_rotational_optimization_demo.cpp.o -MF CMakeFiles/voronota.dir/src/modes/mode_rotational_optimization_demo.cpp.o.d -o CMakeFiles/voronota.dir/src/modes/mode_rotational_optimization_demo.cpp.o -c /build/reproducible-path/voronota-1.29.4307+ds/src/modes/mode_rotational_optimization_demo.cpp +[ 65%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_run_script.cpp.o +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/voronota-1.29.4307+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/voronota.dir/src/modes/mode_run_script.cpp.o -MF CMakeFiles/voronota.dir/src/modes/mode_run_script.cpp.o.d -o CMakeFiles/voronota.dir/src/modes/mode_run_script.cpp.o -c /build/reproducible-path/voronota-1.29.4307+ds/src/modes/mode_run_script.cpp +[ 67%] 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-1.29.4307+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/voronota.dir/src/modes/mode_score_contacts_energy.cpp.o -MF CMakeFiles/voronota.dir/src/modes/mode_score_contacts_energy.cpp.o.d -o CMakeFiles/voronota.dir/src/modes/mode_score_contacts_energy.cpp.o -c /build/reproducible-path/voronota-1.29.4307+ds/src/modes/mode_score_contacts_energy.cpp +[ 69%] 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-1.29.4307+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/voronota.dir/src/modes/mode_score_contacts_energy_stats.cpp.o -MF CMakeFiles/voronota.dir/src/modes/mode_score_contacts_energy_stats.cpp.o.d -o CMakeFiles/voronota.dir/src/modes/mode_score_contacts_energy_stats.cpp.o -c /build/reproducible-path/voronota-1.29.4307+ds/src/modes/mode_score_contacts_energy_stats.cpp +[ 71%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_score_contacts_global_energy_by_cuts.cpp.o +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/voronota-1.29.4307+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/voronota.dir/src/modes/mode_score_contacts_global_energy_by_cuts.cpp.o -MF CMakeFiles/voronota.dir/src/modes/mode_score_contacts_global_energy_by_cuts.cpp.o.d -o CMakeFiles/voronota.dir/src/modes/mode_score_contacts_global_energy_by_cuts.cpp.o -c /build/reproducible-path/voronota-1.29.4307+ds/src/modes/mode_score_contacts_global_energy_by_cuts.cpp +[ 73%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_score_contacts_potential.cpp.o +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/voronota-1.29.4307+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/voronota.dir/src/modes/mode_score_contacts_potential.cpp.o -MF CMakeFiles/voronota.dir/src/modes/mode_score_contacts_potential.cpp.o.d -o CMakeFiles/voronota.dir/src/modes/mode_score_contacts_potential.cpp.o -c /build/reproducible-path/voronota-1.29.4307+ds/src/modes/mode_score_contacts_potential.cpp +[ 76%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_score_contacts_potentials_stats.cpp.o +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/voronota-1.29.4307+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/voronota.dir/src/modes/mode_score_contacts_potentials_stats.cpp.o -MF CMakeFiles/voronota.dir/src/modes/mode_score_contacts_potentials_stats.cpp.o.d -o CMakeFiles/voronota.dir/src/modes/mode_score_contacts_potentials_stats.cpp.o -c /build/reproducible-path/voronota-1.29.4307+ds/src/modes/mode_score_contacts_potentials_stats.cpp +[ 78%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_score_contacts_quality.cpp.o +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/voronota-1.29.4307+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/voronota.dir/src/modes/mode_score_contacts_quality.cpp.o -MF CMakeFiles/voronota.dir/src/modes/mode_score_contacts_quality.cpp.o.d -o CMakeFiles/voronota.dir/src/modes/mode_score_contacts_quality.cpp.o -c /build/reproducible-path/voronota-1.29.4307+ds/src/modes/mode_score_contacts_quality.cpp +[ 80%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_score_scores.cpp.o +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/voronota-1.29.4307+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/voronota.dir/src/modes/mode_score_scores.cpp.o -MF CMakeFiles/voronota.dir/src/modes/mode_score_scores.cpp.o.d -o CMakeFiles/voronota.dir/src/modes/mode_score_scores.cpp.o -c /build/reproducible-path/voronota-1.29.4307+ds/src/modes/mode_score_scores.cpp +[ 82%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_simulate_potential_for_membrane_proteins.cpp.o +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/voronota-1.29.4307+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/voronota.dir/src/modes/mode_simulate_potential_for_membrane_proteins.cpp.o -MF CMakeFiles/voronota.dir/src/modes/mode_simulate_potential_for_membrane_proteins.cpp.o.d -o CMakeFiles/voronota.dir/src/modes/mode_simulate_potential_for_membrane_proteins.cpp.o -c /build/reproducible-path/voronota-1.29.4307+ds/src/modes/mode_simulate_potential_for_membrane_proteins.cpp In file included from /usr/include/c++/14/string:51, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, @@ -669,8 +804,14 @@ /usr/include/c++/14/bits/new_allocator.h:151:55: note: destination object of size 4 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ -[ 43%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_query_balls_clashes.cpp.o -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/voronota-1.29.4307+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/voronota.dir/src/modes/mode_query_balls_clashes.cpp.o -MF CMakeFiles/voronota.dir/src/modes/mode_query_balls_clashes.cpp.o.d -o CMakeFiles/voronota.dir/src/modes/mode_query_balls_clashes.cpp.o -c /build/reproducible-path/voronota-1.29.4307+ds/src/modes/mode_query_balls_clashes.cpp +[ 84%] 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-1.29.4307+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -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-1.29.4307+ds/src/modes/mode_split_atoms_file.cpp +[ 86%] 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-1.29.4307+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -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-1.29.4307+ds/src/modes/mode_vectorize_contact_environments.cpp +[ 89%] 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-1.29.4307+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -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-1.29.4307+ds/src/modes/mode_vectorize_contacts.cpp +[ 91%] 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-1.29.4307+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -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-1.29.4307+ds/src/modes/mode_vectorize_points.cpp In file included from /usr/include/c++/14/bits/stl_tree.h:63, from /usr/include/c++/14/set:62, from /build/reproducible-path/voronota-1.29.4307+ds/src/modes/../apollota/search_for_spherical_collisions.h:4, @@ -705,6 +846,8 @@ /usr/include/c++/14/bits/new_allocator.h:151:55: note: destination object of size 4 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ +[ 93%] 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-1.29.4307+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -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-1.29.4307+ds/src/modes/mode_write_balls_to_atoms_file.cpp In static member function 'static _Up* std::__copy_move<_IsMove, true, std::random_access_iterator_tag>::__copy_m(_Tp*, _Tp*, _Up*) [with _Tp = const unsigned int; _Up = unsigned int; bool _IsMove = false]', inlined from '_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = const unsigned int*; _OI = unsigned int*]' at /usr/include/c++/14/bits/stl_algobase.h:521:30, inlined from '_OI std::__copy_move_a1(_II, _II, _OI) [with bool _IsMove = false; _II = const unsigned int*; _OI = unsigned int*]' at /usr/include/c++/14/bits/stl_algobase.h:548:42, @@ -732,10 +875,10 @@ /usr/include/c++/14/bits/new_allocator.h:151:55: note: destination object of size 4 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ -[ 45%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_query_balls_distances.cpp.o -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/voronota-1.29.4307+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/voronota.dir/src/modes/mode_query_balls_distances.cpp.o -MF CMakeFiles/voronota.dir/src/modes/mode_query_balls_distances.cpp.o.d -o CMakeFiles/voronota.dir/src/modes/mode_query_balls_distances.cpp.o -c /build/reproducible-path/voronota-1.29.4307+ds/src/modes/mode_query_balls_distances.cpp -[ 47%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_query_balls_sequences_pairings_stats.cpp.o -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/voronota-1.29.4307+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/voronota.dir/src/modes/mode_query_balls_sequences_pairings_stats.cpp.o -MF CMakeFiles/voronota.dir/src/modes/mode_query_balls_sequences_pairings_stats.cpp.o.d -o CMakeFiles/voronota.dir/src/modes/mode_query_balls_sequences_pairings_stats.cpp.o -c /build/reproducible-path/voronota-1.29.4307+ds/src/modes/mode_query_balls_sequences_pairings_stats.cpp +[ 95%] 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-1.29.4307+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -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-1.29.4307+ds/src/modes/mode_write_qa_scores_in_casp_format.cpp +[ 97%] Building CXX object CMakeFiles/voronota.dir/src/voronota.cpp.o +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/voronota-1.29.4307+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -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-1.29.4307+ds/src/voronota.cpp In file included from /usr/include/c++/14/string:51, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, @@ -773,6 +916,19 @@ /usr/include/c++/14/bits/new_allocator.h:151:55: note: destination object of size 4 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ +/build/reproducible-path/voronota-1.29.4307+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++/14/string:49, + from /usr/include/c++/14/bits/locale_classes.h:40, + from /usr/include/c++/14/bits/ios_base.h:41, + from /usr/include/c++/14/ios:44, + from /usr/include/c++/14/ostream:40, + from /usr/include/c++/14/iostream:41, + from /build/reproducible-path/voronota-1.29.4307+ds/src/voronota.cpp:1: +/usr/include/c++/14/bits/stl_function.h:1102:11: note: declared here + 1102 | class pointer_to_unary_function : public unary_function<_Arg, _Result> + | ^~~~~~~~~~~~~~~~~~~~~~~~~ In static member function 'static _Up* std::__copy_move<_IsMove, true, std::random_access_iterator_tag>::__copy_m(_Tp*, _Tp*, _Up*) [with _Tp = const unsigned int; _Up = unsigned int; bool _IsMove = false]', inlined from '_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = const unsigned int*; _OI = unsigned int*]' at /usr/include/c++/14/bits/stl_algobase.h:521:30, inlined from '_OI std::__copy_move_a1(_II, _II, _OI) [with bool _IsMove = false; _II = const unsigned int*; _OI = unsigned int*]' at /usr/include/c++/14/bits/stl_algobase.h:548:42, @@ -833,8 +989,6 @@ /usr/include/c++/14/bits/new_allocator.h:151:55: note: destination object of size 4 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ -[ 50%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_query_contacts.cpp.o -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/voronota-1.29.4307+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/voronota.dir/src/modes/mode_query_contacts.cpp.o -MF CMakeFiles/voronota.dir/src/modes/mode_query_contacts.cpp.o.d -o CMakeFiles/voronota.dir/src/modes/mode_query_contacts.cpp.o -c /build/reproducible-path/voronota-1.29.4307+ds/src/modes/mode_query_contacts.cpp In static member function 'static _Up* std::__copy_move<_IsMove, true, std::random_access_iterator_tag>::__copy_m(_Tp*, _Tp*, _Up*) [with _Tp = const unsigned int; _Up = unsigned int; bool _IsMove = false]', inlined from '_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = const unsigned int*; _OI = unsigned int*]' at /usr/include/c++/14/bits/stl_algobase.h:521:30, inlined from '_OI std::__copy_move_a1(_II, _II, _OI) [with bool _IsMove = false; _II = const unsigned int*; _OI = unsigned int*]' at /usr/include/c++/14/bits/stl_algobase.h:548:42, @@ -862,77 +1016,6 @@ /usr/include/c++/14/bits/new_allocator.h:151:55: note: destination object of size 4 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ -[ 52%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_query_contacts_depth_values.cpp.o -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/voronota-1.29.4307+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/voronota.dir/src/modes/mode_query_contacts_depth_values.cpp.o -MF CMakeFiles/voronota.dir/src/modes/mode_query_contacts_depth_values.cpp.o.d -o CMakeFiles/voronota.dir/src/modes/mode_query_contacts_depth_values.cpp.o -c /build/reproducible-path/voronota-1.29.4307+ds/src/modes/mode_query_contacts_depth_values.cpp -In file included from /usr/include/c++/14/bits/stl_tree.h:63, - from /usr/include/c++/14/set:62, - from /build/reproducible-path/voronota-1.29.4307+ds/src/modes/../apollota/search_for_spherical_collisions.h:4, - from /build/reproducible-path/voronota-1.29.4307+ds/src/modes/mode_query_balls_clashes.cpp:1: -In static member function 'static _Up* std::__copy_move<_IsMove, true, std::random_access_iterator_tag>::__copy_m(_Tp*, _Tp*, _Up*) [with _Tp = const unsigned int; _Up = unsigned int; bool _IsMove = false]', - inlined from '_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = const unsigned int*; _OI = unsigned int*]' at /usr/include/c++/14/bits/stl_algobase.h:521:30, - inlined from '_OI std::__copy_move_a1(_II, _II, _OI) [with bool _IsMove = false; _II = const unsigned int*; _OI = unsigned int*]' at /usr/include/c++/14/bits/stl_algobase.h:548:42, - inlined from '_OI std::__copy_move_a(_II, _II, _OI) [with bool _IsMove = false; _II = __gnu_cxx::__normal_iterator >; _OI = unsigned int*]' at /usr/include/c++/14/bits/stl_algobase.h:555:31, - inlined from '_OI std::copy(_II, _II, _OI) [with _II = __gnu_cxx::__normal_iterator >; _OI = unsigned int*]' at /usr/include/c++/14/bits/stl_algobase.h:651:7, - inlined from 'static _ForwardIterator std::__uninitialized_copy::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = unsigned int*]' at /usr/include/c++/14/bits/stl_uninitialized.h:147:27, - inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = unsigned int*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, - inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = unsigned int*; _Tp = unsigned int]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, - inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = unsigned int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:606:31, - inlined from 'static std::vector voronota::apollota::SplittingOfSpheres::order_for_median(const std::vector&, const std::vector&, unsigned int) [with PointType = voronota::apollota::BoundingSpheresHierarchy::Cluster]' at /build/reproducible-path/voronota-1.29.4307+ds/src/modes/../apollota/splitting_of_spheres.h:69:11, - inlined from 'static std::vector > voronota::apollota::SplittingOfSpheres::split_by_median(const std::vector&, const std::vector&, unsigned int) [with PointType = voronota::apollota::BoundingSpheresHierarchy::Cluster]' at /build/reproducible-path/voronota-1.29.4307+ds/src/modes/../apollota/splitting_of_spheres.h:61:42, - inlined from 'static std::vector > voronota::apollota::SplittingOfSpheres::binary_split(const std::vector&, unsigned int) [with PointType = voronota::apollota::BoundingSpheresHierarchy::Cluster]' at /build/reproducible-path/voronota-1.29.4307+ds/src/modes/../apollota/splitting_of_spheres.h:43:51: -/usr/include/c++/14/bits/stl_algobase.h:452:30: warning: 'void* __builtin_memmove(void*, const void*, unsigned int)' writing between 5 and 2147483647 bytes into a region of size 4 overflows the destination [-Wstringop-overflow=] - 452 | __builtin_memmove(__result, __first, sizeof(_Tp) * _Num); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/i386-linux-gnu/c++/14/bits/c++allocator.h:33, - from /usr/include/c++/14/bits/allocator.h:46, - from /usr/include/c++/14/bits/stl_tree.h:64: -In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = unsigned int]', - inlined from 'static _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = unsigned int]' at /usr/include/c++/14/bits/alloc_traits.h:515:28, - inlined from 'std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = unsigned int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:380:33, - inlined from 'void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = unsigned int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:398:44, - inlined from 'std::_Vector_base<_Tp, _Alloc>::_Vector_base(std::size_t, const allocator_type&) [with _Tp = unsigned int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:334:26, - inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = unsigned int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:603:61, - inlined from 'static std::vector voronota::apollota::SplittingOfSpheres::order_for_median(const std::vector&, const std::vector&, unsigned int) [with PointType = voronota::apollota::BoundingSpheresHierarchy::Cluster]' at /build/reproducible-path/voronota-1.29.4307+ds/src/modes/../apollota/splitting_of_spheres.h:69:11, - inlined from 'static std::vector > voronota::apollota::SplittingOfSpheres::split_by_median(const std::vector&, const std::vector&, unsigned int) [with PointType = voronota::apollota::BoundingSpheresHierarchy::Cluster]' at /build/reproducible-path/voronota-1.29.4307+ds/src/modes/../apollota/splitting_of_spheres.h:61:42, - inlined from 'static std::vector > voronota::apollota::SplittingOfSpheres::binary_split(const std::vector&, unsigned int) [with PointType = voronota::apollota::BoundingSpheresHierarchy::Cluster]' at /build/reproducible-path/voronota-1.29.4307+ds/src/modes/../apollota/splitting_of_spheres.h:43:51: -/usr/include/c++/14/bits/new_allocator.h:151:55: note: destination object of size 4 allocated by 'operator new' - 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); - | ^ -In static member function 'static _Up* std::__copy_move<_IsMove, true, std::random_access_iterator_tag>::__copy_m(_Tp*, _Tp*, _Up*) [with _Tp = const unsigned int; _Up = unsigned int; bool _IsMove = false]', - inlined from '_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = const unsigned int*; _OI = unsigned int*]' at /usr/include/c++/14/bits/stl_algobase.h:521:30, - inlined from '_OI std::__copy_move_a1(_II, _II, _OI) [with bool _IsMove = false; _II = const unsigned int*; _OI = unsigned int*]' at /usr/include/c++/14/bits/stl_algobase.h:548:42, - inlined from '_OI std::__copy_move_a(_II, _II, _OI) [with bool _IsMove = false; _II = __gnu_cxx::__normal_iterator >; _OI = unsigned int*]' at /usr/include/c++/14/bits/stl_algobase.h:555:31, - inlined from '_OI std::copy(_II, _II, _OI) [with _II = __gnu_cxx::__normal_iterator >; _OI = unsigned int*]' at /usr/include/c++/14/bits/stl_algobase.h:651:7, - inlined from 'static _ForwardIterator std::__uninitialized_copy::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = unsigned int*]' at /usr/include/c++/14/bits/stl_uninitialized.h:147:27, - inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = unsigned int*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, - inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = unsigned int*; _Tp = unsigned int]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, - inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = unsigned int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:606:31, - inlined from 'static std::vector voronota::apollota::SplittingOfSpheres::order_for_median(const std::vector&, const std::vector&, unsigned int) [with PointType = voronota::apollota::SimpleSphere]' at /build/reproducible-path/voronota-1.29.4307+ds/src/modes/../apollota/splitting_of_spheres.h:69:11, - inlined from 'static std::vector > voronota::apollota::SplittingOfSpheres::split_by_median(const std::vector&, const std::vector&, unsigned int) [with PointType = voronota::apollota::SimpleSphere]' at /build/reproducible-path/voronota-1.29.4307+ds/src/modes/../apollota/splitting_of_spheres.h:61:42, - inlined from 'static std::vector > voronota::apollota::SplittingOfSpheres::binary_split(const std::vector&, unsigned int) [with PointType = voronota::apollota::SimpleSphere]' at /build/reproducible-path/voronota-1.29.4307+ds/src/modes/../apollota/splitting_of_spheres.h:43:51: -/usr/include/c++/14/bits/stl_algobase.h:452:30: warning: 'void* __builtin_memmove(void*, const void*, unsigned int)' writing between 5 and 2147483647 bytes into a region of size 4 overflows the destination [-Wstringop-overflow=] - 452 | __builtin_memmove(__result, __first, sizeof(_Tp) * _Num); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = unsigned int]', - inlined from 'static _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = unsigned int]' at /usr/include/c++/14/bits/alloc_traits.h:515:28, - inlined from 'std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = unsigned int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:380:33, - inlined from 'void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = unsigned int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:398:44, - inlined from 'std::_Vector_base<_Tp, _Alloc>::_Vector_base(std::size_t, const allocator_type&) [with _Tp = unsigned int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:334:26, - inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = unsigned int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:603:61, - inlined from 'static std::vector voronota::apollota::SplittingOfSpheres::order_for_median(const std::vector&, const std::vector&, unsigned int) [with PointType = voronota::apollota::SimpleSphere]' at /build/reproducible-path/voronota-1.29.4307+ds/src/modes/../apollota/splitting_of_spheres.h:69:11, - inlined from 'static std::vector > voronota::apollota::SplittingOfSpheres::split_by_median(const std::vector&, const std::vector&, unsigned int) [with PointType = voronota::apollota::SimpleSphere]' at /build/reproducible-path/voronota-1.29.4307+ds/src/modes/../apollota/splitting_of_spheres.h:61:42, - inlined from 'static std::vector > voronota::apollota::SplittingOfSpheres::binary_split(const std::vector&, unsigned int) [with PointType = voronota::apollota::SimpleSphere]' at /build/reproducible-path/voronota-1.29.4307+ds/src/modes/../apollota/splitting_of_spheres.h:43:51: -/usr/include/c++/14/bits/new_allocator.h:151:55: note: destination object of size 4 allocated by 'operator new' - 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); - | ^ -[ 54%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_query_contacts_interface_exposure_values.cpp.o -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/voronota-1.29.4307+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/voronota.dir/src/modes/mode_query_contacts_interface_exposure_values.cpp.o -MF CMakeFiles/voronota.dir/src/modes/mode_query_contacts_interface_exposure_values.cpp.o.d -o CMakeFiles/voronota.dir/src/modes/mode_query_contacts_interface_exposure_values.cpp.o -c /build/reproducible-path/voronota-1.29.4307+ds/src/modes/mode_query_contacts_interface_exposure_values.cpp -[ 56%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_query_contacts_simulating_unfolding.cpp.o -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/voronota-1.29.4307+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/voronota.dir/src/modes/mode_query_contacts_simulating_unfolding.cpp.o -MF CMakeFiles/voronota.dir/src/modes/mode_query_contacts_simulating_unfolding.cpp.o.d -o CMakeFiles/voronota.dir/src/modes/mode_query_contacts_simulating_unfolding.cpp.o -c /build/reproducible-path/voronota-1.29.4307+ds/src/modes/mode_query_contacts_simulating_unfolding.cpp -[ 58%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_query_contacts_solvation_values.cpp.o -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/voronota-1.29.4307+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/voronota.dir/src/modes/mode_query_contacts_solvation_values.cpp.o -MF CMakeFiles/voronota.dir/src/modes/mode_query_contacts_solvation_values.cpp.o.d -o CMakeFiles/voronota.dir/src/modes/mode_query_contacts_solvation_values.cpp.o -c /build/reproducible-path/voronota-1.29.4307+ds/src/modes/mode_query_contacts_solvation_values.cpp -[ 60%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_reprint_hbp.cpp.o -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/voronota-1.29.4307+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/voronota.dir/src/modes/mode_reprint_hbp.cpp.o -MF CMakeFiles/voronota.dir/src/modes/mode_reprint_hbp.cpp.o.d -o CMakeFiles/voronota.dir/src/modes/mode_reprint_hbp.cpp.o -c /build/reproducible-path/voronota-1.29.4307+ds/src/modes/mode_reprint_hbp.cpp In file included from /usr/include/c++/14/string:51, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, @@ -970,8 +1053,6 @@ /usr/include/c++/14/bits/new_allocator.h:151:55: note: destination object of size 4 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ -[ 63%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_rotational_optimization_demo.cpp.o -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/voronota-1.29.4307+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/voronota.dir/src/modes/mode_rotational_optimization_demo.cpp.o -MF CMakeFiles/voronota.dir/src/modes/mode_rotational_optimization_demo.cpp.o.d -o CMakeFiles/voronota.dir/src/modes/mode_rotational_optimization_demo.cpp.o -c /build/reproducible-path/voronota-1.29.4307+ds/src/modes/mode_rotational_optimization_demo.cpp In static member function 'static _Up* std::__copy_move<_IsMove, true, std::random_access_iterator_tag>::__copy_m(_Tp*, _Tp*, _Up*) [with _Tp = const unsigned int; _Up = unsigned int; bool _IsMove = false]', inlined from '_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = const unsigned int*; _OI = unsigned int*]' at /usr/include/c++/14/bits/stl_algobase.h:521:30, inlined from '_OI std::__copy_move_a1(_II, _II, _OI) [with bool _IsMove = false; _II = const unsigned int*; _OI = unsigned int*]' at /usr/include/c++/14/bits/stl_algobase.h:548:42, @@ -999,51 +1080,6 @@ /usr/include/c++/14/bits/new_allocator.h:151:55: note: destination object of size 4 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ -[ 65%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_run_script.cpp.o -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/voronota-1.29.4307+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/voronota.dir/src/modes/mode_run_script.cpp.o -MF CMakeFiles/voronota.dir/src/modes/mode_run_script.cpp.o.d -o CMakeFiles/voronota.dir/src/modes/mode_run_script.cpp.o -c /build/reproducible-path/voronota-1.29.4307+ds/src/modes/mode_run_script.cpp -[ 67%] 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-1.29.4307+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/voronota.dir/src/modes/mode_score_contacts_energy.cpp.o -MF CMakeFiles/voronota.dir/src/modes/mode_score_contacts_energy.cpp.o.d -o CMakeFiles/voronota.dir/src/modes/mode_score_contacts_energy.cpp.o -c /build/reproducible-path/voronota-1.29.4307+ds/src/modes/mode_score_contacts_energy.cpp -[ 69%] 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-1.29.4307+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/voronota.dir/src/modes/mode_score_contacts_energy_stats.cpp.o -MF CMakeFiles/voronota.dir/src/modes/mode_score_contacts_energy_stats.cpp.o.d -o CMakeFiles/voronota.dir/src/modes/mode_score_contacts_energy_stats.cpp.o -c /build/reproducible-path/voronota-1.29.4307+ds/src/modes/mode_score_contacts_energy_stats.cpp -[ 71%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_score_contacts_global_energy_by_cuts.cpp.o -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/voronota-1.29.4307+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/voronota.dir/src/modes/mode_score_contacts_global_energy_by_cuts.cpp.o -MF CMakeFiles/voronota.dir/src/modes/mode_score_contacts_global_energy_by_cuts.cpp.o.d -o CMakeFiles/voronota.dir/src/modes/mode_score_contacts_global_energy_by_cuts.cpp.o -c /build/reproducible-path/voronota-1.29.4307+ds/src/modes/mode_score_contacts_global_energy_by_cuts.cpp -[ 73%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_score_contacts_potential.cpp.o -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/voronota-1.29.4307+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/voronota.dir/src/modes/mode_score_contacts_potential.cpp.o -MF CMakeFiles/voronota.dir/src/modes/mode_score_contacts_potential.cpp.o.d -o CMakeFiles/voronota.dir/src/modes/mode_score_contacts_potential.cpp.o -c /build/reproducible-path/voronota-1.29.4307+ds/src/modes/mode_score_contacts_potential.cpp -[ 76%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_score_contacts_potentials_stats.cpp.o -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/voronota-1.29.4307+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/voronota.dir/src/modes/mode_score_contacts_potentials_stats.cpp.o -MF CMakeFiles/voronota.dir/src/modes/mode_score_contacts_potentials_stats.cpp.o.d -o CMakeFiles/voronota.dir/src/modes/mode_score_contacts_potentials_stats.cpp.o -c /build/reproducible-path/voronota-1.29.4307+ds/src/modes/mode_score_contacts_potentials_stats.cpp -[ 78%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_score_contacts_quality.cpp.o -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/voronota-1.29.4307+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/voronota.dir/src/modes/mode_score_contacts_quality.cpp.o -MF CMakeFiles/voronota.dir/src/modes/mode_score_contacts_quality.cpp.o.d -o CMakeFiles/voronota.dir/src/modes/mode_score_contacts_quality.cpp.o -c /build/reproducible-path/voronota-1.29.4307+ds/src/modes/mode_score_contacts_quality.cpp -[ 80%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_score_scores.cpp.o -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/voronota-1.29.4307+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/voronota.dir/src/modes/mode_score_scores.cpp.o -MF CMakeFiles/voronota.dir/src/modes/mode_score_scores.cpp.o.d -o CMakeFiles/voronota.dir/src/modes/mode_score_scores.cpp.o -c /build/reproducible-path/voronota-1.29.4307+ds/src/modes/mode_score_scores.cpp -[ 82%] Building CXX object CMakeFiles/voronota.dir/src/modes/mode_simulate_potential_for_membrane_proteins.cpp.o -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/voronota-1.29.4307+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/voronota.dir/src/modes/mode_simulate_potential_for_membrane_proteins.cpp.o -MF CMakeFiles/voronota.dir/src/modes/mode_simulate_potential_for_membrane_proteins.cpp.o.d -o CMakeFiles/voronota.dir/src/modes/mode_simulate_potential_for_membrane_proteins.cpp.o -c /build/reproducible-path/voronota-1.29.4307+ds/src/modes/mode_simulate_potential_for_membrane_proteins.cpp -[ 84%] 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-1.29.4307+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -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-1.29.4307+ds/src/modes/mode_split_atoms_file.cpp -[ 86%] 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-1.29.4307+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -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-1.29.4307+ds/src/modes/mode_vectorize_contact_environments.cpp -[ 89%] 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-1.29.4307+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -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-1.29.4307+ds/src/modes/mode_vectorize_contacts.cpp -[ 91%] 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-1.29.4307+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -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-1.29.4307+ds/src/modes/mode_vectorize_points.cpp -[ 93%] 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-1.29.4307+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -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-1.29.4307+ds/src/modes/mode_write_balls_to_atoms_file.cpp -[ 95%] 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-1.29.4307+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -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-1.29.4307+ds/src/modes/mode_write_qa_scores_in_casp_format.cpp -[ 97%] Building CXX object CMakeFiles/voronota.dir/src/voronota.cpp.o -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/voronota-1.29.4307+ds=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -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-1.29.4307+ds/src/voronota.cpp -/build/reproducible-path/voronota-1.29.4307+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++/14/string:49, - from /usr/include/c++/14/bits/locale_classes.h:40, - from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/ios:44, - from /usr/include/c++/14/ostream:40, - from /usr/include/c++/14/iostream:41, - from /build/reproducible-path/voronota-1.29.4307+ds/src/voronota.cpp:1: -/usr/include/c++/14/bits/stl_function.h:1102:11: note: declared here - 1102 | class pointer_to_unary_function : public unary_function<_Arg, _Result> - | ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:51, from /build/reproducible-path/voronota-1.29.4307+ds/src/modes/../auxiliaries/program_options_handler.h:4, from /build/reproducible-path/voronota-1.29.4307+ds/src/modes/mode_run_script.cpp:1: @@ -1116,7 +1152,7 @@ create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/voronota/ - cd obj-i686-linux-gnu && make -j11 install DESTDIR=/build/reproducible-path/voronota-1.29.4307\+ds/debian/voronota AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd obj-i686-linux-gnu && make -j21 install DESTDIR=/build/reproducible-path/voronota-1.29.4307\+ds/debian/voronota AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/voronota-1.29.4307+ds/obj-i686-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/voronota-1.29.4307+ds -B/build/reproducible-path/voronota-1.29.4307+ds/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -1159,8 +1195,8 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'voronota-dbgsym' in '../voronota-dbgsym_1.29.4307+ds-1_i386.deb'. dpkg-deb: building package 'voronota' in '../voronota_1.29.4307+ds-1_i386.deb'. +dpkg-deb: building package 'voronota-dbgsym' in '../voronota-dbgsym_1.29.4307+ds-1_i386.deb'. dpkg-genbuildinfo --build=binary -O../voronota_1.29.4307+ds-1_i386.buildinfo dpkg-genchanges --build=binary -O../voronota_1.29.4307+ds-1_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1168,12 +1204,14 @@ 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/109783/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/109783/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/28699 and its subdirectories -I: Current time: Tue Feb 18 08:20:13 -12 2025 -I: pbuilder-time-stamp: 1739910013 +I: removing directory /srv/workspace/pbuilder/109783 and its subdirectories +I: Current time: Tue Mar 24 16:48:43 +14 2026 +I: pbuilder-time-stamp: 1774320523