Diff of the two buildlogs: -- --- b1/build.log 2025-11-14 12:52:43.045470685 +0000 +++ b2/build.log 2025-11-14 12:58:04.589852087 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Dec 17 07:11:22 -12 2026 -I: pbuilder-time-stamp: 1797534682 +I: Current time: Sat Nov 15 02:52:44 +14 2025 +I: pbuilder-time-stamp: 1763124764 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -27,53 +27,85 @@ dpkg-source: info: applying c23.patch I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1172927/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/49568/tmp/hooks/D01_modify_environment starting +debug: Running on ionos1-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Nov 14 12:53 /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/49568/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/49568/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' - DISTRIBUTION='unstable' - 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=40 nocheck' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='65ee629df2224c92bddca969c8cdec52' - 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='1172927' - PS1='# ' - PS2='> ' + INVOCATION_ID=4f277f75ab4e4c42a9282ea611152f2b + 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=49568 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.OGDs476j/pbuilderrc_Naxe --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.OGDs476j/b1 --logfile b1/build.log sortmerna_4.3.7-3.dsc' - SUDO_GID='110' - SUDO_HOME='/var/lib/jenkins' - SUDO_UID='105' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://213.165.73.152:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.OGDs476j/pbuilderrc_2RZp --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.OGDs476j/b2 --logfile b2/build.log sortmerna_4.3.7-3.dsc' + SUDO_GID=110 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://46.16.76.132:3128 I: uname -a - Linux ionos5-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 2025 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1172927/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/49568/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -215,7 +247,7 @@ Get: 86 http://deb.debian.org/debian unstable/main amd64 librocksdb-dev amd64 9.10.0-1+b1 [5555 kB] Get: 87 http://deb.debian.org/debian unstable/main amd64 python3-all amd64 3.13.7-1 [1048 B] Get: 88 http://deb.debian.org/debian unstable/main amd64 rapidjson-dev all 1.1.0+dfsg2-7.6 [98.2 kB] -Fetched 49.9 MB in 10s (5148 kB/s) +Fetched 49.9 MB in 18s (2724 kB/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 ... 19866 files and directories currently installed.) @@ -518,8 +550,8 @@ Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' -Local time is now: Thu Dec 17 19:14:19 UTC 2026. -Universal Time is now: Thu Dec 17 19:14:19 UTC 2026. +Local time is now: Fri Nov 14 12:56:57 UTC 2025. +Universal Time is now: Fri Nov 14 12:56:57 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20240727.1) ... @@ -600,7 +632,11 @@ Solving dependencies... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/reproducible-path/sortmerna-4.3.7/ && 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 > ../sortmerna_4.3.7-3_source.changes +I: user script /srv/workspace/pbuilder/49568/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/49568/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/sortmerna-4.3.7/ && 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 > ../sortmerna_4.3.7-3_source.changes dpkg-buildpackage: info: source package sortmerna dpkg-buildpackage: info: source version 4.3.7-3 dpkg-buildpackage: info: source distribution unstable @@ -619,7 +655,7 @@ dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:311: dh_auto_configure --buildsystem=cmake --builddirectory=/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build -- -DPYTHON_EXECUTABLE:FILEPATH=/usr/bin/python3.13 -DPYTHON_LIBRARY:FILEPATH=/usr/lib/python3.13/config-3.13-x86_64-linux-gnu/libpython3.13.so -DPYTHON_INCLUDE_DIR:PATH=/usr/include/python3.13 -DPython_EXECUTABLE=/usr/bin/python3.13 -DPython_LIBRARY=/usr/lib/python3.13/config-3.13-x86_64-linux-gnu/libpython3.13.so -DPython_INCLUDE_DIR=/usr/include/python3.13 -DPython3_EXECUTABLE=/usr/bin/python3.13 -DPython3_LIBRARY=/usr/lib/python3.13/config-3.13-x86_64-linux-gnu/libpython3.13.so -DPython3_INCLUDE_DIR=/usr/include/python3.13 - cd .pybuild/cpython3_3.13/build && PKG_CONFIG=/usr/bin/pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DPYTHON_EXECUTABLE:FILEPATH=/usr/bin/python3.13 -DPYTHON_LIBRARY:FILEPATH=/usr/lib/python3.13/config-3.13-x86_64-linux-gnu/libpython3.13.so -DPYTHON_INCLUDE_DIR:PATH=/usr/include/python3.13 -DPython_EXECUTABLE=/usr/bin/python3.13 -DPython_LIBRARY=/usr/lib/python3.13/config-3.13-x86_64-linux-gnu/libpython3.13.so -DPython_INCLUDE_DIR=/usr/include/python3.13 -DPython3_EXECUTABLE=/usr/bin/python3.13 -DPython3_LIBRARY=/usr/lib/python3.13/config-3.13-x86_64-linux-gnu/libpython3.13.so -DPython3_INCLUDE_DIR=/usr/include/python3.13 ../../.. + cd .pybuild/cpython3_3.13/build && PKG_CONFIG=/usr/bin/pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DBUILD_TESTING:BOOL=OFF -DPYTHON_EXECUTABLE:FILEPATH=/usr/bin/python3.13 -DPYTHON_LIBRARY:FILEPATH=/usr/lib/python3.13/config-3.13-x86_64-linux-gnu/libpython3.13.so -DPYTHON_INCLUDE_DIR:PATH=/usr/include/python3.13 -DPython_EXECUTABLE=/usr/bin/python3.13 -DPython_LIBRARY=/usr/lib/python3.13/config-3.13-x86_64-linux-gnu/libpython3.13.so -DPython_INCLUDE_DIR=/usr/include/python3.13 -DPython3_EXECUTABLE=/usr/bin/python3.13 -DPython3_LIBRARY=/usr/lib/python3.13/config-3.13-x86_64-linux-gnu/libpython3.13.so -DPython3_INCLUDE_DIR=/usr/include/python3.13 ../../.. -- The CXX compiler identification is GNU 15.2.0 -- The C compiler identification is GNU 15.2.0 -- Detecting CXX compiler ABI info @@ -670,11 +706,12 @@ SMR Objects transitive link dependencies: alp;RocksDB::rocksdb-shared;ZLIB::ZLIB SMR Objects COMPILE_OPT: COMPILE_OPT-NOTFOUND COMPILE_FLG: COMPILE_FLG-NOTFOUND package_config_destination: /usr/cmake/sortmerna --- Configuring done (3.1s) +-- Configuring done (2.2s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: + BUILD_TESTING CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR @@ -696,112 +733,112 @@ -- Build files have been written to: /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build dh_auto_build -O--buildsystem=pybuild I: pybuild base:311: dh_auto_build --buildsystem=cmake --builddirectory=/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build -- - cd .pybuild/cpython3_3.13/build && make -j42 INSTALL="install --strip-program=true" VERBOSE=1 + cd .pybuild/cpython3_3.13/build && make -j40 INSTALL="install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build' /usr/bin/cmake -S/build/reproducible-path/sortmerna-4.3.7 -B/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/CMakeFiles /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build' make -f CMakeFiles/build_version.dir/build.make CMakeFiles/build_version.dir/depend -make -f 3rdparty/cmph/CMakeFiles/cmph.dir/build.make 3rdparty/cmph/CMakeFiles/cmph.dir/depend -make -f 3rdparty/alp/CMakeFiles/alp.dir/build.make 3rdparty/alp/CMakeFiles/alp.dir/depend make[3]: Entering directory '/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build' cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sortmerna-4.3.7 /build/reproducible-path/sortmerna-4.3.7 /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/CMakeFiles/build_version.dir/DependInfo.cmake "--color=" -make[3]: Entering directory '/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build' -cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sortmerna-4.3.7 /build/reproducible-path/sortmerna-4.3.7/3rdparty/alp /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/3rdparty/alp /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/3rdparty/alp/CMakeFiles/alp.dir/DependInfo.cmake "--color=" -make[3]: Entering directory '/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build' -cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sortmerna-4.3.7 /build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/3rdparty/cmph /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/3rdparty/cmph/CMakeFiles/cmph.dir/DependInfo.cmake "--color=" -make[3]: Leaving directory '/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build' make[3]: Leaving directory '/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build' +make -f 3rdparty/cmph/CMakeFiles/cmph.dir/build.make 3rdparty/cmph/CMakeFiles/cmph.dir/depend +make[3]: Entering directory '/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build' make -f CMakeFiles/build_version.dir/build.make CMakeFiles/build_version.dir/build -make -f 3rdparty/alp/CMakeFiles/alp.dir/build.make 3rdparty/alp/CMakeFiles/alp.dir/build +cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sortmerna-4.3.7 /build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/3rdparty/cmph /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/3rdparty/cmph/CMakeFiles/cmph.dir/DependInfo.cmake "--color=" +make -f 3rdparty/alp/CMakeFiles/alp.dir/build.make 3rdparty/alp/CMakeFiles/alp.dir/depend make[3]: Entering directory '/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build' make[3]: Entering directory '/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build' +cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sortmerna-4.3.7 /build/reproducible-path/sortmerna-4.3.7/3rdparty/alp /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/3rdparty/alp /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/3rdparty/alp/CMakeFiles/alp.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build' make -f 3rdparty/cmph/CMakeFiles/cmph.dir/build.make 3rdparty/cmph/CMakeFiles/cmph.dir/build make[3]: Entering directory '/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build' -[ 1%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/njn_ioutil.cpp.o -[ 2%] Building CXX object CMakeFiles/build_version.dir/build_version.cpp.o -[ 4%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/njn_localmaxstat.cpp.o -[ 5%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/njn_dynprogproblim.cpp.o -[ 8%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/njn_localmaxstatutil.cpp.o -[ 8%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/njn_localmaxstatmatrix.cpp.o -/usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.7/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++17 -MD -MT CMakeFiles/build_version.dir/build_version.cpp.o -MF CMakeFiles/build_version.dir/build_version.cpp.o.d -o 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-c /build/reproducible-path/sortmerna-4.3.7/3rdparty/alp/sls_pvalues.cpp +cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/3rdparty/cmph && /usr/bin/cc -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT 3rdparty/cmph/CMakeFiles/cmph.dir/vqueue.c.o -MF CMakeFiles/cmph.dir/vqueue.c.o.d -o CMakeFiles/cmph.dir/vqueue.c.o -c /build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph/vqueue.c [ 54%] Built target build_version make[3]: Leaving directory '/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build' [ 54%] Built target cmph @@ -813,61 +850,61 @@ make[3]: Leaving directory '/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build' make -f src/sortmerna/CMakeFiles/smr_objs.dir/build.make 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src/sortmerna/CMakeFiles/smr_objs.dir/alignment.cpp.o -MF CMakeFiles/smr_objs.dir/alignment.cpp.o.d -o CMakeFiles/smr_objs.dir/alignment.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/alignment.cpp -[ 59%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/cmd.cpp.o -[ 60%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/output.cpp.o -[ 63%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/readfeed.cpp.o -[ 64%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/read.cpp.o -cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.7/include -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -W 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src/sortmerna/CMakeFiles/smr_objs.dir/bitvector.cpp.o -cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.7/include -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/readfeed.cpp.o -MF CMakeFiles/smr_objs.dir/readfeed.cpp.o.d -o CMakeFiles/smr_objs.dir/readfeed.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/readfeed.cpp -[ 67%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/kseq_load.cpp.o -[ 69%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/izlib.cpp.o -[ 70%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/summary.cpp.o cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.7/include -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/bitvector.cpp.o -MF CMakeFiles/smr_objs.dir/bitvector.cpp.o.d -o CMakeFiles/smr_objs.dir/bitvector.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/bitvector.cpp -[ 74%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/options.cpp.o -cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/src/sortmerna && /usr/bin/c++ 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src/sortmerna/CMakeFiles/smr_objs.dir/kvdb.cpp.o -MF CMakeFiles/smr_objs.dir/kvdb.cpp.o.d -o CMakeFiles/smr_objs.dir/kvdb.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/kvdb.cpp -[ 85%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/report_fastx.cpp.o cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.7/include -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/options.cpp.o -MF CMakeFiles/smr_objs.dir/options.cpp.o.d -o CMakeFiles/smr_objs.dir/options.cpp.o -c 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src/sortmerna/CMakeFiles/smr_objs.dir/processor.cpp.o -MF CMakeFiles/smr_objs.dir/processor.cpp.o.d -o CMakeFiles/smr_objs.dir/processor.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/processor.cpp -cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.7/include -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/readstats.cpp.o -MF CMakeFiles/smr_objs.dir/readstats.cpp.o.d -o CMakeFiles/smr_objs.dir/readstats.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/readstats.cpp -cd 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-I/build/reproducible-path/sortmerna-4.3.7/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/report_blast.cpp.o -MF CMakeFiles/smr_objs.dir/report_blast.cpp.o.d -o CMakeFiles/smr_objs.dir/report_blast.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/report_blast.cpp cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.7/include -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/report_denovo.cpp.o -MF CMakeFiles/smr_objs.dir/report_denovo.cpp.o.d -o CMakeFiles/smr_objs.dir/report_denovo.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/report_denovo.cpp @@ -880,6 +917,13 @@ /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/izlib.cpp:244:17: note: here 244 | case Z_DATA_ERROR: | ^~~~ +/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/report_biom.cpp: In member function 'virtual void ReportBiom::init(Readfeed&, Runopts&)': +/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/report_biom.cpp:41:33: warning: unused parameter 'readfeed' [-Wunused-parameter] + 41 | void ReportBiom::init(Readfeed& readfeed, Runopts& opts) + | ~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/report_biom.cpp:41:52: warning: unused parameter 'opts' [-Wunused-parameter] + 41 | void ReportBiom::init(Readfeed& readfeed, Runopts& opts) + | ~~~~~~~~~^~~~ /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/report.cpp: In constructor 'Report::Report(Runopts&)': /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/report.cpp:39:25: warning: unused parameter 'opts' [-Wunused-parameter] 39 | Report::Report(Runopts& opts) : pid_str(std::to_string(getpid())), is_zip(false) {} @@ -903,28 +947,13 @@ /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/readfeed.cpp: In member function 'bool Readfeed::define_format(const int&)': /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/readfeed.cpp:857:36: warning: comparison is always false due to limited range of data type [-Wtype-limits] 857 | if (str[i] > 127 || str[i] < 0) { -/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/report_biom.cpp: In member function 'virtual void ReportBiom::init(Readfeed&, Runopts&)': -/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/report_biom.cpp:41:33: warning: unused parameter 'readfeed' [-Wunused-parameter] - 41 | void ReportBiom::init(Readfeed& readfeed, Runopts& opts) - | ~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/report_biom.cpp:41:52: warning: unused parameter 'opts' [-Wunused-parameter] - 41 | void ReportBiom::init(Readfeed& readfeed, Runopts& opts) - | ~~~~~~~~~^~~~ -/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/indexdb.cpp:915:14: warning: 'void {anonymous}::help()' defined but not used [-Wunused-function] - 915 | void help() - | ^~~~ /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/kvdb.cpp: In member function 'int KeyValueDatabase::clear(std::string)': /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/kvdb.cpp:58:41: warning: unused parameter 'dbpath' [-Wunused-parameter] 58 | int KeyValueDatabase::clear(std::string dbpath) | ~~~~~~~~~~~~^~~~~~ -/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/read.cpp: In member function 'void Read::unmarshallJson(KeyValueDatabase&)': -/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/read.cpp:540:46: warning: unused parameter 'kvdb' [-Wunused-parameter] - 540 | void Read::unmarshallJson(KeyValueDatabase & kvdb) - | ~~~~~~~~~~~~~~~~~~~^~~~ -/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/report_fx_base.cpp: In member function 'void ReportFxBase::write_a_read(std::ostream&, Read&, Readstate&, Izlib&, bool, const int&)': -/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/report_fx_base.cpp:201:123: warning: unused parameter 'dbg' [-Wunused-parameter] - 201 | void ReportFxBase::write_a_read(std::ostream& strm, Read& read, Readstate& rstate, Izlib& izlib, bool is_last, const int& dbg) - | ~~~~~~~~~~~^~~ +/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/indexdb.cpp:915:14: warning: 'void {anonymous}::help()' defined but not used [-Wunused-function] + 915 | void help() + | ^~~~ /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/index.cpp: In member function 'void Index::load(uint32_t, uint32_t, std::vector, std::__cxx11::basic_string > >&, Refstats&)': /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/index.cpp:211:58: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 211 | ((NodeElement *&)dst) += 4; @@ -932,6 +961,37 @@ /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/index.cpp:257:82: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 257 | ((NodeElement *&)dst) += 4; | ^~~ +/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/cmd.cpp: In member function 'void CmdSession::cmdIndex(Runopts&, std::string&)': +/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/cmd.cpp:250:68: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] + 250 | if (index.positions_tbl[it->id].arr[i].seq == std::stoi(refid)) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/cmd.cpp: In member function 'void CmdSession::cmdTest(Runopts&, std::string&)': +/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/cmd.cpp:317:36: warning: unused parameter 'opts' [-Wunused-parameter] + 317 | void CmdSession::cmdTest(Runopts & opts, std::string & cmd) + | ~~~~~~~~~~^~~~ +/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/cmd.cpp:317:56: warning: unused parameter 'cmd' [-Wunused-parameter] + 317 | void CmdSession::cmdTest(Runopts & opts, std::string & cmd) + | ~~~~~~~~~~~~~~^~~ +In file included from /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/paralleltraversal.cpp:47: +/build/reproducible-path/sortmerna-4.3.7/include/ThreadPool.hpp: In member function 'void ThreadPool::threadEntry(int)': +/build/reproducible-path/sortmerna-4.3.7/include/ThreadPool.hpp:92:38: warning: unused parameter 'i' [-Wunused-parameter] + 92 | void threadEntry(int i) + | ~~~~^ +/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/paralleltraversal.cpp: In function 'void traverse(Runopts&, Index&, References&, Readstats&, Refstats&, Read&, bool)': +/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/paralleltraversal.cpp:292:99: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] + 292 | bool is_last_idx = (index.index_num == opts.indexfiles.size() - 1) && (index.part == refstats.num_index_parts[index.index_num] - 1); + | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/sortmerna-4.3.7/include/kseq_load.hpp:40, + from /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/readstats.cpp:52: +/build/reproducible-path/sortmerna-4.3.7/include/kseq.h:171:20: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function] + 171 | static int kseq_read(kseq_t *seq) \ + | ^~~~~~~~~ +/build/reproducible-path/sortmerna-4.3.7/include/kseq.h:221:9: note: in expansion of macro '__KSEQ_READ' + 221 | __KSEQ_READ + | ^~~~~~~~~~~ +/build/reproducible-path/sortmerna-4.3.7/include/kseq_load.hpp:43:1: note: in expansion of macro 'KSEQ_INIT' + 43 | KSEQ_INIT(gzFile, gzread) + | ^~~~~~~~~ /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp: In member function 'void Runopts::opt_log(const std::string&)': /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp:284:42: warning: unused parameter 'val' [-Wunused-parameter] 284 | void Runopts::opt_log(const std::string& val) @@ -972,10 +1032,6 @@ /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp:343:43: warning: unused parameter 'val' [-Wunused-parameter] 343 | void Runopts::opt_sout(const std::string& val) | ~~~~~~~~~~~~~~~~~~~^~~ -/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/cmd.cpp: In member function 'void CmdSession::cmdIndex(Runopts&, std::string&)': -/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/cmd.cpp:250:68: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] - 250 | if (index.positions_tbl[it->id].arr[i].seq == std::stoi(refid)) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp: In member function 'void Runopts::opt_fastx(const std::string&)': /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp:471:44: warning: unused parameter 'val' [-Wunused-parameter] 471 | void Runopts::opt_fastx(const std::string &val) @@ -984,13 +1040,6 @@ /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp:484:42: warning: unused parameter 'val' [-Wunused-parameter] 484 | void Runopts::opt_sam(const std::string &val) | ~~~~~~~~~~~~~~~~~~~^~~ -/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/cmd.cpp: In member function 'void CmdSession::cmdTest(Runopts&, std::string&)': -/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/cmd.cpp:317:36: warning: unused parameter 'opts' [-Wunused-parameter] - 317 | void CmdSession::cmdTest(Runopts & opts, std::string & cmd) - | ~~~~~~~~~~^~~~ -/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/cmd.cpp:317:56: warning: unused parameter 'cmd' [-Wunused-parameter] - 317 | void CmdSession::cmdTest(Runopts & opts, std::string & cmd) - | ~~~~~~~~~~~~~~^~~ /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp: In member function 'void Runopts::opt_no_best(const std::string&)': /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp:593:46: warning: unused parameter 'val' [-Wunused-parameter] 593 | void Runopts::opt_no_best(const std::string &val) @@ -1054,30 +1103,18 @@ /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp:1198:45: warning: unused parameter 'val' [-Wunused-parameter] 1198 | void Runopts::opt_filter(const std::string& val) | ~~~~~~~~~~~~~~~~~~~^~~ +/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/read.cpp: In member function 'void Read::unmarshallJson(KeyValueDatabase&)': +/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/read.cpp:540:46: warning: unused parameter 'kvdb' [-Wunused-parameter] + 540 | void Read::unmarshallJson(KeyValueDatabase & kvdb) + | ~~~~~~~~~~~~~~~~~~~^~~~ +/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/report_fx_base.cpp: In member function 'void ReportFxBase::write_a_read(std::ostream&, Read&, Readstate&, Izlib&, bool, const int&)': +/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/report_fx_base.cpp:201:123: warning: unused parameter 'dbg' [-Wunused-parameter] + 201 | void ReportFxBase::write_a_read(std::ostream& strm, Read& read, Readstate& rstate, Izlib& izlib, bool is_last, const int& dbg) + | ~~~~~~~~~~~^~~ /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp: In member function 'void Runopts::process(int, char**, bool)': 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'/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build' @@ -1110,14 +1147,13 @@ make[2]: Leaving directory '/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/CMakeFiles 0 make[1]: Leaving directory '/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build' - dh_auto_test -O--buildsystem=pybuild -I: pybuild base:311: dh_auto_test --buildsystem=cmake --builddirectory=/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build -- +dh: command-omitted: The call to "dh_auto_test -O--buildsystem=pybuild" was omitted due to "DEB_BUILD_OPTIONS=nocheck" create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install --destdir=debian/sortmerna/ -O--buildsystem=pybuild I: pybuild base:311: dh_auto_install --buildsystem=cmake 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