Diff of the two buildlogs: -- --- b1/build.log 2025-08-28 23:38:25.966876268 +0000 +++ b2/build.log 2025-08-28 23:41:20.619098660 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Aug 28 11:36:20 -12 2025 -I: pbuilder-time-stamp: 1756424180 +I: Current time: Thu Oct 1 20:01:26 +14 2026 +I: pbuilder-time-stamp: 1790834486 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration @@ -26,53 +26,85 @@ dpkg-source: info: applying pyhon3.12-syntax.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1130807/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1064117/tmp/hooks/D01_modify_environment starting +debug: Running on ionos15-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Oct 1 06:01 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/1064117/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1064117/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=40 ' - DISTRIBUTION='forky' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' + DIRSTACK=() + DISTRIBUTION=forky + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='0c4e931f56444532bf885edb8a5db89c' - 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='1130807' - PS1='# ' - PS2='> ' + INVOCATION_ID=bfeab9ca48604d5184d023fab50f6861 + 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=1064117 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.NZQSgQFu/pbuilderrc_bDRl --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.NZQSgQFu/b1 --logfile b1/build.log sortmerna_4.3.7-2.dsc' - SUDO_GID='111' - SUDO_HOME='/var/lib/jenkins' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://46.16.76.132:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.NZQSgQFu/pbuilderrc_iPI9 --distribution forky --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.NZQSgQFu/b2 --logfile b2/build.log sortmerna_4.3.7-2.dsc' + SUDO_GID=111 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos11-amd64 6.12.41+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.41-1 (2025-08-12) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.41+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.41-1 (2025-08-12) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1130807/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1064117/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -212,7 +244,7 @@ Get: 84 http://deb.debian.org/debian forky/main amd64 librocksdb-dev amd64 9.10.0-1+b1 [5555 kB] Get: 85 http://deb.debian.org/debian forky/main amd64 python3-all amd64 3.13.5-1 [1048 B] Get: 86 http://deb.debian.org/debian forky/main amd64 rapidjson-dev all 1.1.0+dfsg2-7.4 [98.1 kB] -Fetched 49.3 MB in 1s (34.8 MB/s) +Fetched 49.3 MB in 16s (3133 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 ... 19855 files and directories currently installed.) @@ -509,8 +541,8 @@ Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' -Local time is now: Thu Aug 28 23:37:32 UTC 2025. -Universal Time is now: Thu Aug 28 23:37:32 UTC 2025. +Local time is now: Thu Oct 1 06:03:09 UTC 2026. +Universal Time is now: Thu Oct 1 06:03:09 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20240727.1) ... @@ -583,7 +615,11 @@ Building tag database... -> Finished parsing the build-deps 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_4.3.7-2_source.changes +I: user script /srv/workspace/pbuilder/1064117/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for forky +I: user script /srv/workspace/pbuilder/1064117/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_4.3.7-2_source.changes dpkg-buildpackage: info: source package sortmerna dpkg-buildpackage: info: source version 4.3.7-2 dpkg-buildpackage: info: source distribution unstable @@ -653,8 +689,8 @@ 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 (3.7s) --- Generating done (0.6s) +-- Configuring done (1.1s) +-- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: @@ -679,7 +715,7 @@ -- 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 -j40 "INSTALL=install --strip-program=true" VERBOSE=1 + cd .pybuild/cpython3_3.13/build && make -j42 "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 @@ -695,95 +731,95 @@ 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[3]: Leaving 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[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]: Leaving 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' make -f 3rdparty/alp/CMakeFiles/alp.dir/build.make 3rdparty/alp/CMakeFiles/alp.dir/build 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' -[ 5%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/bmz.c.o -[ 4%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/bdz.c.o -[ 5%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/njn_dynprogprob.cpp.o -[ 5%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/njn_dynprogproblim.cpp.o -[ 7%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/bdz_ph.c.o -[ 9%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/bmz8.c.o -[ 9%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/brz.c.o +make[3]: Entering directory '/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build' +[ 1%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/chd_ph.c.o +[ 7%] Building CXX object CMakeFiles/build_version.dir/build_version.cpp.o +[ 7%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/bmz.c.o +[ 8%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/njn_dynprogprobproto.cpp.o +[ 8%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/njn_dynprogproblim.cpp.o +[ 11%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/bdz_ph.c.o +[ 11%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/bdz.c.o +[ 8%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/njn_dynprogprob.cpp.o +[ 12%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/njn_ioutil.cpp.o +[ 14%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/brz.c.o +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 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-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/bdz.c.o -MF CMakeFiles/cmph.dir/bdz.c.o.d -o CMakeFiles/cmph.dir/bdz.c.o -c /build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph/bdz.c -cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/3rdparty/alp && /usr/bin/c++ -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 -std=gnu++11 -MD -MT 3rdparty/alp/CMakeFiles/alp.dir/njn_dynprogprob.cpp.o -MF CMakeFiles/alp.dir/njn_dynprogprob.cpp.o.d -o CMakeFiles/alp.dir/njn_dynprogprob.cpp.o -c 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3rdparty/alp/CMakeFiles/alp.dir/sls_alp.cpp.o +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 +[ 53%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/buffer_manager.c.o +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=. 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3rdparty/cmph/CMakeFiles/cmph.dir/buffer_manager.c.o -MF CMakeFiles/cmph.dir/buffer_manager.c.o.d -o CMakeFiles/cmph.dir/buffer_manager.c.o -c /build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph/buffer_manager.c +cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/3rdparty/alp && /usr/bin/c++ -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 -std=gnu++11 -MD -MT 3rdparty/alp/CMakeFiles/alp.dir/sls_pvalues.cpp.o -MF CMakeFiles/alp.dir/sls_pvalues.cpp.o.d -o CMakeFiles/alp.dir/sls_pvalues.cpp.o -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/vstack.c.o -MF CMakeFiles/cmph.dir/vstack.c.o.d -o CMakeFiles/cmph.dir/vstack.c.o -c /build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph/vstack.c make[3]: Leaving directory '/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build' [ 54%] Built target build_version make[3]: Leaving directory '/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build' @@ -796,59 +832,59 @@ 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 src/sortmerna/CMakeFiles/smr_objs.dir/build make[3]: Entering directory '/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build' -[ 57%] Building CXX 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src/sortmerna/CMakeFiles/smr_objs.dir/indexdb.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/cmd.cpp.o -MF CMakeFiles/smr_objs.dir/cmd.cpp.o.d -o CMakeFiles/smr_objs.dir/cmd.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/cmd.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 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/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/bitvector.cpp -[ 67%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/kvdb.cpp.o +[ 66%] 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/cmd.cpp.o -MF CMakeFiles/smr_objs.dir/cmd.cpp.o.d -o CMakeFiles/smr_objs.dir/cmd.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/cmd.cpp +[ 67%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/indexdb.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/izlib.cpp.o -MF CMakeFiles/smr_objs.dir/izlib.cpp.o.d -o CMakeFiles/smr_objs.dir/izlib.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/izlib.cpp -[ 69%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/summary.cpp.o +[ 70%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/processor.cpp.o +[ 70%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/output.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/index.cpp.o -MF CMakeFiles/smr_objs.dir/index.cpp.o.d -o CMakeFiles/smr_objs.dir/index.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/index.cpp -[ 70%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/paralleltraversal.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/indexdb.cpp.o -MF CMakeFiles/smr_objs.dir/indexdb.cpp.o.d -o CMakeFiles/smr_objs.dir/indexdb.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/indexdb.cpp -[ 71%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/output.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 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CMakeFiles/smr_objs.dir/indexdb.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/indexdb.cpp +[ 74%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/paralleltraversal.cpp.o [ 74%] 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 -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/output.cpp.o -MF CMakeFiles/smr_objs.dir/output.cpp.o.d -o CMakeFiles/smr_objs.dir/output.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/output.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/options.cpp.o -MF CMakeFiles/smr_objs.dir/options.cpp.o.d -o CMakeFiles/smr_objs.dir/options.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp [ 76%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/readfeed.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/summary.cpp.o -MF CMakeFiles/smr_objs.dir/summary.cpp.o.d -o CMakeFiles/smr_objs.dir/summary.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/summary.cpp -[ 77%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/references.cpp.o -[ 78%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/readstats.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/paralleltraversal.cpp.o -MF CMakeFiles/smr_objs.dir/paralleltraversal.cpp.o.d -o CMakeFiles/smr_objs.dir/paralleltraversal.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/paralleltraversal.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 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/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/read.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/references.cpp.o -MF CMakeFiles/smr_objs.dir/references.cpp.o.d -o CMakeFiles/smr_objs.dir/references.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/references.cpp -[ 83%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/refstats.cpp.o -[ 83%] Building C object src/sortmerna/CMakeFiles/smr_objs.dir/ssw.c.o -[ 83%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/traverse_bursttrie.cpp.o -[ 84%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/util.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/output.cpp.o -MF CMakeFiles/smr_objs.dir/output.cpp.o.d -o CMakeFiles/smr_objs.dir/output.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/output.cpp +[ 78%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/references.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 -[ 85%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/otumap.cpp.o -[ 87%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/report_fastx.cpp.o -[ 90%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/report_fx_base.cpp.o -[ 90%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/report.cpp.o +[ 80%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/otumap.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/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 /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/util.cpp.o -MF CMakeFiles/smr_objs.dir/util.cpp.o.d -o CMakeFiles/smr_objs.dir/util.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/util.cpp -[ 91%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/report_fx_other.cpp.o -[ 92%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/report_biom.cpp.o +[ 81%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/refstats.cpp.o +[ 83%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/util.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/references.cpp.o -MF CMakeFiles/smr_objs.dir/references.cpp.o.d -o CMakeFiles/smr_objs.dir/references.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/references.cpp +[ 85%] Building C object src/sortmerna/CMakeFiles/smr_objs.dir/ssw.c.o +[ 85%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/traverse_bursttrie.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/otumap.cpp.o -MF CMakeFiles/smr_objs.dir/otumap.cpp.o.d -o CMakeFiles/smr_objs.dir/otumap.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/otumap.cpp +[ 88%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/report.cpp.o +[ 88%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/report_fx_base.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 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CMakeFiles/smr_objs.dir/otumap.cpp.o.d -o CMakeFiles/smr_objs.dir/otumap.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/otumap.cpp +[ 94%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/report_sam.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/util.cpp.o -MF CMakeFiles/smr_objs.dir/util.cpp.o.d -o CMakeFiles/smr_objs.dir/util.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/util.cpp +[ 95%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/report_biom.cpp.o +[ 97%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/report_denovo.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/report.cpp.o -MF CMakeFiles/smr_objs.dir/report.cpp.o.d -o CMakeFiles/smr_objs.dir/report.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/report.cpp -[ 97%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/report_sam.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/report_fx_base.cpp.o -MF CMakeFiles/smr_objs.dir/report_fx_base.cpp.o.d -o CMakeFiles/smr_objs.dir/report_fx_base.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/report_fx_base.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_fastx.cpp.o -MF CMakeFiles/smr_objs.dir/report_fastx.cpp.o.d -o CMakeFiles/smr_objs.dir/report_fastx.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/report_fastx.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_fx_other.cpp.o -MF CMakeFiles/smr_objs.dir/report_fx_other.cpp.o.d -o CMakeFiles/smr_objs.dir/report_fx_other.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/report_fx_other.cpp @@ -900,32 +936,17 @@ /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/cmd.cpp: In member function 'void CmdSession::cmdIndex(Runopts&, std::string&)': 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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/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/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/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/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) @@ -974,6 +995,10 @@ /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/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::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) @@ -994,11 +1019,6 @@ /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp:740:46: warning: unused parameter 'val' [-Wunused-parameter] 740 | void Runopts::opt_version(const std::string &val) | ~~~~~~~~~~~~~~~~~~~^~~ -In file included from 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-/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/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/options.cpp: In member function 'void Runopts::process(int, char**, bool)': /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp:1368:50: warning: unused parameter 'dryrun' [-Wunused-parameter] 1368 | void Runopts::process(int argc, char**argv, bool dryrun) | ~~~~~^~~~~~ +/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/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] @@ -1061,6 +1093,10 @@ /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/paralleltraversal.cpp: In function 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../../3rdparty/cmph/CMakeFiles/cmph.dir/fch_buckets.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/graph.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/hash.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/jenkins_hash.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/miller_rabin.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/select.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/vqueue.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/vstack.c.o /usr/lib/x86_64-linux-gnu/librocksdb.so.9.10.0 -ldl /usr/lib/x86_64-linux-gnu/libz.so make[3]: Leaving directory '/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build' @@ -1100,7 +1136,7 @@ dh_prep -O--buildsystem=pybuild dh_auto_install --destdir=debian/sortmerna/ -O--buildsystem=pybuild I: pybuild base:311: dh_auto_install --buildsystem=cmake --builddirectory=/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build --destdir=/build/reproducible-path/sortmerna-4.3.7/debian/sortmerna -- - cd .pybuild/cpython3_3.13/build && make -j40 install 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