Diff of the two buildlogs: -- --- b1/build.log 2024-10-30 11:14:58.123609010 +0000 +++ b2/build.log 2024-10-30 11:17:06.011059052 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Dec 2 05:36:18 -12 2025 -I: pbuilder-time-stamp: 1764696978 +I: Current time: Thu Oct 31 01:15:01 +14 2024 +I: pbuilder-time-stamp: 1730286901 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -29,51 +29,83 @@ dpkg-source: info: applying gcc-13.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/3323337/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2343279/tmp/hooks/D01_modify_environment starting +debug: Running on infom01-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 30 11:15 /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/2343279/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2343279/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="32" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.32(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='amd64' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='b42e7f8a24ea43d19ea5aa7942ca9c1f' - 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='3323337' - PS1='# ' - PS2='> ' + INVOCATION_ID=173c139ecdfa489b902ee32e8ef3c97b + 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=2343279 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.0GT5Ctsu/pbuilderrc_hWsw --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.0GT5Ctsu/b1 --logfile b1/build.log sortmerna_4.3.7-1.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.0GT5Ctsu/pbuilderrc_meb0 --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.0GT5Ctsu/b2 --logfile b2/build.log sortmerna_4.3.7-1.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' I: uname -a - Linux infom02-amd64 6.10.11+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.10.11-1~bpo12+1 (2024-10-03) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-26-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.112-1 (2024-09-30) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/3323337/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2343279/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -219,7 +251,7 @@ Get: 90 http://deb.debian.org/debian trixie/main amd64 librocksdb-dev amd64 9.3.1-1+b1 [5295 kB] Get: 91 http://deb.debian.org/debian trixie/main amd64 python3-all amd64 3.12.6-1 [1040 B] Get: 92 http://deb.debian.org/debian trixie/main amd64 rapidjson-dev all 1.1.0+dfsg2-7.3 [98.0 kB] -Fetched 55.6 MB in 1s (42.2 MB/s) +Fetched 55.6 MB in 3s (20.2 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-minimal: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 ... 19949 files and directories currently installed.) @@ -538,8 +570,8 @@ Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Tue Dec 2 17:37:13 UTC 2025. -Universal Time is now: Tue Dec 2 17:37:13 UTC 2025. +Local time is now: Wed Oct 30 11:16:23 UTC 2024. +Universal Time is now: Wed Oct 30 11:16:23 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... @@ -616,7 +648,11 @@ 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_4.3.7-1_source.changes +I: user script /srv/workspace/pbuilder/2343279/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/2343279/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_4.3.7-1_source.changes dpkg-buildpackage: info: source package sortmerna dpkg-buildpackage: info: source version 4.3.7-1 dpkg-buildpackage: info: source distribution unstable @@ -654,8 +690,8 @@ CMAKE_CXX_COMPILER_ID = GNU CMAKE_CONFIGURATION_TYPES = CMAKE_HOST_SYSTEM_NAME = Linux -CMAKE_HOST_SYSTEM_VERSION = 6.10.11+bpo-amd64 -CMAKE_HOST_SYSTEM = Linux-6.10.11+bpo-amd64 +CMAKE_HOST_SYSTEM_VERSION = 6.1.0-26-cloud-amd64 +CMAKE_HOST_SYSTEM = Linux-6.1.0-26-cloud-amd64 CMAKE_BINARY_DIR = /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build CMAKE_CURRENT_BINARY_DIR = /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build RUNTIME_OUTPUT_DIRECTORY_RELEASE = @@ -686,7 +722,7 @@ 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 (2.3s) +-- Configuring done (1.2s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: @@ -724,89 +760,89 @@ make[3]: Entering directory '/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build' cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/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_3.12/build /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build/CMakeFiles/build_version.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build' -cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/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_3.12/build /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build/3rdparty/alp /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build/3rdparty/alp/CMakeFiles/alp.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build' +cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/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_3.12/build /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build/3rdparty/alp /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build/3rdparty/alp/CMakeFiles/alp.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/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_3.12/build /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build/3rdparty/cmph /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build/3rdparty/cmph/CMakeFiles/cmph.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build' +make -f 3rdparty/alp/CMakeFiles/alp.dir/build.make 3rdparty/alp/CMakeFiles/alp.dir/build +make[3]: Leaving directory '/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build' make -f CMakeFiles/build_version.dir/build.make CMakeFiles/build_version.dir/build make[3]: Entering directory '/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build' +make[3]: Entering directory '/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build' make[3]: Leaving directory '/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build' -make[3]: Leaving directory '/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build' -make -f 3rdparty/alp/CMakeFiles/alp.dir/build.make 3rdparty/alp/CMakeFiles/alp.dir/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_3.12/build' -make[3]: Entering directory '/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build' -[ 1%] Building CXX object CMakeFiles/build_version.dir/build_version.cpp.o [ 2%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/njn_dynprogprob.cpp.o -[ 5%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/bmz8.c.o -[ 5%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/njn_ioutil.cpp.o -[ 8%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/njn_dynprogprobproto.cpp.o -[ 8%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/bdz.c.o -[ 9%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/bmz.c.o -[ 11%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/bdz_ph.c.o -cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/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/bmz8.c.o -MF CMakeFiles/cmph.dir/bmz8.c.o.d -o CMakeFiles/cmph.dir/bmz8.c.o -c /build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph/bmz8.c +[ 2%] Building CXX object CMakeFiles/build_version.dir/build_version.cpp.o +[ 7%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/njn_dynprogprobproto.cpp.o +[ 7%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/njn_random.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 CMakeFiles/build_version.dir/build_version.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build/build_version.cpp cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/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 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-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_dynprogprobproto.cpp.o -MF CMakeFiles/alp.dir/njn_dynprogprobproto.cpp.o.d -o CMakeFiles/alp.dir/njn_dynprogprobproto.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/3rdparty/alp/njn_dynprogprobproto.cpp +cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/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_random.cpp.o -MF CMakeFiles/alp.dir/njn_random.cpp.o.d -o CMakeFiles/alp.dir/njn_random.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/3rdparty/alp/njn_random.cpp +/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build/build_version.cpp:4:44: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] + 4 | const char* sortmerna_build_compile_date = __DATE__; + | ^~~~~~~~ +[ 7%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/njn_ioutil.cpp.o +[ 8%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/njn_dynprogproblim.cpp.o +[ 14%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/njn_localmaxstatutil.cpp.o +cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/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_dynprogproblim.cpp.o -MF CMakeFiles/alp.dir/njn_dynprogproblim.cpp.o.d -o 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/build/reproducible-path/sortmerna-4.3.7/3rdparty/alp/sls_pvalues.cpp [ 47%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/hash.c.o cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/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/hash.c.o -MF CMakeFiles/cmph.dir/hash.c.o.d -o CMakeFiles/cmph.dir/hash.c.o -c /build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph/hash.c [ 49%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/jenkins_hash.c.o @@ -829,30 +865,30 @@ make[3]: Leaving directory '/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build' make -f src/sortmerna/CMakeFiles/smr_objs.dir/build.make 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src/sortmerna/CMakeFiles/smr_objs.dir/kseq_load.cpp.o +[ 63%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/kvdb.cpp.o +[ 63%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/indexdb.cpp.o cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/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/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 -[ 67%] Building CXX object 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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 +[ 67%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/kseq_load.cpp.o +[ 69%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/options.cpp.o cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/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 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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 +[ 71%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/paralleltraversal.cpp.o +cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/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 /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/izlib.cpp: In member function 'int Izlib::inflatez(std::ifstream&)': /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/izlib.cpp:243:29: warning: this statement may fall through [-Wimplicit-fallthrough=] 243 | ret = Z_DATA_ERROR; /* and fall through */ @@ -862,9 +898,17 @@ | ^~~~ [ 73%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/processor.cpp.o cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/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 /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) + | ~~~~~~~~~~~~^~~~~~ +[ 76%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/readfeed.cpp.o +cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/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 /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) @@ -905,10 +949,6 @@ /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/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/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) @@ -944,6 +984,10 @@ /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp:750:45: warning: unused parameter 'narg' [-Wunused-parameter] 750 | void Runopts::opt_unknown(char **argv, int &narg, char * opt) | ~~~~~^~~~ +/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; + | ^~~ /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp: In member function 'void Runopts::opt_F(const std::string&)': /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp:784:40: warning: unused parameter 'val' [-Wunused-parameter] 784 | void Runopts::opt_F(const std::string &val) @@ -960,6 +1004,14 @@ /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp:819:40: warning: unused parameter 'val' [-Wunused-parameter] 819 | void Runopts::opt_v(const std::string &val) | ~~~~~~~~~~~~~~~~~~~^~~ +/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; + | ^~~ +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::opt_dbg_put_db(const std::string&)': /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp:937:49: warning: unused parameter 'val' [-Wunused-parameter] 937 | void Runopts::opt_dbg_put_db(const std::string& val) @@ -968,8 +1020,6 @@ /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp:980:42: warning: unused parameter 'val' [-Wunused-parameter] 980 | void Runopts::opt_cmd(const std::string &val) | ~~~~~~~~~~~~~~~~~~~^~~ -[ 74%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/read.cpp.o -cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/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/read.cpp.o -MF CMakeFiles/smr_objs.dir/read.cpp.o.d -o CMakeFiles/smr_objs.dir/read.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/read.cpp /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp: In member function 'void Runopts::opt_tmpdir(const std::string&)': /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp:1036:45: warning: unused parameter 'val' [-Wunused-parameter] 1036 | void Runopts::opt_tmpdir(const std::string &val) @@ -982,16 +1032,14 @@ /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) | ~~~~~~~~~~~~~~~~~~~^~~ -[ 76%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/readfeed.cpp.o -cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/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 -/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/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::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) @@ -999,24 +1047,10 @@ /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: 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; - | ^~~ -/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; - | ^~~ -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); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 77%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/readstats.cpp.o -cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/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 In file included from /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/paralleltraversal.cpp:41: /build/reproducible-path/sortmerna-4.3.7/include/kseq_load.hpp: At global scope: /build/reproducible-path/sortmerna-4.3.7/include/kseq.h:171:20: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function] @@ -1028,6 +1062,8 @@ /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) | ^~~~~~~~~ +[ 77%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/readstats.cpp.o +cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/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 /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/readfeed.cpp: In member function 'void Readfeed::init(std::vector >&, const int&)': /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/readfeed.cpp:105:69: warning: unused parameter 'dbg' [-Wunused-parameter] 105 | void Readfeed::init(std::vector& readfiles, const int& dbg) @@ -1053,6 +1089,8 @@ | ~~~~~~~~~~~~~~~~~~~^~~~ [ 78%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/references.cpp.o cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/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 +[ 80%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/refstats.cpp.o +cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/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/refstats.cpp.o -MF CMakeFiles/smr_objs.dir/refstats.cpp.o.d -o CMakeFiles/smr_objs.dir/refstats.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/refstats.cpp 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] @@ -1064,8 +1102,6 @@ /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) | ^~~~~~~~~ -[ 80%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/refstats.cpp.o -cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/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/refstats.cpp.o -MF CMakeFiles/smr_objs.dir/refstats.cpp.o.d -o CMakeFiles/smr_objs.dir/refstats.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/refstats.cpp [ 81%] Building C object src/sortmerna/CMakeFiles/smr_objs.dir/ssw.c.o cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build/src/sortmerna && /usr/bin/cc -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 -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 src/sortmerna/CMakeFiles/smr_objs.dir/ssw.c.o -MF CMakeFiles/smr_objs.dir/ssw.c.o.d -o CMakeFiles/smr_objs.dir/ssw.c.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/ssw.c [ 83%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/traverse_bursttrie.cpp.o @@ -1078,20 +1114,26 @@ cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/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 [ 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_3.12/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 -[ 91%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/report_fx_other.cpp.o -[ 91%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/report_fastx.cpp.o +[ 90%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/report_fastx.cpp.o cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/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 +[ 91%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/report_fx_other.cpp.o cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/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 [ 92%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/report_blast.cpp.o cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/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_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 -[ 94%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/report_denovo.cpp.o -cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/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 -[ 95%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/report_biom.cpp.o -cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/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_biom.cpp.o -MF CMakeFiles/smr_objs.dir/report_biom.cpp.o.d -o CMakeFiles/smr_objs.dir/report_biom.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/report_biom.cpp /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) {} | ~~~~~~~~~^~~~ +[ 94%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/report_denovo.cpp.o +cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/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 +[ 95%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/report_biom.cpp.o +cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/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_biom.cpp.o -MF CMakeFiles/smr_objs.dir/report_biom.cpp.o.d -o CMakeFiles/smr_objs.dir/report_biom.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/report_biom.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_3.12/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_sam.cpp.o -MF CMakeFiles/smr_objs.dir/report_sam.cpp.o.d -o CMakeFiles/smr_objs.dir/report_sam.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/report_sam.cpp +/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/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) @@ -1099,12 +1141,6 @@ /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) | ~~~~~~~~~^~~~ -[ 97%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/report_sam.cpp.o -cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/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_sam.cpp.o -MF CMakeFiles/smr_objs.dir/report_sam.cpp.o.d -o CMakeFiles/smr_objs.dir/report_sam.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/report_sam.cpp -/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) - | ~~~~~~~~~~~^~~ make[3]: Leaving directory '/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build' [ 97%] Built target smr_objs make -f src/sortmerna/CMakeFiles/sortmerna.dir/build.make src/sortmerna/CMakeFiles/sortmerna.dir/depend @@ -1119,7 +1155,7 @@ cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build/src/sortmerna && /usr/bin/cmake -E cmake_link_script CMakeFiles/sortmerna.dir/link.txt --verbose=1 /usr/bin/c++ -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 -Wl,-z,relro -Wl,-z,now 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Binutils for Debian) 2.43.1 make[3]: Leaving directory '/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build' [100%] Built target sortmerna @@ -1151,8 +1187,8 @@ debian/rules execute_after_dh_install make[1]: Entering directory '/build/reproducible-path/sortmerna-4.3.7' find debian -name cmake -type d | xargs rm -rvf -removed 'debian/sortmerna/usr/cmake/sortmerna/sortmernaConfig.cmake' removed 'debian/sortmerna/usr/cmake/sortmerna/sortmernaConfigVersion.cmake' +removed 'debian/sortmerna/usr/cmake/sortmerna/sortmernaConfig.cmake' removed directory 'debian/sortmerna/usr/cmake/sortmerna' removed directory 'debian/sortmerna/usr/cmake' make[1]: Leaving directory '/build/reproducible-path/sortmerna-4.3.7' @@ -1195,8 +1231,8 @@ dh_gencontrol -O--buildsystem=pybuild dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild -dpkg-deb: building package 'sortmerna' in '../sortmerna_4.3.7-1_amd64.deb'. dpkg-deb: building package 'sortmerna-dbgsym' in '../sortmerna-dbgsym_4.3.7-1_amd64.deb'. +dpkg-deb: building package 'sortmerna' in '../sortmerna_4.3.7-1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../sortmerna_4.3.7-1_amd64.buildinfo dpkg-genchanges --build=binary -O../sortmerna_4.3.7-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1204,12 +1240,14 @@ 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/2343279/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2343279/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/3323337 and its subdirectories -I: Current time: Tue Dec 2 05:37:57 -12 2025 -I: pbuilder-time-stamp: 1764697077 +I: removing directory /srv/workspace/pbuilder/2343279 and its subdirectories +I: Current time: Thu Oct 31 01:17:05 +14 2024 +I: pbuilder-time-stamp: 1730287025