Diff of the two buildlogs: -- --- b1/build.log 2024-05-09 20:40:31.845910744 +0000 +++ b2/build.log 2024-05-09 20:43:26.686469784 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Jun 11 15:00:28 -12 2025 -I: pbuilder-time-stamp: 1749697228 +I: Current time: Fri May 10 10:40:34 +14 2024 +I: pbuilder-time-stamp: 1715287234 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -33,52 +33,84 @@ 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/1470472/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2021789/tmp/hooks/D01_modify_environment starting +debug: Running on ionos11-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 May 9 20:40 /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/2021789/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2021789/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' - DISTRIBUTION='trixie' - 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]="21" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.21(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=20 ' + 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='c674c5182fea4045a203bfcd3efa8a04' - 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='1470472' - PS1='# ' - PS2='> ' + INVOCATION_ID=f3475b1ae96b4370b8e753ce78a6fdaf + 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=2021789 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.rTgIGS3A/pbuilderrc_hgsV --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.rTgIGS3A/b1 --logfile b1/build.log sortmerna_4.3.6-3.dsc' - SUDO_GID='110' - SUDO_UID='105' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://213.165.73.152:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.rTgIGS3A/pbuilderrc_xBFV --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.rTgIGS3A/b2 --logfile b2/build.log sortmerna_4.3.6-3.dsc' + SUDO_GID=111 + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://46.16.76.132:3128 I: uname -a - Linux ionos5-amd64 6.6.13+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.6.13-1~bpo12+1 (2024-02-15) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-21-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Jun 10 17:46 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1470472/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 7 11:25 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2021789/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -194,7 +226,7 @@ Get: 64 http://deb.debian.org/debian trixie/main amd64 libzstd-dev amd64 1.5.5+dfsg2-2 [358 kB] Get: 65 http://deb.debian.org/debian trixie/main amd64 librocksdb-dev amd64 8.9.1-2 [4952 kB] Get: 66 http://deb.debian.org/debian trixie/main amd64 rapidjson-dev all 1.1.0+dfsg2-7.2 [97.8 kB] -Fetched 45.9 MB in 8s (5874 kB/s) +Fetched 45.9 MB in 1s (47.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libproc2-0: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 ... 19699 files and directories currently installed.) @@ -473,7 +505,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/sortmerna-4.3.6/ && 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_4.3.6-3_source.changes +I: user script /srv/workspace/pbuilder/2021789/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/2021789/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/sortmerna-4.3.6/ && 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_4.3.6-3_source.changes dpkg-buildpackage: info: source package sortmerna dpkg-buildpackage: info: source version 4.3.6-3 dpkg-buildpackage: info: source distribution unstable @@ -505,8 +541,8 @@ CMAKE_CXX_COMPILER_ID = GNU CMAKE_CONFIGURATION_TYPES = CMAKE_HOST_SYSTEM_NAME = Linux -CMAKE_HOST_SYSTEM_VERSION = 6.6.13+bpo-amd64 -CMAKE_HOST_SYSTEM = Linux-6.6.13+bpo-amd64 +CMAKE_HOST_SYSTEM_VERSION = 6.1.0-21-amd64 +CMAKE_HOST_SYSTEM = Linux-6.1.0-21-amd64 PROJECT_BINARY_DIR = /build/reproducible-path/sortmerna-4.3.6/obj-x86_64-linux-gnu CMAKE_BINARY_DIR = /build/reproducible-path/sortmerna-4.3.6/obj-x86_64-linux-gnu CMAKE_CURRENT_BINARY_DIR = /build/reproducible-path/sortmerna-4.3.6/obj-x86_64-linux-gnu @@ -539,7 +575,7 @@ 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 (9.1s) +-- Configuring done (1.7s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: @@ -555,7 +591,7 @@ -- Build files have been written to: /build/reproducible-path/sortmerna-4.3.6/obj-x86_64-linux-gnu dh_auto_build - cd obj-x86_64-linux-gnu && make -j42 "INSTALL=install --strip-program=true" VERBOSE=1 + cd obj-x86_64-linux-gnu && make -j20 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/sortmerna-4.3.6/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/sortmerna-4.3.6 -B/build/reproducible-path/sortmerna-4.3.6/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/sortmerna-4.3.6/obj-x86_64-linux-gnu/CMakeFiles /build/reproducible-path/sortmerna-4.3.6/obj-x86_64-linux-gnu//CMakeFiles/progress.marks @@ -567,101 +603,101 @@ make[3]: Entering directory '/build/reproducible-path/sortmerna-4.3.6/obj-x86_64-linux-gnu' cd /build/reproducible-path/sortmerna-4.3.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sortmerna-4.3.6 /build/reproducible-path/sortmerna-4.3.6 /build/reproducible-path/sortmerna-4.3.6/obj-x86_64-linux-gnu /build/reproducible-path/sortmerna-4.3.6/obj-x86_64-linux-gnu /build/reproducible-path/sortmerna-4.3.6/obj-x86_64-linux-gnu/CMakeFiles/build_version.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/sortmerna-4.3.6/obj-x86_64-linux-gnu' -make[3]: Entering directory '/build/reproducible-path/sortmerna-4.3.6/obj-x86_64-linux-gnu' cd /build/reproducible-path/sortmerna-4.3.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sortmerna-4.3.6 /build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph /build/reproducible-path/sortmerna-4.3.6/obj-x86_64-linux-gnu /build/reproducible-path/sortmerna-4.3.6/obj-x86_64-linux-gnu/3rdparty/cmph /build/reproducible-path/sortmerna-4.3.6/obj-x86_64-linux-gnu/3rdparty/cmph/CMakeFiles/cmph.dir/DependInfo.cmake "--color=" +make[3]: Entering directory '/build/reproducible-path/sortmerna-4.3.6/obj-x86_64-linux-gnu' cd /build/reproducible-path/sortmerna-4.3.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sortmerna-4.3.6 /build/reproducible-path/sortmerna-4.3.6/3rdparty/alp /build/reproducible-path/sortmerna-4.3.6/obj-x86_64-linux-gnu /build/reproducible-path/sortmerna-4.3.6/obj-x86_64-linux-gnu/3rdparty/alp /build/reproducible-path/sortmerna-4.3.6/obj-x86_64-linux-gnu/3rdparty/alp/CMakeFiles/alp.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sortmerna-4.3.6/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/sortmerna-4.3.6/obj-x86_64-linux-gnu' +make -f 3rdparty/cmph/CMakeFiles/cmph.dir/build.make 3rdparty/cmph/CMakeFiles/cmph.dir/build make -f 3rdparty/alp/CMakeFiles/alp.dir/build.make 3rdparty/alp/CMakeFiles/alp.dir/build -make -f CMakeFiles/build_version.dir/build.make CMakeFiles/build_version.dir/build make[3]: Leaving directory '/build/reproducible-path/sortmerna-4.3.6/obj-x86_64-linux-gnu' -make -f 3rdparty/cmph/CMakeFiles/cmph.dir/build.make 3rdparty/cmph/CMakeFiles/cmph.dir/build make[3]: 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/build/reproducible-path/sortmerna-4.3.6/obj-x86_64-linux-gnu/3rdparty/cmph && /usr/bin/cc -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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-4.3.6/3rdparty/cmph/bdz.c +cd /build/reproducible-path/sortmerna-4.3.6/obj-x86_64-linux-gnu/3rdparty/cmph && /usr/bin/cc -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT 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/usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.6/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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-4.3.6/obj-x86_64-linux-gnu/build_version.cpp -cd /build/reproducible-path/sortmerna-4.3.6/obj-x86_64-linux-gnu/3rdparty/alp && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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 CMakeFiles/alp.dir/njn_dynprogproblim.cpp.o -c /build/reproducible-path/sortmerna-4.3.6/3rdparty/alp/njn_dynprogproblim.cpp cd /build/reproducible-path/sortmerna-4.3.6/obj-x86_64-linux-gnu/3rdparty/alp && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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 /build/reproducible-path/sortmerna-4.3.6/3rdparty/alp/njn_dynprogprob.cpp -[ 9%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/bdz.c.o -[ 9%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/njn_localmaxstat.cpp.o -[ 11%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/njn_localmaxstatutil.cpp.o +[ 12%] Building CXX object 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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-4.3.6/3rdparty/alp/njn_random.cpp +[ 26%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/sls_alignment_evaluer.cpp.o +[ 28%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/chm.c.o +cd /build/reproducible-path/sortmerna-4.3.6/obj-x86_64-linux-gnu/3rdparty/alp && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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_alignment_evaluer.cpp.o -MF CMakeFiles/alp.dir/sls_alignment_evaluer.cpp.o.d -o CMakeFiles/alp.dir/sls_alignment_evaluer.cpp.o -c /build/reproducible-path/sortmerna-4.3.6/3rdparty/alp/sls_alignment_evaluer.cpp cd 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CMakeFiles/alp.dir/sls_pvalues.cpp.o.d -o CMakeFiles/alp.dir/sls_pvalues.cpp.o -c /build/reproducible-path/sortmerna-4.3.6/3rdparty/alp/sls_pvalues.cpp -[ 38%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/cmph.c.o -[ 39%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/cmph_structs.c.o -cd /build/reproducible-path/sortmerna-4.3.6/obj-x86_64-linux-gnu/3rdparty/alp && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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_basic.cpp.o -MF CMakeFiles/alp.dir/sls_basic.cpp.o.d -o CMakeFiles/alp.dir/sls_basic.cpp.o -c /build/reproducible-path/sortmerna-4.3.6/3rdparty/alp/sls_basic.cpp -cd /build/reproducible-path/sortmerna-4.3.6/obj-x86_64-linux-gnu/3rdparty/cmph && /usr/bin/cc -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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/cmph_structs.c.o -MF CMakeFiles/cmph.dir/cmph_structs.c.o.d -o CMakeFiles/cmph.dir/cmph_structs.c.o -c /build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph/cmph_structs.c -[ 40%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/compressed_rank.c.o +make[3]: Leaving directory '/build/reproducible-path/sortmerna-4.3.6/obj-x86_64-linux-gnu' +[ 28%] Built target build_version +[ 29%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/sls_alp.cpp.o +cd /build/reproducible-path/sortmerna-4.3.6/obj-x86_64-linux-gnu/3rdparty/alp && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/alp -g -O2 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/usr/bin/cc -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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/miller_rabin.c.o -MF CMakeFiles/cmph.dir/miller_rabin.c.o.d -o CMakeFiles/cmph.dir/miller_rabin.c.o -c /build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph/miller_rabin.c +[ 46%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/jenkins_hash.c.o cd /build/reproducible-path/sortmerna-4.3.6/obj-x86_64-linux-gnu/3rdparty/cmph && /usr/bin/cc -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT 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-[ 54%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/vstack.c.o +[ 49%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/vqueue.c.o cd /build/reproducible-path/sortmerna-4.3.6/obj-x86_64-linux-gnu/3rdparty/cmph && /usr/bin/cc -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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-4.3.6/3rdparty/cmph/vqueue.c +[ 50%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/vstack.c.o cd /build/reproducible-path/sortmerna-4.3.6/obj-x86_64-linux-gnu/3rdparty/cmph && /usr/bin/cc -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -g -O2 -Werror=implicit-function-declaration 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/build/reproducible-path/sortmerna-4.3.6/3rdparty/alp/sls_basic.cpp +[ 53%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/sls_alp_sim.cpp.o +cd /build/reproducible-path/sortmerna-4.3.6/obj-x86_64-linux-gnu/3rdparty/alp && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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_alp_sim.cpp.o -MF CMakeFiles/alp.dir/sls_alp_sim.cpp.o.d -o CMakeFiles/alp.dir/sls_alp_sim.cpp.o -c /build/reproducible-path/sortmerna-4.3.6/3rdparty/alp/sls_alp_sim.cpp +[ 54%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/sls_pvalues.cpp.o +cd /build/reproducible-path/sortmerna-4.3.6/obj-x86_64-linux-gnu/3rdparty/alp && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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-4.3.6/3rdparty/alp/sls_pvalues.cpp make[3]: Leaving directory '/build/reproducible-path/sortmerna-4.3.6/obj-x86_64-linux-gnu' [ 54%] Built target cmph make[3]: Leaving directory '/build/reproducible-path/sortmerna-4.3.6/obj-x86_64-linux-gnu' @@ -672,66 +708,46 @@ make[3]: Leaving directory '/build/reproducible-path/sortmerna-4.3.6/obj-x86_64-linux-gnu' 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-4.3.6/obj-x86_64-linux-gnu' -[ 64%] Building CXX object 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/build/reproducible-path/sortmerna-4.3.6/src/sortmerna/read.cpp -[ 97%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/readfeed.cpp.o +[ 71%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/alignment.cpp.o +[ 74%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/readstats.cpp.o +[ 74%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/processor.cpp.o +[ 76%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/summary.cpp.o +[ 77%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/output.cpp.o +cd /build/reproducible-path/sortmerna-4.3.6/obj-x86_64-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.6/include -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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-4.3.6/src/sortmerna/alignment.cpp cd /build/reproducible-path/sortmerna-4.3.6/obj-x86_64-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.6/include -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/bitvector.cpp.o -MF CMakeFiles/smr_objs.dir/bitvector.cpp.o.d -o CMakeFiles/smr_objs.dir/bitvector.cpp.o -c /build/reproducible-path/sortmerna-4.3.6/src/sortmerna/bitvector.cpp +cd /build/reproducible-path/sortmerna-4.3.6/obj-x86_64-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.6/include -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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-4.3.6/src/sortmerna/izlib.cpp +cd /build/reproducible-path/sortmerna-4.3.6/obj-x86_64-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.6/include -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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-4.3.6/src/sortmerna/index.cpp cd /build/reproducible-path/sortmerna-4.3.6/obj-x86_64-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.6/include -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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-4.3.6/src/sortmerna/indexdb.cpp +cd /build/reproducible-path/sortmerna-4.3.6/obj-x86_64-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.6/include -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -fstack-protector-strong 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/build/reproducible-path/sortmerna-4.3.6/src/sortmerna/options.cpp +[ 80%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/refstats.cpp.o cd /build/reproducible-path/sortmerna-4.3.6/obj-x86_64-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.6/include -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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-4.3.6/src/sortmerna/output.cpp cd /build/reproducible-path/sortmerna-4.3.6/obj-x86_64-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.6/include -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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-4.3.6/src/sortmerna/summary.cpp cd /build/reproducible-path/sortmerna-4.3.6/obj-x86_64-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.6/include -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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-4.3.6/src/sortmerna/paralleltraversal.cpp +cd /build/reproducible-path/sortmerna-4.3.6/obj-x86_64-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.6/include -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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/processor.cpp.o -MF CMakeFiles/smr_objs.dir/processor.cpp.o.d -o CMakeFiles/smr_objs.dir/processor.cpp.o -c /build/reproducible-path/sortmerna-4.3.6/src/sortmerna/processor.cpp +[ 81%] Building C object src/sortmerna/CMakeFiles/smr_objs.dir/ssw.c.o +cd /build/reproducible-path/sortmerna-4.3.6/obj-x86_64-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.6/include -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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-4.3.6/src/sortmerna/read.cpp cd /build/reproducible-path/sortmerna-4.3.6/obj-x86_64-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.6/include -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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-4.3.6/src/sortmerna/readfeed.cpp +cd /build/reproducible-path/sortmerna-4.3.6/obj-x86_64-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.6/include -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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-4.3.6/src/sortmerna/readstats.cpp +cd /build/reproducible-path/sortmerna-4.3.6/obj-x86_64-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.6/include -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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-4.3.6/src/sortmerna/references.cpp cd /build/reproducible-path/sortmerna-4.3.6/obj-x86_64-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.6/include -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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-4.3.6/src/sortmerna/refstats.cpp cd /build/reproducible-path/sortmerna-4.3.6/obj-x86_64-linux-gnu/src/sortmerna && /usr/bin/cc -I/build/reproducible-path/sortmerna-4.3.6/include -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/alp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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-4.3.6/src/sortmerna/ssw.c +[ 83%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/traverse_bursttrie.cpp.o cd /build/reproducible-path/sortmerna-4.3.6/obj-x86_64-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.6/include -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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/traverse_bursttrie.cpp.o -MF CMakeFiles/smr_objs.dir/traverse_bursttrie.cpp.o.d -o CMakeFiles/smr_objs.dir/traverse_bursttrie.cpp.o -c /build/reproducible-path/sortmerna-4.3.6/src/sortmerna/traverse_bursttrie.cpp -cd /build/reproducible-path/sortmerna-4.3.6/obj-x86_64-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.6/include -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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-4.3.6/src/sortmerna/otumap.cpp -cd /build/reproducible-path/sortmerna-4.3.6/obj-x86_64-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.6/include -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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-4.3.6/src/sortmerna/report.cpp -cd /build/reproducible-path/sortmerna-4.3.6/obj-x86_64-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.6/include -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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-4.3.6/src/sortmerna/report_fx_base.cpp -cd /build/reproducible-path/sortmerna-4.3.6/obj-x86_64-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.6/include -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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-4.3.6/src/sortmerna/report_fastx.cpp -cd /build/reproducible-path/sortmerna-4.3.6/obj-x86_64-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.6/include -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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-4.3.6/src/sortmerna/report_fx_other.cpp -cd /build/reproducible-path/sortmerna-4.3.6/obj-x86_64-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.6/include -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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-4.3.6/src/sortmerna/report_blast.cpp -cd /build/reproducible-path/sortmerna-4.3.6/obj-x86_64-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.6/include -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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-4.3.6/src/sortmerna/report_denovo.cpp -cd /build/reproducible-path/sortmerna-4.3.6/obj-x86_64-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.6/include -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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-4.3.6/src/sortmerna/report_biom.cpp -cd /build/reproducible-path/sortmerna-4.3.6/obj-x86_64-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.6/include -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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-4.3.6/src/sortmerna/report_sam.cpp /build/reproducible-path/sortmerna-4.3.6/src/sortmerna/izlib.cpp: In member function 'int Izlib::inflatez(std::ifstream&)': /build/reproducible-path/sortmerna-4.3.6/src/sortmerna/izlib.cpp:243:29: warning: this statement may fall through [-Wimplicit-fallthrough=] 243 | ret = Z_DATA_ERROR; /* and fall through */ @@ -739,13 +755,10 @@ /build/reproducible-path/sortmerna-4.3.6/src/sortmerna/izlib.cpp:244:17: note: here 244 | case Z_DATA_ERROR: | ^~~~ -/build/reproducible-path/sortmerna-4.3.6/src/sortmerna/report_biom.cpp: In member function 'virtual void ReportBiom::init(Readfeed&, Runopts&)': -/build/reproducible-path/sortmerna-4.3.6/src/sortmerna/report_biom.cpp:41:33: warning: unused parameter 'readfeed' [-Wunused-parameter] - 41 | void ReportBiom::init(Readfeed& readfeed, Runopts& opts) - | ~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/sortmerna-4.3.6/src/sortmerna/report_biom.cpp:41:52: warning: unused parameter 'opts' [-Wunused-parameter] - 41 | void ReportBiom::init(Readfeed& readfeed, Runopts& opts) - | ~~~~~~~~~^~~~ +[ 84%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/util.cpp.o +cd /build/reproducible-path/sortmerna-4.3.6/obj-x86_64-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.6/include -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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-4.3.6/src/sortmerna/util.cpp +[ 85%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/otumap.cpp.o +cd /build/reproducible-path/sortmerna-4.3.6/obj-x86_64-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.6/include -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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-4.3.6/src/sortmerna/otumap.cpp /build/reproducible-path/sortmerna-4.3.6/src/sortmerna/readfeed.cpp: In member function 'void Readfeed::init(std::vector >&, const int&)': /build/reproducible-path/sortmerna-4.3.6/src/sortmerna/readfeed.cpp:105:69: warning: unused parameter 'dbg' [-Wunused-parameter] 105 | void Readfeed::init(std::vector& readfiles, const int& dbg) @@ -765,32 +778,6 @@ /build/reproducible-path/sortmerna-4.3.6/src/sortmerna/readfeed.cpp: In member function 'bool Readfeed::define_format(const int&)': /build/reproducible-path/sortmerna-4.3.6/src/sortmerna/readfeed.cpp:857:36: warning: comparison is always false due to limited range of data type [-Wtype-limits] 857 | if (str[i] > 127 || str[i] < 0) { -/build/reproducible-path/sortmerna-4.3.6/src/sortmerna/report.cpp: In constructor 'Report::Report(Runopts&)': -/build/reproducible-path/sortmerna-4.3.6/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) {} - | ~~~~~~~~~^~~~ -/build/reproducible-path/sortmerna-4.3.6/src/sortmerna/indexdb.cpp:916:14: warning: 'void {anonymous}::help()' defined but not used [-Wunused-function] - 916 | void help() - | ^~~~ -/build/reproducible-path/sortmerna-4.3.6/src/sortmerna/kvdb.cpp: In member function 'int KeyValueDatabase::clear(std::string)': -/build/reproducible-path/sortmerna-4.3.6/src/sortmerna/kvdb.cpp:58:41: warning: unused parameter 'dbpath' [-Wunused-parameter] - 58 | int KeyValueDatabase::clear(std::string dbpath) - | ~~~~~~~~~~~~^~~~~~ -/build/reproducible-path/sortmerna-4.3.6/src/sortmerna/read.cpp: In member function 'void Read::unmarshallJson(KeyValueDatabase&)': -/build/reproducible-path/sortmerna-4.3.6/src/sortmerna/read.cpp:540:46: warning: unused parameter 'kvdb' [-Wunused-parameter] - 540 | void Read::unmarshallJson(KeyValueDatabase & kvdb) - | ~~~~~~~~~~~~~~~~~~~^~~~ -/build/reproducible-path/sortmerna-4.3.6/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-4.3.6/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-4.3.6/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-4.3.6/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-4.3.6/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-4.3.6/src/sortmerna/options.cpp: In member function 'void Runopts::opt_log(const std::string&)': /build/reproducible-path/sortmerna-4.3.6/src/sortmerna/options.cpp:284:42: warning: unused parameter 'val' [-Wunused-parameter] 284 | void Runopts::opt_log(const std::string& val) @@ -847,10 +834,6 @@ /build/reproducible-path/sortmerna-4.3.6/src/sortmerna/options.cpp:636:15: warning: unused variable 'end' [-Wunused-variable] 636 | char *end = 0; | ^~~ -/build/reproducible-path/sortmerna-4.3.6/src/sortmerna/cmd.cpp: In member function 'void CmdSession::cmdIndex(Runopts&, std::string&)': -/build/reproducible-path/sortmerna-4.3.6/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-4.3.6/src/sortmerna/options.cpp: In member function 'void Runopts::opt_full_search(const std::string&)': /build/reproducible-path/sortmerna-4.3.6/src/sortmerna/options.cpp:651:50: warning: unused parameter 'val' [-Wunused-parameter] 651 | void Runopts::opt_full_search(const std::string &val) @@ -859,13 +842,6 @@ /build/reproducible-path/sortmerna-4.3.6/src/sortmerna/options.cpp:661:41: warning: unused parameter 'val' [-Wunused-parameter] 661 | void Runopts::opt_SQ(const std::string &val) | ~~~~~~~~~~~~~~~~~~~^~~ -/build/reproducible-path/sortmerna-4.3.6/src/sortmerna/cmd.cpp: In member function 'void CmdSession::cmdTest(Runopts&, std::string&)': -/build/reproducible-path/sortmerna-4.3.6/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-4.3.6/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-4.3.6/src/sortmerna/options.cpp: In member function 'void Runopts::opt_version(const std::string&)': /build/reproducible-path/sortmerna-4.3.6/src/sortmerna/options.cpp:740:46: warning: unused parameter 'val' [-Wunused-parameter] 740 | void Runopts::opt_version(const std::string &val) @@ -905,17 +881,6 @@ /build/reproducible-path/sortmerna-4.3.6/src/sortmerna/options.cpp:1036:45: warning: unused parameter 'val' [-Wunused-parameter] 1036 | void Runopts::opt_tmpdir(const std::string &val) | ~~~~~~~~~~~~~~~~~~~^~~ -In file included from /build/reproducible-path/sortmerna-4.3.6/include/kseq_load.hpp:40, - from /build/reproducible-path/sortmerna-4.3.6/src/sortmerna/readstats.cpp:52: -/build/reproducible-path/sortmerna-4.3.6/include/kseq.h:171:20: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function] - 171 | static int kseq_read(kseq_t *seq) \ - | ^~~~~~~~~ -/build/reproducible-path/sortmerna-4.3.6/include/kseq.h:221:9: note: in expansion of macro '__KSEQ_READ' - 221 | __KSEQ_READ - | ^~~~~~~~~~~ -/build/reproducible-path/sortmerna-4.3.6/include/kseq_load.hpp:43:1: note: in expansion of macro 'KSEQ_INIT' - 43 | KSEQ_INIT(gzFile, gzread) - | ^~~~~~~~~ /build/reproducible-path/sortmerna-4.3.6/src/sortmerna/options.cpp: In member function 'void Runopts::opt_align(const std::string&)': /build/reproducible-path/sortmerna-4.3.6/src/sortmerna/options.cpp:1193:44: warning: unused parameter 'val' [-Wunused-parameter] 1193 | void Runopts::opt_align(const std::string& val) @@ -924,19 +889,69 @@ /build/reproducible-path/sortmerna-4.3.6/src/sortmerna/options.cpp:1198:45: warning: unused parameter 'val' [-Wunused-parameter] 1198 | void Runopts::opt_filter(const std::string& val) | ~~~~~~~~~~~~~~~~~~~^~~ +/build/reproducible-path/sortmerna-4.3.6/src/sortmerna/options.cpp: In member function 'void Runopts::process(int, char**, bool)': +/build/reproducible-path/sortmerna-4.3.6/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-4.3.6/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-4.3.6/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-4.3.6/src/sortmerna/index.cpp:257:82: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] + 257 | ((NodeElement *&)dst) += 4; + | ^~~ +[ 87%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/report.cpp.o +cd /build/reproducible-path/sortmerna-4.3.6/obj-x86_64-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.6/include -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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-4.3.6/src/sortmerna/report.cpp +/build/reproducible-path/sortmerna-4.3.6/src/sortmerna/kvdb.cpp: In member function 'int KeyValueDatabase::clear(std::string)': +/build/reproducible-path/sortmerna-4.3.6/src/sortmerna/kvdb.cpp:58:41: warning: unused parameter 'dbpath' [-Wunused-parameter] + 58 | int KeyValueDatabase::clear(std::string dbpath) + | ~~~~~~~~~~~~^~~~~~ +/build/reproducible-path/sortmerna-4.3.6/src/sortmerna/read.cpp: In member function 'void Read::unmarshallJson(KeyValueDatabase&)': +/build/reproducible-path/sortmerna-4.3.6/src/sortmerna/read.cpp:540:46: warning: unused parameter 'kvdb' [-Wunused-parameter] + 540 | void Read::unmarshallJson(KeyValueDatabase & kvdb) + | ~~~~~~~~~~~~~~~~~~~^~~~ +/build/reproducible-path/sortmerna-4.3.6/src/sortmerna/indexdb.cpp:916:14: warning: 'void {anonymous}::help()' defined but not used [-Wunused-function] + 916 | void help() + | ^~~~ +/build/reproducible-path/sortmerna-4.3.6/src/sortmerna/cmd.cpp: In member function 'void CmdSession::cmdIndex(Runopts&, std::string&)': +/build/reproducible-path/sortmerna-4.3.6/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-4.3.6/src/sortmerna/cmd.cpp: In member function 'void CmdSession::cmdTest(Runopts&, std::string&)': +/build/reproducible-path/sortmerna-4.3.6/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-4.3.6/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-4.3.6/src/sortmerna/paralleltraversal.cpp:47: /build/reproducible-path/sortmerna-4.3.6/include/ThreadPool.hpp: In member function 'void ThreadPool::threadEntry(int)': /build/reproducible-path/sortmerna-4.3.6/include/ThreadPool.hpp:92:38: warning: unused parameter 'i' [-Wunused-parameter] 92 | void threadEntry(int i) | ~~~~^ -/build/reproducible-path/sortmerna-4.3.6/src/sortmerna/options.cpp: In member function 'void Runopts::process(int, char**, bool)': -/build/reproducible-path/sortmerna-4.3.6/src/sortmerna/options.cpp:1368:50: warning: unused parameter 'dryrun' [-Wunused-parameter] - 1368 | void Runopts::process(int argc, char**argv, bool dryrun) - | ~~~~~^~~~~~ +[ 88%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/report_fx_base.cpp.o +cd /build/reproducible-path/sortmerna-4.3.6/obj-x86_64-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.6/include -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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-4.3.6/src/sortmerna/report_fx_base.cpp /build/reproducible-path/sortmerna-4.3.6/src/sortmerna/paralleltraversal.cpp: In function 'void traverse(Runopts&, Index&, References&, Readstats&, Refstats&, Read&, bool)': /build/reproducible-path/sortmerna-4.3.6/src/sortmerna/paralleltraversal.cpp:289:99: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] 289 | bool is_last_idx = (index.index_num == opts.indexfiles.size() - 1) && (index.part == refstats.num_index_parts[index.index_num] - 1); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 90%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/report_fastx.cpp.o +cd /build/reproducible-path/sortmerna-4.3.6/obj-x86_64-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.6/include -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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-4.3.6/src/sortmerna/report_fastx.cpp +/build/reproducible-path/sortmerna-4.3.6/src/sortmerna/report.cpp: In constructor 'Report::Report(Runopts&)': +/build/reproducible-path/sortmerna-4.3.6/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) {} + | ~~~~~~~~~^~~~ +In file included from /build/reproducible-path/sortmerna-4.3.6/include/kseq_load.hpp:40, + from /build/reproducible-path/sortmerna-4.3.6/src/sortmerna/readstats.cpp:52: +/build/reproducible-path/sortmerna-4.3.6/include/kseq.h:171:20: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function] + 171 | static int kseq_read(kseq_t *seq) \ + | ^~~~~~~~~ +/build/reproducible-path/sortmerna-4.3.6/include/kseq.h:221:9: note: in expansion of macro '__KSEQ_READ' + 221 | __KSEQ_READ + | ^~~~~~~~~~~ +/build/reproducible-path/sortmerna-4.3.6/include/kseq_load.hpp:43:1: note: in expansion of macro 'KSEQ_INIT' + 43 | KSEQ_INIT(gzFile, gzread) + | ^~~~~~~~~ In file included from /build/reproducible-path/sortmerna-4.3.6/src/sortmerna/paralleltraversal.cpp:41: /build/reproducible-path/sortmerna-4.3.6/include/kseq_load.hpp: At global scope: /build/reproducible-path/sortmerna-4.3.6/include/kseq.h:171:20: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function] @@ -948,6 +963,27 @@ /build/reproducible-path/sortmerna-4.3.6/include/kseq_load.hpp:43:1: note: in expansion of macro 'KSEQ_INIT' 43 | KSEQ_INIT(gzFile, gzread) | ^~~~~~~~~ +[ 91%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/report_fx_other.cpp.o +cd /build/reproducible-path/sortmerna-4.3.6/obj-x86_64-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.6/include -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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-4.3.6/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-4.3.6/obj-x86_64-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.6/include -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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-4.3.6/src/sortmerna/report_blast.cpp +[ 94%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/report_denovo.cpp.o +cd /build/reproducible-path/sortmerna-4.3.6/obj-x86_64-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.6/include -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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-4.3.6/src/sortmerna/report_denovo.cpp +[ 95%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/report_biom.cpp.o +cd /build/reproducible-path/sortmerna-4.3.6/obj-x86_64-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.6/include -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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-4.3.6/src/sortmerna/report_biom.cpp +/build/reproducible-path/sortmerna-4.3.6/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-4.3.6/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-4.3.6/src/sortmerna/report_biom.cpp: In member function 'virtual void ReportBiom::init(Readfeed&, Runopts&)': +/build/reproducible-path/sortmerna-4.3.6/src/sortmerna/report_biom.cpp:41:33: warning: unused parameter 'readfeed' [-Wunused-parameter] + 41 | void ReportBiom::init(Readfeed& readfeed, Runopts& opts) + | ~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/sortmerna-4.3.6/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-4.3.6/obj-x86_64-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.6/include -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/concurrentqueue 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/usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu/crtn.o GNU ld (GNU Binutils for Debian) 2.42 make[3]: Leaving directory '/build/reproducible-path/sortmerna-4.3.6/obj-x86_64-linux-gnu' [100%] Built target sortmerna @@ -973,7 +1009,7 @@ create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/sortmerna/ - cd obj-x86_64-linux-gnu && make -j42 install DESTDIR=/build/reproducible-path/sortmerna-4.3.6/debian/sortmerna AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd obj-x86_64-linux-gnu && make -j20 install DESTDIR=/build/reproducible-path/sortmerna-4.3.6/debian/sortmerna AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/sortmerna-4.3.6/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/sortmerna-4.3.6 -B/build/reproducible-path/sortmerna-4.3.6/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -991,8 +1027,8 @@ debian/rules execute_after_dh_install make[1]: Entering directory '/build/reproducible-path/sortmerna-4.3.6' find debian -name cmake -type d | xargs rm -rvf -removed 'debian/sortmerna/usr/cmake/sortmerna/sortmernaConfigVersion.cmake' removed 'debian/sortmerna/usr/cmake/sortmerna/sortmernaConfig.cmake' +removed 'debian/sortmerna/usr/cmake/sortmerna/sortmernaConfigVersion.cmake' removed directory 'debian/sortmerna/usr/cmake/sortmerna' removed directory 'debian/sortmerna/usr/cmake' make[1]: Leaving directory '/build/reproducible-path/sortmerna-4.3.6' @@ -1043,12 +1079,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/2021789/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2021789/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/1470472 and its subdirectories -I: Current time: Wed Jun 11 15:03:30 -12 2025 -I: pbuilder-time-stamp: 1749697410 +I: removing directory /srv/workspace/pbuilder/2021789 and its subdirectories +I: Current time: Fri May 10 10:43:26 +14 2024 +I: pbuilder-time-stamp: 1715287406