Diff of the two buildlogs: -- --- b1/build.log 2024-05-25 21:06:08.168858346 +0000 +++ b2/build.log 2024-05-25 21:07:13.230095789 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat May 25 09:03:06 -12 2024 -I: pbuilder-time-stamp: 1716670986 +I: Current time: Sat Jun 28 17:29:11 +14 2025 +I: pbuilder-time-stamp: 1751081351 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-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/3819639/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3014000/tmp/hooks/D01_modify_environment starting +debug: Running on ionos5-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 Jun 28 03:29 /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/3014000/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3014000/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=20 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="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=42 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='f6c3534f4ab34ca6ac2c534ded42b703' - 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='3819639' - PS1='# ' - PS2='> ' + INVOCATION_ID=bdaa8cbba48f4b22b5840782fee0be62 + 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=3014000 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.ybtGtdE3/pbuilderrc_vdPg --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ybtGtdE3/b1 --logfile b1/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+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://46.16.76.132:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.ybtGtdE3/pbuilderrc_r42B --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ybtGtdE3/b2 --logfile b2/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-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos11-amd64 6.1.0-21-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.7.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.7.12-1~bpo12+1 (2024-05-06) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 25 07:42 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/3819639/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Jun 27 14:06 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/3014000/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -193,7 +225,7 @@ Get: 63 http://deb.debian.org/debian unstable/main amd64 libzstd-dev amd64 1.5.5+dfsg2-2 [358 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 librocksdb-dev amd64 8.9.1-2 [4952 kB] Get: 65 http://deb.debian.org/debian unstable/main amd64 rapidjson-dev all 1.1.0+dfsg2-7.2 [97.8 kB] -Fetched 45.9 MB in 2s (26.1 MB/s) +Fetched 45.9 MB in 3s (18.2 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 ... 19718 files and directories currently installed.) @@ -468,7 +500,11 @@ 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/3014000/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/3014000/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 @@ -500,8 +536,8 @@ CMAKE_CXX_COMPILER_ID = GNU CMAKE_CONFIGURATION_TYPES = CMAKE_HOST_SYSTEM_NAME = Linux -CMAKE_HOST_SYSTEM_VERSION = 6.1.0-21-amd64 -CMAKE_HOST_SYSTEM = Linux-6.1.0-21-amd64 +CMAKE_HOST_SYSTEM_VERSION = 6.7.12+bpo-amd64 +CMAKE_HOST_SYSTEM = Linux-6.7.12+bpo-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 @@ -534,8 +570,8 @@ SMR Objects transitive link dependencies: alp;RocksDB::rocksdb-shared;ZLIB::ZLIB SMR Objects COMPILE_OPT: COMPILE_OPT-NOTFOUND COMPILE_FLG: COMPILE_FLG-NOTFOUND package_config_destination: /usr/cmake/sortmerna --- Configuring done (4.3s) --- Generating done (0.1s) +-- Configuring done (0.8s) +-- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: @@ -550,114 +586,114 @@ -- 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 -j20 "INSTALL=install --strip-program=true" VERBOSE=1 + cd obj-x86_64-linux-gnu && make -j42 "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 make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/sortmerna-4.3.6/obj-x86_64-linux-gnu' make -f CMakeFiles/build_version.dir/build.make CMakeFiles/build_version.dir/depend -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 -f 3rdparty/cmph/CMakeFiles/cmph.dir/build.make 3rdparty/cmph/CMakeFiles/cmph.dir/depend make -f 3rdparty/alp/CMakeFiles/alp.dir/build.make 3rdparty/alp/CMakeFiles/alp.dir/depend make[3]: Entering directory '/build/reproducible-path/sortmerna-4.3.6/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=" +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' 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 CMakeFiles/build_version.dir/build.make 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-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 -/build/reproducible-path/sortmerna-4.3.6/obj-x86_64-linux-gnu/build_version.cpp:4:44: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] - 4 | const char* sortmerna_build_compile_date = __DATE__; - | ^~~~~~~~ -[ 9%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/njn_dynprogprobproto.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 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/build/reproducible-path/sortmerna-4.3.6/3rdparty/alp/njn_localmaxstat.cpp -[ 15%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/bmz8.c.o +[ 16%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/chd_ph.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/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-4.3.6/3rdparty/alp/njn_dynprogprobproto.cpp +[ 16%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/compressed_rank.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/bmz8.c.o -MF CMakeFiles/cmph.dir/bmz8.c.o.d -o CMakeFiles/cmph.dir/bmz8.c.o -c /build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph/bmz8.c -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_localmaxstatmatrix.cpp.o -MF CMakeFiles/alp.dir/njn_localmaxstatmatrix.cpp.o.d -o CMakeFiles/alp.dir/njn_localmaxstatmatrix.cpp.o -c /build/reproducible-path/sortmerna-4.3.6/3rdparty/alp/njn_localmaxstatmatrix.cpp -[ 16%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/brz.c.o +[ 22%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/njn_dynprogprob.cpp.o +[ 22%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/njn_dynprogproblim.cpp.o +[ 22%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/compressed_seq.c.o +[ 22%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/chd.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/brz.c.o -MF CMakeFiles/cmph.dir/brz.c.o.d -o CMakeFiles/cmph.dir/brz.c.o -c /build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph/brz.c -[ 16%] Built target build_version -[ 18%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/njn_localmaxstatutil.cpp.o -[ 19%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/buffer_entry.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/njn_localmaxstatutil.cpp.o -MF CMakeFiles/alp.dir/njn_localmaxstatutil.cpp.o.d -o CMakeFiles/alp.dir/njn_localmaxstatutil.cpp.o -c /build/reproducible-path/sortmerna-4.3.6/3rdparty/alp/njn_localmaxstatutil.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/buffer_entry.c.o -MF CMakeFiles/cmph.dir/buffer_entry.c.o.d -o CMakeFiles/cmph.dir/buffer_entry.c.o -c /build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph/buffer_entry.c -[ 21%] 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/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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CMakeFiles/cmph.dir/chd.c.o -c /build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph/chd.c +[ 26%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/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 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 -[ 36%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/compressed_rank.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 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42%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/njn_localmaxstatmatrix.cpp.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/graph.c.o -MF CMakeFiles/cmph.dir/graph.c.o.d -o CMakeFiles/cmph.dir/graph.c.o -c /build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph/graph.c -[ 43%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/hash.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 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-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/hash.c.o -MF CMakeFiles/cmph.dir/hash.c.o.d -o CMakeFiles/cmph.dir/hash.c.o -c /build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph/hash.c -[ 45%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/jenkins_hash.c.o -[ 46%] 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 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CMakeFiles/cmph.dir/jenkins_hash.c.o -c /build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph/jenkins_hash.c -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 -[ 47%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/miller_rabin.c.o +[ 45%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/sls_alignment_evaluer.cpp.o +[ 40%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/njn_localmaxstatutil.cpp.o +[ 50%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/njn_localmaxstat.cpp.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/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 -[ 49%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/select.c.o +[ 50%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/sls_alp_regression.cpp.o +[ 52%] 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.cpp.o -MF CMakeFiles/alp.dir/sls_alp.cpp.o.d -o CMakeFiles/alp.dir/sls_alp.cpp.o -c /build/reproducible-path/sortmerna-4.3.6/3rdparty/alp/sls_alp.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/select.c.o -MF CMakeFiles/cmph.dir/select.c.o.d -o CMakeFiles/cmph.dir/select.c.o -c 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/build/reproducible-path/sortmerna-4.3.6/3rdparty/alp/sls_alignment_evaluer.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/sls_alp_data.cpp.o -MF CMakeFiles/alp.dir/sls_alp_data.cpp.o.d -o CMakeFiles/alp.dir/sls_alp_data.cpp.o -c /build/reproducible-path/sortmerna-4.3.6/3rdparty/alp/sls_alp_data.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/sls_alp_regression.cpp.o -MF CMakeFiles/alp.dir/sls_alp_regression.cpp.o.d -o CMakeFiles/alp.dir/sls_alp_regression.cpp.o -c /build/reproducible-path/sortmerna-4.3.6/3rdparty/alp/sls_alp_regression.cpp +/build/reproducible-path/sortmerna-4.3.6/obj-x86_64-linux-gnu/build_version.cpp:4:44: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] + 4 | const char* sortmerna_build_compile_date = __DATE__; + | ^~~~~~~~ +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 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 -[ 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 build_version +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' [ 54%] Built target alp @@ -667,48 +703,77 @@ 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' -[ 56%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/alignment.cpp.o -[ 57%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/bitvector.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 -[ 59%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/cmd.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/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/cmd.cpp.o -MF CMakeFiles/smr_objs.dir/cmd.cpp.o.d -o CMakeFiles/smr_objs.dir/cmd.cpp.o -c /build/reproducible-path/sortmerna-4.3.6/src/sortmerna/cmd.cpp [ 60%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/index.cpp.o -[ 61%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/izlib.cpp.o +[ 60%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/cmd.cpp.o +[ 60%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/izlib.cpp.o +[ 60%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/bitvector.cpp.o +[ 63%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/alignment.cpp.o +[ 63%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/indexdb.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/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/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 +[ 64%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/paralleltraversal.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 +[ 66%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/kseq_load.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/cmd.cpp.o -MF CMakeFiles/smr_objs.dir/cmd.cpp.o.d -o CMakeFiles/smr_objs.dir/cmd.cpp.o -c /build/reproducible-path/sortmerna-4.3.6/src/sortmerna/cmd.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 -[ 63%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/indexdb.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/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 -[ 64%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/kvdb.cpp.o -[ 66%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/kseq_load.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/kvdb.cpp.o -MF CMakeFiles/smr_objs.dir/kvdb.cpp.o.d -o CMakeFiles/smr_objs.dir/kvdb.cpp.o -c /build/reproducible-path/sortmerna-4.3.6/src/sortmerna/kvdb.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 +[ 67%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/kvdb.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/kseq_load.cpp.o -MF CMakeFiles/smr_objs.dir/kseq_load.cpp.o.d -o CMakeFiles/smr_objs.dir/kseq_load.cpp.o -c /build/reproducible-path/sortmerna-4.3.6/src/sortmerna/kseq_load.cpp -[ 67%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/options.cpp.o +[ 69%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/options.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/kvdb.cpp.o -MF CMakeFiles/smr_objs.dir/kvdb.cpp.o.d -o CMakeFiles/smr_objs.dir/kvdb.cpp.o -c /build/reproducible-path/sortmerna-4.3.6/src/sortmerna/kvdb.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/options.cpp.o -MF CMakeFiles/smr_objs.dir/options.cpp.o.d -o CMakeFiles/smr_objs.dir/options.cpp.o -c /build/reproducible-path/sortmerna-4.3.6/src/sortmerna/options.cpp -[ 69%] 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/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 -[ 70%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/paralleltraversal.cpp.o -[ 73%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/summary.cpp.o +[ 71%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/refstats.cpp.o +[ 71%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/output.cpp.o [ 73%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/processor.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/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/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/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 [ 74%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/readfeed.cpp.o -[ 76%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/references.cpp.o [ 77%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/readstats.cpp.o +[ 77%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/summary.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/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/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 [ 78%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/read.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/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 +[ 80%] 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/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 +[ 81%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/references.cpp.o +[ 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/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 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 +[ 84%] 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/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 +[ 87%] 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/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 +[ 87%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/util.cpp.o +[ 90%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/report_blast.cpp.o +[ 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/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 -[ 80%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/traverse_bursttrie.cpp.o -[ 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/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 -[ 83%] 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/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 +[ 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/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 -[ 84%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/util.cpp.o +[ 92%] 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/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/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 +[ 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/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_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.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 +[ 95%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/report_biom.cpp.o +[ 97%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/report_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 -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/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/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 */ + | ^ +/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/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) @@ -728,27 +793,24 @@ /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/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 */ - | ^ -/build/reproducible-path/sortmerna-4.3.6/src/sortmerna/izlib.cpp:244:17: note: here - 244 | case Z_DATA_ERROR: - | ^~~~ -[ 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/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) + | ~~~~~~~~~^~~~ /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) | ~~~~~~~~~~~~^~~~~~ -[ 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 -[ 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 -[ 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 -[ 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 +/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/indexdb.cpp:916:14: warning: 'void {anonymous}::help()' defined but not used [-Wunused-function] 916 | void help() | ^~~~ @@ -756,6 +818,17 @@ /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/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) + | ~~~~~~~~~~~~~~^~~ /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) @@ -804,6 +877,15 @@ /build/reproducible-path/sortmerna-4.3.6/src/sortmerna/options.cpp:484:42: warning: unused parameter 'val' [-Wunused-parameter] 484 | void Runopts::opt_sam(const std::string &val) | ~~~~~~~~~~~~~~~~~~~^~~ +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/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_no_best(const std::string&)': /build/reproducible-path/sortmerna-4.3.6/src/sortmerna/options.cpp:593:46: warning: unused parameter 'val' [-Wunused-parameter] 593 | void Runopts::opt_no_best(const std::string &val) @@ -859,12 +941,6 @@ /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) | ~~~~~~~~~~~~~~~~~~~^~~ -/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)) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ -[ 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 /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) @@ -877,33 +953,10 @@ /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/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/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/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); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 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 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] @@ -915,10 +968,6 @@ /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/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/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] @@ -930,19 +979,6 @@ /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) | ^~~~~~~~~ -[ 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 -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/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) - | ~~~~~~~~~^~~~ make[3]: Leaving directory '/build/reproducible-path/sortmerna-4.3.6/obj-x86_64-linux-gnu' [ 97%] Built target smr_objs make 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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 @@ -986,8 +1022,8 @@ 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/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-4.3.6' @@ -1038,12 +1074,14 @@ 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/3014000/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3014000/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/3819639 and its subdirectories -I: Current time: Sat May 25 09:06:07 -12 2024 -I: pbuilder-time-stamp: 1716671167 +I: removing directory /srv/workspace/pbuilder/3014000 and its subdirectories +I: Current time: Sat Jun 28 17:30:10 +14 2025 +I: pbuilder-time-stamp: 1751081410