Diff of the two buildlogs: -- --- b1/build.log 2025-03-23 12:19:34.486317503 +0000 +++ b2/build.log 2025-03-23 12:25:15.363028441 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Mar 23 00:18:14 -12 2025 -I: pbuilder-time-stamp: 1742732294 +I: Current time: Sun Apr 26 08:42:36 +14 2026 +I: pbuilder-time-stamp: 1777142556 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -22,51 +22,83 @@ dpkg-source: info: unpacking sideretro_1.1.6-2.debian.tar.xz I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/746214/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3938917/tmp/hooks/D01_modify_environment starting +debug: Running on infom02-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 Apr 25 18:43 /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/3938917/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3938917/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='amd64' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='f7f20429c1c94b28a137381be6708e26' - 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='746214' - PS1='# ' - PS2='> ' + INVOCATION_ID=5b19ab9cf308478a9f1fc1194bb38070 + 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=3938917 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.WHBspe8S/pbuilderrc_0rdP --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.WHBspe8S/b1 --logfile b1/build.log sideretro_1.1.6-2.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.WHBspe8S/pbuilderrc_HVTY --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.WHBspe8S/b2 --logfile b2/build.log sideretro_1.1.6-2.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' I: uname -a - Linux infom01-amd64 6.1.0-32-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.129-1 (2025-03-06) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.12-1~bpo12+1 (2025-02-23) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Mar 4 11:20 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/746214/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Mar 4 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/3938917/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -280,7 +312,7 @@ Get: 160 http://deb.debian.org/debian trixie/main amd64 python3-snowballstemmer all 2.2.0-4 [58.0 kB] Get: 161 http://deb.debian.org/debian trixie/main amd64 sphinx-common all 8.1.3-5 [617 kB] Get: 162 http://deb.debian.org/debian trixie/main amd64 python3-sphinx all 8.1.3-5 [468 kB] -Fetched 77.6 MB in 1s (117 MB/s) +Fetched 77.6 MB in 4s (20.1 MB/s) Preconfiguring packages ... Selecting previously unselected package libpython3.13-minimal:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19786 files and directories currently installed.) @@ -808,8 +840,8 @@ Setting up tzdata (2025a-2) ... Current default time zone: 'Etc/UTC' -Local time is now: Sun Mar 23 12:19:09 UTC 2025. -Universal Time is now: Sun Mar 23 12:19:09 UTC 2025. +Local time is now: Sat Apr 25 18:46:41 UTC 2026. +Universal Time is now: Sat Apr 25 18:46:41 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... @@ -965,7 +997,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/sideretro-1.1.6/ && 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 > ../sideretro_1.1.6-2_source.changes +I: user script /srv/workspace/pbuilder/3938917/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/3938917/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/sideretro-1.1.6/ && 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 > ../sideretro_1.1.6-2_source.changes dpkg-buildpackage: info: source package sideretro dpkg-buildpackage: info: source version 1.1.6-2 dpkg-buildpackage: info: source distribution unstable @@ -1022,69 +1058,69 @@ [1/70] /usr/bin/meson --internal vcstagger config.h.in config.h 1.1.6 /build/reproducible-path/sideretro-1.1.6 @version@ '(.*)' git describe --tags --dirty=+ [2/70] cc -Isrc/libsider.a.p -Isrc -I../src -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -MD -MQ src/libsider.a.p/chr.c.o -MF src/libsider.a.p/chr.c.o.d -o src/libsider.a.p/chr.c.o -c ../src/chr.c [3/70] cc -Isrc/libsider.a.p -Isrc -I../src -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -MD -MQ src/libsider.a.p/dbscan.c.o -MF src/libsider.a.p/dbscan.c.o.d -o src/libsider.a.p/dbscan.c.o -c ../src/dbscan.c -[4/70] cc -Isrc/libsider.a.p -Isrc -I../src -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -MD -MQ src/libsider.a.p/blacklist.c.o -MF src/libsider.a.p/blacklist.c.o.d -o src/libsider.a.p/blacklist.c.o -c ../src/blacklist.c -[5/70] cc -Isrc/libsider.a.p -Isrc -I../src -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -MD -MQ src/libsider.a.p/array.c.o -MF src/libsider.a.p/array.c.o.d -o src/libsider.a.p/array.c.o -c ../src/array.c +[4/70] cc -Isrc/libsider.a.p -Isrc -I../src -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -MD -MQ src/libsider.a.p/array.c.o -MF src/libsider.a.p/array.c.o.d -o src/libsider.a.p/array.c.o -c ../src/array.c +[5/70] cc -Isrc/libsider.a.p -Isrc -I../src -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -MD -MQ src/libsider.a.p/correlation.c.o -MF src/libsider.a.p/correlation.c.o.d -o src/libsider.a.p/correlation.c.o -c ../src/correlation.c [6/70] cc -Isrc/libsider.a.p -Isrc -I../src -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -MD -MQ src/libsider.a.p/bed.c.o -MF src/libsider.a.p/bed.c.o.d -o src/libsider.a.p/bed.c.o -c ../src/bed.c -[7/70] cc -Isrc/libsider.a.p -Isrc -I../src -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -MD -MQ src/libsider.a.p/bitree.c.o -MF src/libsider.a.p/bitree.c.o.d -o src/libsider.a.p/bitree.c.o -c ../src/bitree.c +[7/70] cc -Isrc/libsider.a.p -Isrc -I../src -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -MD -MQ src/libsider.a.p/blacklist.c.o -MF src/libsider.a.p/blacklist.c.o.d -o src/libsider.a.p/blacklist.c.o -c ../src/blacklist.c [8/70] cc -Isrc/libsider.a.p -Isrc -I../src -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -MD -MQ src/libsider.a.p/db_merge.c.o -MF src/libsider.a.p/db_merge.c.o.d -o src/libsider.a.p/db_merge.c.o -c ../src/db_merge.c -[9/70] cc -Isrc/libsider.a.p -Isrc -I../src -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -MD -MQ src/libsider.a.p/correlation.c.o -MF src/libsider.a.p/correlation.c.o.d -o src/libsider.a.p/correlation.c.o -c ../src/correlation.c -[10/70] cc -Isrc/libsider.a.p -Isrc -I../src -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -MD -MQ src/libsider.a.p/dedup.c.o -MF src/libsider.a.p/dedup.c.o.d -o src/libsider.a.p/dedup.c.o -c ../src/dedup.c -[11/70] cc -Isrc/libsider.a.p -Isrc -I../src -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -MD -MQ src/libsider.a.p/cluster.c.o -MF src/libsider.a.p/cluster.c.o.d -o src/libsider.a.p/cluster.c.o -c ../src/cluster.c +[9/70] cc -Isrc/libsider.a.p -Isrc -I../src -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -MD -MQ src/libsider.a.p/bitree.c.o -MF src/libsider.a.p/bitree.c.o.d -o src/libsider.a.p/bitree.c.o -c ../src/bitree.c +[10/70] cc -Isrc/libsider.a.p -Isrc -I../src -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -MD -MQ src/libsider.a.p/cluster.c.o -MF src/libsider.a.p/cluster.c.o.d -o src/libsider.a.p/cluster.c.o -c ../src/cluster.c +[11/70] cc -Isrc/libsider.a.p -Isrc -I../src -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -MD -MQ src/libsider.a.p/dedup.c.o -MF src/libsider.a.p/dedup.c.o.d -o src/libsider.a.p/dedup.c.o -c ../src/dedup.c [12/70] cc -Isrc/libsider.a.p -Isrc -I../src -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -MD -MQ src/libsider.a.p/exon.c.o -MF src/libsider.a.p/exon.c.o.d -o src/libsider.a.p/exon.c.o -c ../src/exon.c -[13/70] cc -Isrc/libsider.a.p -Isrc -I../src -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -MD -MQ src/libsider.a.p/fasta.c.o -MF src/libsider.a.p/fasta.c.o.d -o src/libsider.a.p/fasta.c.o -c ../src/fasta.c -[14/70] cc -Isrc/libsider.a.p -Isrc -I../src -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -MD -MQ src/libsider.a.p/gz.c.o -MF src/libsider.a.p/gz.c.o.d -o src/libsider.a.p/gz.c.o -c ../src/gz.c -[15/70] cc -Isrc/libsider.a.p -Isrc -I../src -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat 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-DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -MD -MQ src/libsider.a.p/str.c.o -MF src/libsider.a.p/str.c.o.d -o src/libsider.a.p/str.c.o -c ../src/str.c [31/70] cc -Isrc/libsider.a.p -Isrc -I../src -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -MD -MQ src/libsider.a.p/merge_call.c.o -MF src/libsider.a.p/merge_call.c.o.d -o src/libsider.a.p/merge_call.c.o -c ../src/merge_call.c -[32/70] cc -Isrc/sider.p -Isrc -I../src -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ src/sider.p/main.c.o -MF src/sider.p/main.c.o.d -o src/sider.p/main.c.o -c ../src/main.c -[33/70] cc -Isrc/libsider.a.p -Isrc -I../src -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -MD -MQ src/libsider.a.p/retrocopy.c.o -MF src/libsider.a.p/retrocopy.c.o.d -o src/libsider.a.p/retrocopy.c.o -c ../src/retrocopy.c -[34/70] cc -Isrc/libsider.a.p -Isrc -I../src -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -MD -MQ src/libsider.a.p/utils.c.o -MF src/libsider.a.p/utils.c.o.d -o src/libsider.a.p/utils.c.o -c ../src/utils.c -[35/70] cc -Isrc/libsider.a.p -Isrc -I../src -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -MD -MQ src/libsider.a.p/vcf.c.o -MF src/libsider.a.p/vcf.c.o.d -o src/libsider.a.p/vcf.c.o -c ../src/vcf.c -[36/70] cc -Isrc/libsider.a.p -Isrc -I../src -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -MD -MQ src/libsider.a.p/wrapper.c.o -MF src/libsider.a.p/wrapper.c.o.d -o src/libsider.a.p/wrapper.c.o -c ../src/wrapper.c -[37/70] rm -f src/libsider.a && gcc-ar csrDT src/libsider.a src/libsider.a.p/abnormal.c.o src/libsider.a.p/array.c.o src/libsider.a.p/bed.c.o src/libsider.a.p/bitree.c.o src/libsider.a.p/blacklist.c.o src/libsider.a.p/chr.c.o src/libsider.a.p/cluster.c.o src/libsider.a.p/correlation.c.o src/libsider.a.p/db.c.o src/libsider.a.p/db_merge.c.o src/libsider.a.p/dbscan.c.o src/libsider.a.p/dedup.c.o src/libsider.a.p/exon.c.o src/libsider.a.p/fasta.c.o src/libsider.a.p/genotype.c.o src/libsider.a.p/gff.c.o src/libsider.a.p/gz.c.o src/libsider.a.p/hash.c.o src/libsider.a.p/ibitree.c.o src/libsider.a.p/io.c.o src/libsider.a.p/list.c.o src/libsider.a.p/log.c.o src/libsider.a.p/logger.c.o src/libsider.a.p/make_vcf.c.o src/libsider.a.p/merge_call.c.o src/libsider.a.p/process_sample.c.o src/libsider.a.p/retrocopy.c.o src/libsider.a.p/sam.c.o src/libsider.a.p/set.c.o src/libsider.a.p/str.c.o src/libsider.a.p/thpool.c.o src/libsider.a.p/utils.c.o src/libsider.a.p/vcf.c.o src/libsider.a.p/wrapper.c.o -[38/70] cc -Itests/check_sider.p -Itests -I../tests -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -MD -MQ tests/check_sider.p/check_sider_bed.c.o -MF tests/check_sider.p/check_sider_bed.c.o.d -o tests/check_sider.p/check_sider_bed.c.o -c ../tests/check_sider_bed.c -[39/70] cc -Itests/check_sider.p -Itests -I../tests -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -MD -MQ tests/check_sider.p/check_sider_chr.c.o -MF tests/check_sider.p/check_sider_chr.c.o.d -o tests/check_sider.p/check_sider_chr.c.o -c ../tests/check_sider_chr.c +[32/70] cc -Isrc/libsider.a.p -Isrc -I../src -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -MD -MQ src/libsider.a.p/retrocopy.c.o -MF src/libsider.a.p/retrocopy.c.o.d -o src/libsider.a.p/retrocopy.c.o -c ../src/retrocopy.c +[33/70] cc -Isrc/libsider.a.p -Isrc -I../src -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -MD -MQ src/libsider.a.p/thpool.c.o -MF src/libsider.a.p/thpool.c.o.d -o src/libsider.a.p/thpool.c.o -c ../src/thpool.c +[34/70] cc -Isrc/libsider.a.p -Isrc -I../src -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -MD -MQ src/libsider.a.p/wrapper.c.o -MF src/libsider.a.p/wrapper.c.o.d -o src/libsider.a.p/wrapper.c.o -c ../src/wrapper.c +[35/70] cc -Itests/check_sider.p -Itests -I../tests -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -MD -MQ tests/check_sider.p/check_sider_bed.c.o -MF tests/check_sider.p/check_sider_bed.c.o.d -o tests/check_sider.p/check_sider_bed.c.o -c ../tests/check_sider_bed.c +[36/70] cc -Itests/check_sider.p -Itests -I../tests -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -MD -MQ tests/check_sider.p/check_sider_chr.c.o -MF tests/check_sider.p/check_sider_chr.c.o.d -o tests/check_sider.p/check_sider_chr.c.o -c ../tests/check_sider_chr.c +[37/70] cc -Isrc/libsider.a.p -Isrc -I../src -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -MD -MQ src/libsider.a.p/utils.c.o -MF src/libsider.a.p/utils.c.o.d -o src/libsider.a.p/utils.c.o -c ../src/utils.c +[38/70] cc -Itests/check_sider.p -Itests -I../tests -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -MD -MQ tests/check_sider.p/check_sider_bitree.c.o -MF tests/check_sider.p/check_sider_bitree.c.o.d -o tests/check_sider.p/check_sider_bitree.c.o -c ../tests/check_sider_bitree.c +[39/70] cc -Isrc/libsider.a.p -Isrc -I../src -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -MD -MQ src/libsider.a.p/vcf.c.o -MF src/libsider.a.p/vcf.c.o.d -o src/libsider.a.p/vcf.c.o -c ../src/vcf.c [40/70] cc -Itests/check_sider.p -Itests -I../tests -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -MD -MQ tests/check_sider.p/check_sider_abnormal.c.o -MF tests/check_sider.p/check_sider_abnormal.c.o.d -o tests/check_sider.p/check_sider_abnormal.c.o -c ../tests/check_sider_abnormal.c -[41/70] cc -Itests/check_sider.p -Itests -I../tests -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -MD -MQ tests/check_sider.p/check_sider_correlation.c.o -MF tests/check_sider.p/check_sider_correlation.c.o.d -o tests/check_sider.p/check_sider_correlation.c.o -c ../tests/check_sider_correlation.c -[42/70] cc -Itests/check_sider.p -Itests -I../tests -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -MD -MQ tests/check_sider.p/check_sider_bitree.c.o -MF tests/check_sider.p/check_sider_bitree.c.o.d -o tests/check_sider.p/check_sider_bitree.c.o -c ../tests/check_sider_bitree.c -[43/70] cc -Itests/check_sider.p -Itests -I../tests -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -MD -MQ tests/check_sider.p/check_sider_blacklist.c.o -MF tests/check_sider.p/check_sider_blacklist.c.o.d -o tests/check_sider.p/check_sider_blacklist.c.o -c ../tests/check_sider_blacklist.c -[44/70] cc -Itests/check_sider.p -Itests -I../tests -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -MD -MQ tests/check_sider.p/check_sider_cluster.c.o -MF tests/check_sider.p/check_sider_cluster.c.o.d -o tests/check_sider.p/check_sider_cluster.c.o -c ../tests/check_sider_cluster.c -[45/70] cc -Itests/check_sider.p -Itests -I../tests -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -MD -MQ tests/check_sider.p/check_sider_db_merge.c.o -MF tests/check_sider.p/check_sider_db_merge.c.o.d -o tests/check_sider.p/check_sider_db_merge.c.o -c ../tests/check_sider_db_merge.c -[46/70] cc -Itests/check_sider.p -Itests -I../tests -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -MD -MQ tests/check_sider.p/check_sider_dedup.c.o -MF tests/check_sider.p/check_sider_dedup.c.o.d -o tests/check_sider.p/check_sider_dedup.c.o -c ../tests/check_sider_dedup.c -[47/70] cc -Itests/check_sider.p -Itests -I../tests -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -MD -MQ tests/check_sider.p/check_sider_array.c.o -MF tests/check_sider.p/check_sider_array.c.o.d -o tests/check_sider.p/check_sider_array.c.o -c ../tests/check_sider_array.c -[48/70] cc -Itests/check_sider.p -Itests -I../tests -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -MD -MQ tests/check_sider.p/check_sider_db.c.o -MF tests/check_sider.p/check_sider_db.c.o.d -o tests/check_sider.p/check_sider_db.c.o -c ../tests/check_sider_db.c -[49/70] cc -Itests/check_sider.p -Itests -I../tests -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -MD -MQ tests/check_sider.p/check_sider_dbscan.c.o -MF tests/check_sider.p/check_sider_dbscan.c.o.d -o tests/check_sider.p/check_sider_dbscan.c.o -c ../tests/check_sider_dbscan.c +[41/70] cc -Itests/check_sider.p -Itests -I../tests -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -MD -MQ tests/check_sider.p/check_sider_cluster.c.o -MF tests/check_sider.p/check_sider_cluster.c.o.d -o tests/check_sider.p/check_sider_cluster.c.o -c ../tests/check_sider_cluster.c +[42/70] cc -Itests/check_sider.p -Itests -I../tests -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -MD -MQ tests/check_sider.p/check_sider_correlation.c.o -MF tests/check_sider.p/check_sider_correlation.c.o.d -o tests/check_sider.p/check_sider_correlation.c.o -c ../tests/check_sider_correlation.c +[43/70] rm -f src/libsider.a && gcc-ar csrDT src/libsider.a src/libsider.a.p/abnormal.c.o src/libsider.a.p/array.c.o src/libsider.a.p/bed.c.o src/libsider.a.p/bitree.c.o src/libsider.a.p/blacklist.c.o src/libsider.a.p/chr.c.o src/libsider.a.p/cluster.c.o src/libsider.a.p/correlation.c.o src/libsider.a.p/db.c.o src/libsider.a.p/db_merge.c.o src/libsider.a.p/dbscan.c.o src/libsider.a.p/dedup.c.o src/libsider.a.p/exon.c.o src/libsider.a.p/fasta.c.o src/libsider.a.p/genotype.c.o src/libsider.a.p/gff.c.o src/libsider.a.p/gz.c.o src/libsider.a.p/hash.c.o src/libsider.a.p/ibitree.c.o src/libsider.a.p/io.c.o src/libsider.a.p/list.c.o src/libsider.a.p/log.c.o src/libsider.a.p/logger.c.o src/libsider.a.p/make_vcf.c.o src/libsider.a.p/merge_call.c.o src/libsider.a.p/process_sample.c.o src/libsider.a.p/retrocopy.c.o src/libsider.a.p/sam.c.o src/libsider.a.p/set.c.o src/libsider.a.p/str.c.o src/libsider.a.p/thpool.c.o src/libsider.a.p/utils.c.o src/libsider.a.p/vcf.c.o src/libsider.a.p/wrapper.c.o +[44/70] cc -Itests/check_sider.p -Itests -I../tests -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -MD -MQ tests/check_sider.p/check_sider_dedup.c.o -MF tests/check_sider.p/check_sider_dedup.c.o.d -o tests/check_sider.p/check_sider_dedup.c.o -c ../tests/check_sider_dedup.c +[45/70] cc -Itests/check_sider.p -Itests -I../tests -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -MD -MQ tests/check_sider.p/check_sider_dbscan.c.o -MF tests/check_sider.p/check_sider_dbscan.c.o.d -o tests/check_sider.p/check_sider_dbscan.c.o -c ../tests/check_sider_dbscan.c +[46/70] cc -Itests/check_sider.p -Itests -I../tests -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -MD -MQ tests/check_sider.p/check_sider_array.c.o -MF tests/check_sider.p/check_sider_array.c.o.d -o tests/check_sider.p/check_sider_array.c.o -c ../tests/check_sider_array.c +[47/70] cc -Itests/check_sider.p -Itests -I../tests -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -MD -MQ tests/check_sider.p/check_sider_db_merge.c.o -MF tests/check_sider.p/check_sider_db_merge.c.o.d -o tests/check_sider.p/check_sider_db_merge.c.o -c ../tests/check_sider_db_merge.c +[48/70] cc -Itests/check_sider.p -Itests -I../tests -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -MD -MQ tests/check_sider.p/check_sider_blacklist.c.o -MF tests/check_sider.p/check_sider_blacklist.c.o.d -o tests/check_sider.p/check_sider_blacklist.c.o -c ../tests/check_sider_blacklist.c +[49/70] cc -Itests/check_sider.p -Itests -I../tests -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -MD -MQ tests/check_sider.p/check_sider_db.c.o -MF tests/check_sider.p/check_sider_db.c.o.d -o tests/check_sider.p/check_sider_db.c.o -c ../tests/check_sider_db.c [50/70] cc -Itests/check_sider.p -Itests -I../tests -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -MD -MQ tests/check_sider.p/check_sider_genotype.c.o -MF tests/check_sider.p/check_sider_genotype.c.o.d -o tests/check_sider.p/check_sider_genotype.c.o -c ../tests/check_sider_genotype.c [51/70] cc -Itests/check_sider.p -Itests -I../tests -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -MD -MQ tests/check_sider.p/check_sider_fasta.c.o -MF tests/check_sider.p/check_sider_fasta.c.o.d -o tests/check_sider.p/check_sider_fasta.c.o -c ../tests/check_sider_fasta.c -[52/70] cc -Itests/check_sider.p -Itests -I../tests -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -MD -MQ tests/check_sider.p/check_sider_process_sample.c.o -MF tests/check_sider.p/check_sider_process_sample.c.o.d -o tests/check_sider.p/check_sider_process_sample.c.o -c ../tests/check_sider_process_sample.c -[53/70] cc -Itests/check_sider.p -Itests -I../tests -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -MD -MQ tests/check_sider.p/check_sider_exon.c.o -MF tests/check_sider.p/check_sider_exon.c.o.d -o tests/check_sider.p/check_sider_exon.c.o -c ../tests/check_sider_exon.c -[54/70] cc -Itests/check_sider.p -Itests -I../tests -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -MD -MQ tests/check_sider.p/check_sider_io.c.o -MF tests/check_sider.p/check_sider_io.c.o.d -o tests/check_sider.p/check_sider_io.c.o -c ../tests/check_sider_io.c -[55/70] cc -Itests/check_sider.p -Itests -I../tests -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -MD -MQ tests/check_sider.p/check_sider_main.c.o -MF tests/check_sider.p/check_sider_main.c.o.d -o tests/check_sider.p/check_sider_main.c.o -c ../tests/check_sider_main.c -[56/70] cc -Itests/check_sider.p -Itests -I../tests -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -MD -MQ tests/check_sider.p/check_sider_retrocopy.c.o -MF tests/check_sider.p/check_sider_retrocopy.c.o.d -o tests/check_sider.p/check_sider_retrocopy.c.o -c ../tests/check_sider_retrocopy.c -[57/70] cc -Itests/check_sider.p -Itests -I../tests -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -MD -MQ tests/check_sider.p/check_sider_gz.c.o -MF tests/check_sider.p/check_sider_gz.c.o.d -o tests/check_sider.p/check_sider_gz.c.o -c ../tests/check_sider_gz.c +[52/70] cc -Itests/check_sider.p -Itests -I../tests -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -MD -MQ tests/check_sider.p/check_sider_exon.c.o -MF tests/check_sider.p/check_sider_exon.c.o.d -o tests/check_sider.p/check_sider_exon.c.o -c ../tests/check_sider_exon.c +[53/70] cc -Itests/check_sider.p -Itests -I../tests -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -MD -MQ tests/check_sider.p/check_sider_main.c.o -MF tests/check_sider.p/check_sider_main.c.o.d -o tests/check_sider.p/check_sider_main.c.o -c ../tests/check_sider_main.c +[54/70] cc -Itests/check_sider.p -Itests -I../tests -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -MD -MQ tests/check_sider.p/check_sider_gff.c.o -MF tests/check_sider.p/check_sider_gff.c.o.d -o tests/check_sider.p/check_sider_gff.c.o -c ../tests/check_sider_gff.c +[55/70] cc -Itests/check_sider.p -Itests -I../tests -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -MD -MQ tests/check_sider.p/check_sider_retrocopy.c.o -MF tests/check_sider.p/check_sider_retrocopy.c.o.d -o tests/check_sider.p/check_sider_retrocopy.c.o -c ../tests/check_sider_retrocopy.c +[56/70] cc -Itests/check_sider.p -Itests -I../tests -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -MD -MQ tests/check_sider.p/check_sider_process_sample.c.o -MF tests/check_sider.p/check_sider_process_sample.c.o.d -o tests/check_sider.p/check_sider_process_sample.c.o -c ../tests/check_sider_process_sample.c +[57/70] cc -Itests/check_sider.p -Itests -I../tests -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -MD -MQ tests/check_sider.p/check_sider_io.c.o -MF tests/check_sider.p/check_sider_io.c.o.d -o tests/check_sider.p/check_sider_io.c.o -c ../tests/check_sider_io.c [58/70] cc -Itests/check_sider.p -Itests -I../tests -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -MD -MQ tests/check_sider.p/check_sider_ibitree.c.o -MF tests/check_sider.p/check_sider_ibitree.c.o.d -o tests/check_sider.p/check_sider_ibitree.c.o -c ../tests/check_sider_ibitree.c -[59/70] cc -Itests/check_sider.p -Itests -I../tests -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -MD -MQ tests/check_sider.p/check_sider_gff.c.o -MF tests/check_sider.p/check_sider_gff.c.o.d -o tests/check_sider.p/check_sider_gff.c.o -c ../tests/check_sider_gff.c -[60/70] cc -Itests/check_sider.p -Itests -I../tests -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -MD -MQ tests/check_sider.p/check_sider_list.c.o -MF tests/check_sider.p/check_sider_list.c.o.d -o tests/check_sider.p/check_sider_list.c.o -c ../tests/check_sider_list.c -[61/70] cc -Itests/check_sider.p -Itests -I../tests -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -MD -MQ tests/check_sider.p/check_sider_sam.c.o -MF tests/check_sider.p/check_sider_sam.c.o.d -o tests/check_sider.p/check_sider_sam.c.o -c ../tests/check_sider_sam.c -[62/70] cc -o src/sider src/sider.p/main.c.o -Wl,--as-needed -Wl,--no-undefined -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group src/libsider.a -pthread /usr/lib/x86_64-linux-gnu/libsqlite3.so /usr/lib/x86_64-linux-gnu/libhts.so /usr/lib/x86_64-linux-gnu/libz.so -lm -ldl -Wl,--end-group -[63/70] cc -Itests/check_sider.p -Itests -I../tests -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -MD -MQ tests/check_sider.p/check_sider_vcf.c.o -MF tests/check_sider.p/check_sider_vcf.c.o.d -o tests/check_sider.p/check_sider_vcf.c.o -c ../tests/check_sider_vcf.c +[59/70] cc -Itests/check_sider.p -Itests -I../tests -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -MD -MQ tests/check_sider.p/check_sider_sam.c.o -MF tests/check_sider.p/check_sider_sam.c.o.d -o tests/check_sider.p/check_sider_sam.c.o -c ../tests/check_sider_sam.c +[60/70] cc -Itests/check_sider.p -Itests -I../tests -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -MD -MQ tests/check_sider.p/check_sider_gz.c.o -MF tests/check_sider.p/check_sider_gz.c.o.d -o tests/check_sider.p/check_sider_gz.c.o -c ../tests/check_sider_gz.c +[61/70] cc -o src/sider src/sider.p/main.c.o -Wl,--as-needed -Wl,--no-undefined -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group src/libsider.a -pthread /usr/lib/x86_64-linux-gnu/libsqlite3.so /usr/lib/x86_64-linux-gnu/libhts.so /usr/lib/x86_64-linux-gnu/libz.so -lm -ldl -Wl,--end-group +[62/70] cc -Itests/check_sider.p -Itests -I../tests -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -MD -MQ tests/check_sider.p/check_sider_vcf.c.o -MF tests/check_sider.p/check_sider_vcf.c.o.d -o tests/check_sider.p/check_sider_vcf.c.o -c ../tests/check_sider_vcf.c +[63/70] cc -Itests/check_sider.p -Itests -I../tests -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -MD -MQ tests/check_sider.p/check_sider_list.c.o -MF tests/check_sider.p/check_sider_list.c.o.d -o tests/check_sider.p/check_sider_list.c.o -c ../tests/check_sider_list.c [64/70] cc -Itests/check_sider.p -Itests -I../tests -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -MD -MQ tests/check_sider.p/check_sider_str.c.o -MF tests/check_sider.p/check_sider_str.c.o.d -o tests/check_sider.p/check_sider_str.c.o -c ../tests/check_sider_str.c -[65/70] cc -Itests/check_sider.p -Itests -I../tests -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -MD -MQ tests/check_sider.p/check_sider_hash.c.o -MF tests/check_sider.p/check_sider_hash.c.o.d -o tests/check_sider.p/check_sider_hash.c.o -c ../tests/check_sider_hash.c -[66/70] cc -Itests/check_sider.p -Itests -I../tests -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -MD -MQ tests/check_sider.p/check_sider_set.c.o -MF tests/check_sider.p/check_sider_set.c.o.d -o tests/check_sider.p/check_sider_set.c.o -c ../tests/check_sider_set.c +[65/70] cc -Itests/check_sider.p -Itests -I../tests -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -MD -MQ tests/check_sider.p/check_sider_set.c.o -MF tests/check_sider.p/check_sider_set.c.o.d -o tests/check_sider.p/check_sider_set.c.o -c ../tests/check_sider_set.c +[66/70] cc -Itests/check_sider.p -Itests -I../tests -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -MD -MQ tests/check_sider.p/check_sider_hash.c.o -MF tests/check_sider.p/check_sider_hash.c.o.d -o tests/check_sider.p/check_sider_hash.c.o -c ../tests/check_sider_hash.c [67/70] cc -Itests/check_sider.p -Itests -I../tests -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -MD -MQ tests/check_sider.p/check_sider_wrapper.c.o -MF tests/check_sider.p/check_sider_wrapper.c.o.d -o tests/check_sider.p/check_sider_wrapper.c.o -c ../tests/check_sider_wrapper.c ../tests/check_sider_wrapper.c: In function ‘test_xfprintf_fn’: ../tests/check_sider_wrapper.c:281:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] @@ -1131,7 +1167,7 @@ ninja: Entering directory `/build/reproducible-path/sideretro-1.1.6/obj-x86_64-linux-gnu' [1/65] Generating config.h with a custom command 1/1 all RUNNING ->>> MALLOC_PERTURB_=230 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MESON_TEST_ITERATION=1 /build/reproducible-path/sideretro-1.1.6/obj-x86_64-linux-gnu/tests/check_sider +>>> UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MALLOC_PERTURB_=137 MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 MESON_TEST_ITERATION=1 /build/reproducible-path/sideretro-1.1.6/obj-x86_64-linux-gnu/tests/check_sider ――――――――――――――――――――――――――――――――――――― ✀ ――――――――――――――――――――――――――――――――――――― Running suite(s): ProcessSample ok 1 - ../tests/check_sider_process_sample.c:Core:test_sider: Passed @@ -1286,7 +1322,7 @@ ok 133 - ../tests/check_sider_wrapper.c:Abort:test_xpopen_w_abort: Passed DBMerge ok 134 - ../tests/check_sider_db_merge.c:Core:test_db_merge: Passed -ok 135 - ../tests/check_sider_db_merge.c:Core:test_db_merge_in_line: Passed +not ok 135 - ../tests/check_sider_db_merge.c:Core:test_db_merge_in_line: Test timeout expired Set ok 136 - ../tests/check_sider_set.c:Core:test_set_free: Passed ok 137 - ../tests/check_sider_set.c:Core:test_set_insert: Passed @@ -1320,88 +1356,263 @@ ok 163 - ../tests/check_sider_bed.c:Abort:test_chrom_end_fatal: Passed ok 164 - ../tests/check_sider_bed.c:Abort:test_close_fatal: Passed Blacklist -ok 165 - ../tests/check_sider_blacklist.c:Core:test_blacklist_index_dump_from_gff: Passed -ok 166 - ../tests/check_sider_blacklist.c:Core:test_blacklist_index_dump_from_bed: Passed +not ok 165 - ../tests/check_sider_blacklist.c:Core:test_blacklist_index_dump_from_gff: Test timeout expired +not ok 166 - ../tests/check_sider_blacklist.c:Core:test_blacklist_index_dump_from_bed: Test timeout expired ok 167 - ../tests/check_sider_blacklist.c:Core:test_blacklist_lookup: Passed Retrocopy ok 168 - ../tests/check_sider_retrocopy.c:Core:test_retrocopy: Passed Dedup -ok 169 - ../tests/check_sider_dedup.c:Core:test_dedup: Passed - Genotype -[E::idx_find_and_load] Could not retrieve index file for '/tmp/ponga_unsorted.bam.VfFxTl' -ok 170 - ../tests/check_sider_genotype.c:Core:test_genotype: Passed - FASTA -ok 171 - ../tests/check_sider_fasta.c:Core:test_fasta_read: Passed -ok 172 - ../tests/check_sider_fasta.c:Core:test_empty_file: Passed -ok 173 - ../tests/check_sider_fasta.c:Abort:test_open_fatal: Passed -ok 174 - ../tests/check_sider_fasta.c:Abort:test_contig_fatal: Passed -ok 175 - ../tests/check_sider_fasta.c:Abort:test_seq1_fatal: Passed -ok 176 - ../tests/check_sider_fasta.c:Abort:test_seq2_fatal: Passed -ok 177 - ../tests/check_sider_fasta.c:Abort:test_close_fatal: Passed - VCF -ok 178 - ../tests/check_sider_vcf.c:Core:test_vcf: Passed - GZ -ok 179 - ../tests/check_sider_gz.c:Core:test_read1: Passed -ok 180 - ../tests/check_sider_gz.c:Core:test_read2: Passed -ok 181 - ../tests/check_sider_gz.c:Core:test_read_long_line: Passed -ok 182 - ../tests/check_sider_gz.c:Abort:test_open_fatal: Passed -ok 183 - ../tests/check_sider_gz.c:Abort:test_close_fatal: Passed -ok 184 - ../tests/check_sider_gz.c:Abort:test_read_fatal1: Passed -ok 185 - ../tests/check_sider_gz.c:Abort:test_read_fatal2: Passed -100%: Checks: 185, Failures: 0, Errors: 0 -1..185 +all time out (After 30 seconds) ―――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――― -1/1 all OK 6.86s +1/1 all TIMEOUT 30.02s killed by signal 15 SIGTERM -Ok: 1 +Summary of Failures: + +1/1 all TIMEOUT 30.02s killed by signal 15 SIGTERM + +Ok: 0 Expected Fail: 0 Fail: 0 Unexpected Pass: 0 Skipped: 0 -Timeout: 0 +Timeout: 1 Full log written to /build/reproducible-path/sideretro-1.1.6/obj-x86_64-linux-gnu/meson-logs/testlog.txt - create-stamp debian/debhelper-build-stamp - dh_prep - dh_auto_install --destdir=debian/sideretro/ - cd obj-x86_64-linux-gnu && DESTDIR=/build/reproducible-path/sideretro-1.1.6/debian/sideretro LC_ALL=C.UTF-8 ninja install -[1/68] Generating config.h with a custom command -[1/2] Installing files -Installing src/sider to /build/reproducible-path/sideretro-1.1.6/debian/sideretro/usr/bin -Installing docs/sider.1 to /build/reproducible-path/sideretro-1.1.6/debian/sideretro/usr/share/man/man1 - dh_installdocs - dh_installchangelogs - dh_installman - dh_perl - dh_link - dh_strip_nondeterminism - dh_compress - dh_fixperms - dh_missing - dh_dwz -a - dh_strip -a - dh_makeshlibs -a - dh_shlibdeps -a - dh_installdeb - dh_gencontrol - dh_md5sums - dh_builddeb -dpkg-deb: building package 'sideretro-dbgsym' in '../sideretro-dbgsym_1.1.6-2_amd64.deb'. -dpkg-deb: building package 'sideretro' in '../sideretro_1.1.6-2_amd64.deb'. - dpkg-genbuildinfo --build=binary -O../sideretro_1.1.6-2_amd64.buildinfo - dpkg-genchanges --build=binary -O../sideretro_1.1.6-2_amd64.changes -dpkg-genchanges: info: binary-only upload (no source code included) - dpkg-source --after-build . -dpkg-buildpackage: info: binary-only upload (no source included) -dpkg-genchanges: info: not including original source code in upload + cd obj-x86_64-linux-gnu && tail -v -n \+0 meson-logs/testlog.txt +==> meson-logs/testlog.txt <== +Log of Meson test suite run on 2026-04-26T08:47:41.587435 + +Inherited environment: DEB_HOST_MULTIARCH=x86_64-linux-gnu LC_ALL=C.UTF-8 DEB_HOST_GNU_SYSTEM=linux-gnu DEB_BUILD_GNU_TYPE=x86_64-linux-gnu DEB_TARGET_ARCH_LIBC=gnu SUDO_UID=104 DEB_BUILD_ARCH_ENDIAN=little DEB_BUILD_GNU_SYSTEM=linux-gnu DEB_BUILD_ARCH_BITS=64 DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DEB_HOST_ARCH=amd64 DEB_TARGET_ARCH_ENDIAN=little PWD=/build/reproducible-path/sideretro-1.1.6 SOURCE_DATE_EPOCH=1742233420 MAIL=/var/mail/root OLDPWD=/ PBUILDER_PKGDATADIR=/usr/share/pbuilder DEB_HOST_ARCH_BITS=64 LANG=C MAKEFLAGS='' DEB_TARGET_ARCH=amd64 DEB_HOST_GNU_CPU=x86_64 DEB_BUILD_ARCH_LIBC=gnu BUILDUSERNAME=pbuilder2 MFLAGS='' DEB_TARGET_ARCH_BITS=64 DEB_BUILD_ARCH_CPU=amd64 LD_PRELOAD='' DEB_HOST_ARCH_OS=linux SHLVL=3 DEB_HOST_ARCH_CPU=amd64 MAKELEVEL=1 PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build DEB_BUILD_ARCH_ABI=base LANGUAGE=et_EE:et PBUILDER_SYSCONFDIR=/etc DEB_BUILD_ARCH=amd64 DEB_HOST_ARCH_LIBC=gnu TZ=/usr/share/zoneinfo/Etc/GMT-14 INVOCATION_ID=ebf02bff11d14b6ab8532555d407ba1c SUDO_GID=109 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.WHBspe8S/pbuilderrc_HVTY --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.WHBspe8S/b2 --logfile b2/build.log sideretro_1.1.6-2.dsc' DEB_TARGET_ARCH_CPU=amd64 DEB_HOST_GNU_TYPE=x86_64-linux-gnu DEB_BUILD_ARCH_OS=linux LOGNAME=pbuilder2 BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' DEB_TARGET_MULTIARCH=x86_64-linux-gnu DEB_BUILD_GNU_CPU=x86_64 DEB_TARGET_ARCH_OS=linux USER=pbuilder2 DEB_HOST_ARCH_ABI=base DEB_BUILD_MULTIARCH=x86_64-linux-gnu DEB_TARGET_GNU_TYPE=x86_64-linux-gnu DEB_TARGET_ARCH_ABI=base _=/usr/bin/env SUDO_USER=jenkins PBUILDER_PKGLIBDIR=/usr/lib/pbuilder DEB_TARGET_GNU_CPU=x86_64 DEBIAN_FRONTEND=noninteractive HOME=/build/reproducible-path/sideretro-1.1.6/debian/.debhelper/generated/_source/home DEB_RULES_REQUIRES_ROOT=no DEB_TARGET_GNU_SYSTEM=linux-gnu DEB_HOST_ARCH_ENDIAN=little TERM=unknown DEB_BUILD_MAINT_OPTIONS=hardening=+all PBUILDER_OPERATION=build SHELL=/bin/bash DH_INTERNAL_BUILDFLAGS=1 ASFLAGS='' ASFLAGS_FOR_BUILD='' CFLAGS='-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection' CFLAGS_FOR_BUILD='-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection' CPPFLAGS='-Wdate-time -D_FORTIFY_SOURCE=2' CPPFLAGS_FOR_BUILD='-Wdate-time -D_FORTIFY_SOURCE=2' CXXFLAGS='-g -O2 -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection' CXXFLAGS_FOR_BUILD='-g -O2 -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection' DFLAGS=-frelease DFLAGS_FOR_BUILD=-frelease FCFLAGS='-g -O2 -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -fcf-protection' FCFLAGS_FOR_BUILD='-g -O2 -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -fcf-protection' FFLAGS='-g -O2 -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -fcf-protection' FFLAGS_FOR_BUILD='-g -O2 -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -fcf-protection' LDFLAGS='-Wl,-z,relro -Wl,-z,now' LDFLAGS_FOR_BUILD='-Wl,-z,relro -Wl,-z,now' OBJCFLAGS='-g -O2 -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection' OBJCFLAGS_FOR_BUILD='-g -O2 -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection' OBJCXXFLAGS='-g -O2 -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection' OBJCXXFLAGS_FOR_BUILD='-g -O2 -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection' XDG_RUNTIME_DIR=/tmp/dh-xdg-rundir-U3JIqqma MESON_TESTTHREADS=12 DEB_PYTHON_INSTALL_LAYOUT=deb + +==================================== 1/1 ===================================== +test: all +start time: 18:47:41 +duration: 30.02s +result: killed by signal 15 SIGTERM +command: UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MALLOC_PERTURB_=137 MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 MESON_TEST_ITERATION=1 /build/reproducible-path/sideretro-1.1.6/obj-x86_64-linux-gnu/tests/check_sider +----------------------------------- stdout ----------------------------------- +Running suite(s): ProcessSample +ok 1 - ../tests/check_sider_process_sample.c:Core:test_sider: Passed + List +ok 2 - ../tests/check_sider_list.c:Core:test_list_new: Passed +ok 3 - ../tests/check_sider_list.c:Core:test_list_ins_prev: Passed +ok 4 - ../tests/check_sider_list.c:Core:test_list_ins_next: Passed +ok 5 - ../tests/check_sider_list.c:Core:test_list_ins_prev_link: Passed +ok 6 - ../tests/check_sider_list.c:Core:test_list_ins_next_link: Passed +ok 7 - ../tests/check_sider_list.c:Core:test_list_remove: Passed +ok 8 - ../tests/check_sider_list.c:Core:test_list_remove_link: Passed +ok 9 - ../tests/check_sider_list.c:Core:test_list_foreach: Passed + Hash +ok 10 - ../tests/check_sider_hash.c:Core:test_hash_free: Passed +ok 11 - ../tests/check_sider_hash.c:Core:test_hash_insert: Passed +ok 12 - ../tests/check_sider_hash.c:Core:test_hash_lookup: Passed +ok 13 - ../tests/check_sider_hash.c:Core:test_hash_replace: Passed +ok 14 - ../tests/check_sider_hash.c:Core:test_hash_remove: Passed +ok 15 - ../tests/check_sider_hash.c:Core:test_hash_contains: Passed +ok 16 - ../tests/check_sider_hash.c:Core:test_hash_int: Passed +ok 17 - ../tests/check_sider_hash.c:Core:test_hash_direct: Passed +ok 18 - ../tests/check_sider_hash.c:Core:test_hash_many_insertions: Passed +ok 19 - ../tests/check_sider_hash.c:Misc:test_hash_foreach: Passed +ok 20 - ../tests/check_sider_hash.c:Misc:test_hash_iter: Passed +ok 21 - ../tests/check_sider_hash.c:Misc:test_hash_get_keys_as_list: Passed +ok 22 - ../tests/check_sider_hash.c:Misc:test_hash_get_values_as_list: Passed +ok 23 - ../tests/check_sider_hash.c:Misc:test_hash_get_keys_as_array: Passed +ok 24 - ../tests/check_sider_hash.c:Misc:test_hash_get_values_as_array: Passed + Array +ok 25 - ../tests/check_sider_array.c:CoreFree:test_array: Passed +ok 26 - ../tests/check_sider_array.c:CoreFree:test_array_uniq: Passed +ok 27 - ../tests/check_sider_array.c:CoreFree:test_array_find_with_equal_fun: Passed +ok 28 - ../tests/check_sider_array.c:CoreNull:test_array_find: Passed +ok 29 - ../tests/check_sider_array.c:CoreNull:test_array_remove: Passed +ok 30 - ../tests/check_sider_array.c:CoreNull:test_array_remove_index: Passed +ok 31 - ../tests/check_sider_array.c:Free:test_array_no_free_segment: Passed + Utils +ok 32 - ../tests/check_sider_utils.c:Core:test_fequal: Passed +ok 33 - ../tests/check_sider_utils.c:Core:test_equalstring: Passed +ok 34 - ../tests/check_sider_utils.c:Core:test_casequalstring: Passed +ok 35 - ../tests/check_sider_utils.c:Core:test_cmpstringp: Passed +ok 36 - ../tests/check_sider_utils.c:Core:test_casecmpstringp: Passed +ok 37 - ../tests/check_sider_utils.c:Core:test_chomp: Passed +ok 38 - ../tests/check_sider_utils.c:Core:test_trimc: Passed +ok 39 - ../tests/check_sider_utils.c:Core:test_trim: Passed +ok 40 - ../tests/check_sider_utils.c:Core:test_upper: Passed +ok 41 - ../tests/check_sider_utils.c:Core:test_lower: Passed +ok 42 - ../tests/check_sider_utils.c:Core:test_path_dir: Passed +ok 43 - ../tests/check_sider_utils.c:Core:test_path_file: Passed +ok 44 - ../tests/check_sider_utils.c:Core:test_which: Passed +ok 45 - ../tests/check_sider_utils.c:Core:test_exists: Passed +ok 46 - ../tests/check_sider_utils.c:Core:test_xstrdup_concat: Passed +ok 47 - ../tests/check_sider_utils.c:Core:test_xasprintf_concat: Passed +ok 48 - ../tests/check_sider_utils.c:Core:test_mkdir_p: Passed +ok 49 - ../tests/check_sider_utils.c:Core:test_setup_signal: Passed +ok 50 - ../tests/check_sider_utils.c:Core:test_buf_expand: Passed +ok 51 - ../tests/check_sider_utils.c:Core:test_entry_size: Passed + SAM +ok 52 - ../tests/check_sider_sam.c:Core:test_sam_to_bam: Passed +ok 53 - ../tests/check_sider_sam.c:Core:test_sam_to_bam_fp: Passed +ok 54 - ../tests/check_sider_sam.c:Core:test_sam_test_sorted_order: Passed + BiTree +ok 55 - ../tests/check_sider_bitree.c:Core:test_bitree: Passed + IBiTree +ok 56 - ../tests/check_sider_ibitree.c:Core:test_ibitree_insert: Passed +ok 57 - ../tests/check_sider_ibitree.c:Core:test_ibitree_lookup: Passed +ok 58 - ../tests/check_sider_ibitree.c:Core:test_ibitree_lookup_frac: Passed +ok 59 - ../tests/check_sider_ibitree.c:Core:test_ibitree_lookup_either: Passed + String +ok 60 - ../tests/check_sider_str.c:Core:test_string_new: Passed +ok 61 - ../tests/check_sider_str.c:Core:test_string_sized_new: Passed +ok 62 - ../tests/check_sider_str.c:Core:test_string_set: Passed +ok 63 - ../tests/check_sider_str.c:Core:test_string_concat: Passed +ok 64 - ../tests/check_sider_str.c:Core:test_string_printf: Passed +ok 65 - ../tests/check_sider_str.c:Core:test_string_concat_printf: Passed +ok 66 - ../tests/check_sider_str.c:Core:test_string_free: Passed +ok 67 - ../tests/check_sider_str.c:Core:test_string_clear: Passed + DB +ok 68 - ../tests/check_sider_db.c:Core:test_db_open: Passed +ok 69 - ../tests/check_sider_db.c:Core:test_db_exec: Passed +ok 70 - ../tests/check_sider_db.c:Core:test_db_prepare: Passed +ok 71 - ../tests/check_sider_db.c:Core:test_db_schema: Passed +ok 72 - ../tests/check_sider_db.c:Abort:test_db_open_abort: Passed +ok 73 - ../tests/check_sider_db.c:Abort:test_db_close_abort: Passed +ok 74 - ../tests/check_sider_db.c:Abort:test_db_exec_abort: Passed +ok 75 - ../tests/check_sider_db.c:Abort:test_db_prepare_abort: Passed +ok 76 - ../tests/check_sider_db.c:Abort:test_db_step_abort: Passed +ok 77 - ../tests/check_sider_db.c:Abort:test_db_reset_abort: Passed +ok 78 - ../tests/check_sider_db.c:Abort:test_db_bind_int_abort: Passed +ok 79 - ../tests/check_sider_db.c:Abort:test_db_bind_int64_abort: Passed +ok 80 - ../tests/check_sider_db.c:Abort:test_db_bind_double_abort: Passed +ok 81 - ../tests/check_sider_db.c:Abort:test_db_bind_text_abort: Passed +ok 82 - ../tests/check_sider_db.c:Abort:test_db_column_int_abort: Passed +ok 83 - ../tests/check_sider_db.c:Abort:test_db_column_int64_abort: Passed +ok 84 - ../tests/check_sider_db.c:Abort:test_db_column_double_abort: Passed +ok 85 - ../tests/check_sider_db.c:Abort:test_db_column_text_abort: Passed + Chr +ok 86 - ../tests/check_sider_chr.c:Core:test_chr_std_lookup: Passed + Exon +ok 87 - ../tests/check_sider_exon.c:Core:test_exon_tree_index_dump: Passed +ok 88 - ../tests/check_sider_exon.c:Core:test_exon_tree_lookup_dump: Passed + Abnormal +ok 89 - ../tests/check_sider_abnormal.c:Core:test_abnormal_filter_sorted: Passed +ok 90 - ../tests/check_sider_abnormal.c:Core:test_abnormal_filter_unsorted: Passed + GFF +ok 91 - ../tests/check_sider_gff.c:Core:test_gff_header: Passed +ok 92 - ../tests/check_sider_gff.c:Core:test_gff_read: Passed +ok 93 - ../tests/check_sider_gff.c:Core:test_gff_filter: Passed +ok 94 - ../tests/check_sider_gff.c:Core:test_gff_looks_like_gff_file: Passed +ok 95 - ../tests/check_sider_gff.c:Abort:test_open_fatal: Passed +ok 96 - ../tests/check_sider_gff.c:Abort:test_seqname_fatal: Passed +ok 97 - ../tests/check_sider_gff.c:Abort:test_source_fatal: Passed +ok 98 - ../tests/check_sider_gff.c:Abort:test_feature_fatal: Passed +ok 99 - ../tests/check_sider_gff.c:Abort:test_start_fatal: Passed +ok 100 - ../tests/check_sider_gff.c:Abort:test_end_fatal: Passed +ok 101 - ../tests/check_sider_gff.c:Abort:test_score_fatal: Passed +ok 102 - ../tests/check_sider_gff.c:Abort:test_strand_fatal: Passed +ok 103 - ../tests/check_sider_gff.c:Abort:test_frame_fatal: Passed +ok 104 - ../tests/check_sider_gff.c:Abort:test_key_value_fatal: Passed +ok 105 - ../tests/check_sider_gff.c:Abort:test_close_fatal: Passed + IO +ok 106 - ../tests/check_sider_io.c:Core:test_read_file_lines: Passed + DBSCAN +ok 107 - ../tests/check_sider_dbscan.c:Core:test_dbscan: Passed + Cluster +ok 108 - ../tests/check_sider_cluster.c:Core:test_cluster_without_genotype_support: Passed +ok 109 - ../tests/check_sider_cluster.c:Core:test_cluster_with_genotype_support: Passed + Wrapper +ok 110 - ../tests/check_sider_wrapper.c:Core:test_xmalloc: Passed +ok 111 - ../tests/check_sider_wrapper.c:Core:test_xcalloc: Passed +ok 112 - ../tests/check_sider_wrapper.c:Core:test_xrealloc: Passed +ok 113 - ../tests/check_sider_wrapper.c:Core:test_xstrdup: Passed +ok 114 - ../tests/check_sider_wrapper.c:Core:test_xfree: Passed +ok 115 - ../tests/check_sider_wrapper.c:Core:test_xfopen: Passed +ok 116 - ../tests/check_sider_wrapper.c:Core:test_xfdopen: Passed +ok 117 - ../tests/check_sider_wrapper.c:Core:test_xfclose: Passed +ok 118 - ../tests/check_sider_wrapper.c:Core:test_xfflush: Passed +ok 119 - ../tests/check_sider_wrapper.c:Core:test_xpopen: Passed +ok 120 - ../tests/check_sider_wrapper.c:Core:test_xmkdir: Passed +ok 121 - ../tests/check_sider_wrapper.c:Core:test_xasprintf: Passed +ok 122 - ../tests/check_sider_wrapper.c:Core:test_xfprintf: Passed +ok 123 - ../tests/check_sider_wrapper.c:Core:test_xsigaction: Passed +ok 124 - ../tests/check_sider_wrapper.c:Abort:test_xfopen_rw_abort: Passed +ok 125 - ../tests/check_sider_wrapper.c:Abort:test_xfopen_w_abort: Passed +ok 126 - ../tests/check_sider_wrapper.c:Abort:test_xfopen_r_abort: Passed +ok 127 - ../tests/check_sider_wrapper.c:Abort:test_xfdopen_rw_abort: Passed +ok 128 - ../tests/check_sider_wrapper.c:Abort:test_xfdopen_w_abort: Passed +ok 129 - ../tests/check_sider_wrapper.c:Abort:test_xfdopen_r_abort: Passed +ok 130 - ../tests/check_sider_wrapper.c:Abort:test_xmkdir_abort: Passed +ok 131 - ../tests/check_sider_wrapper.c:Abort:test_xsigaction_abort: Passed +ok 132 - ../tests/check_sider_wrapper.c:Abort:test_xpopen_r_abort: Passed +ok 133 - ../tests/check_sider_wrapper.c:Abort:test_xpopen_w_abort: Passed + DBMerge +ok 134 - ../tests/check_sider_db_merge.c:Core:test_db_merge: Passed +not ok 135 - ../tests/check_sider_db_merge.c:Core:test_db_merge_in_line: Test timeout expired + Set +ok 136 - ../tests/check_sider_set.c:Core:test_set_free: Passed +ok 137 - ../tests/check_sider_set.c:Core:test_set_insert: Passed +ok 138 - ../tests/check_sider_set.c:Core:test_set_remove: Passed +ok 139 - ../tests/check_sider_set.c:Core:test_set_union: Passed +ok 140 - ../tests/check_sider_set.c:Core:test_set_intersection: Passed +ok 141 - ../tests/check_sider_set.c:Core:test_set_difference: Passed +ok 142 - ../tests/check_sider_set.c:Core:test_set_is_subset: Passed +ok 143 - ../tests/check_sider_set.c:Core:test_set_is_equal: Passed +ok 144 - ../tests/check_sider_set.c:Core:test_set_is_member: Passed + Correlation +ok 145 - ../tests/check_sider_correlation.c:Core:test_pearson: Passed +ok 146 - ../tests/check_sider_correlation.c:Core:test_spearman: Passed +ok 147 - ../tests/check_sider_correlation.c:Core:test_spearman_eq: Passed +ok 148 - ../tests/check_sider_correlation.c:Core:test_spearman_permutation_test: Passed + BED +ok 149 - ../tests/check_sider_bed.c:Core:test_bed_header: Passed +ok 150 - ../tests/check_sider_bed.c:Core:test_beds: Passed +ok 151 - ../tests/check_sider_bed.c:Core:test_beds: Passed +ok 152 - ../tests/check_sider_bed.c:Core:test_beds: Passed +ok 153 - ../tests/check_sider_bed.c:Core:test_beds: Passed +ok 154 - ../tests/check_sider_bed.c:Core:test_beds: Passed +ok 155 - ../tests/check_sider_bed.c:Core:test_beds: Passed +ok 156 - ../tests/check_sider_bed.c:Core:test_beds: Passed +ok 157 - ../tests/check_sider_bed.c:Core:test_beds: Passed +ok 158 - ../tests/check_sider_bed.c:Core:test_beds: Passed +ok 159 - ../tests/check_sider_bed.c:Core:test_beds: Passed +ok 160 - ../tests/check_sider_bed.c:Abort:test_open_fatal: Passed +ok 161 - ../tests/check_sider_bed.c:Abort:test_chrom_fatal: Passed +ok 162 - ../tests/check_sider_bed.c:Abort:test_chrom_start_fatal: Passed +ok 163 - ../tests/check_sider_bed.c:Abort:test_chrom_end_fatal: Passed +ok 164 - ../tests/check_sider_bed.c:Abort:test_close_fatal: Passed + Blacklist +not ok 165 - ../tests/check_sider_blacklist.c:Core:test_blacklist_index_dump_from_gff: Test timeout expired +not ok 166 - ../tests/check_sider_blacklist.c:Core:test_blacklist_index_dump_from_bed: Test timeout expired +ok 167 - ../tests/check_sider_blacklist.c:Core:test_blacklist_lookup: Passed + Retrocopy +ok 168 - ../tests/check_sider_retrocopy.c:Core:test_retrocopy: Passed + Dedup +============================================================================== + + +Summary of Failures: + +1/1 all TIMEOUT 30.02s killed by signal 15 SIGTERM + +Ok: 0 +Expected Fail: 0 +Fail: 0 +Unexpected Pass: 0 +Skipped: 0 +Timeout: 1 +dh_auto_test: error: cd obj-x86_64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb LC_ALL=C.UTF-8 MESON_TESTTHREADS=12 meson test --verbose returned exit code 1 +make: *** [debian/rules:6: binary] Error 25 +dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 I: copying local configuration +E: Failed autobuilding of package +I: user script /srv/workspace/pbuilder/3938917/tmp/hooks/C01_cleanup starting +debug output: disk usage on i-capture-the-hostname at Sat Apr 25 18:48:11 UTC 2026 +Filesystem Size Used Avail Use% Mounted on +tmpfs 12G 0 12G 0% /dev/shm + +I: user script /srv/workspace/pbuilder/3938917/tmp/hooks/C01_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/746214 and its subdirectories -I: Current time: Sun Mar 23 00:19:33 -12 2025 -I: pbuilder-time-stamp: 1742732373 +I: removing directory /srv/workspace/pbuilder/3938917 and its subdirectories