Diff of the two buildlogs: -- --- b1/build.log 2025-03-24 06:59:56.725903996 +0000 +++ b2/build.log 2025-03-24 07:02:24.531307303 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Mar 23 18:58:00 -12 2025 -I: pbuilder-time-stamp: 1742799480 +I: Current time: Mon Apr 27 03:22:59 +14 2026 +I: pbuilder-time-stamp: 1777209779 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -22,52 +22,84 @@ 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/827/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/4018767/tmp/hooks/D01_modify_environment starting +debug: Running on codethink03-arm64. +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 26 13:23 /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/4018767/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/4018767/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='arm64' - 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]="aarch64-unknown-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=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='d29e10f2d32c4ccc9006345e33f06ec6' - 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='827' - PS1='# ' - PS2='> ' + INVOCATION_ID=5f56035afb4543828f206323c0672354 + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-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=4018767 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.soV8AeuH/pbuilderrc_jJgH --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.soV8AeuH/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' - http_proxy='http://192.168.101.4:3128' + 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.soV8AeuH/pbuilderrc_vvuL --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.soV8AeuH/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' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink04-arm64 6.1.0-32-cloud-arm64 #1 SMP Debian 6.1.129-1 (2025-03-06) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-32-cloud-arm64 #1 SMP Debian 6.1.129-1 (2025-03-06) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Mar 4 11:20 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/827/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Mar 4 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/4018767/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -281,7 +313,7 @@ Get: 160 http://deb.debian.org/debian trixie/main arm64 python3-snowballstemmer all 2.2.0-4 [58.0 kB] Get: 161 http://deb.debian.org/debian trixie/main arm64 sphinx-common all 8.1.3-5 [617 kB] Get: 162 http://deb.debian.org/debian trixie/main arm64 python3-sphinx all 8.1.3-5 [468 kB] -Fetched 74.5 MB in 1s (102 MB/s) +Fetched 74.5 MB in 1s (144 MB/s) Preconfiguring packages ... Selecting previously unselected package libpython3.13-minimal:arm64. (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 ... 19899 files and directories currently installed.) @@ -809,8 +841,8 @@ Setting up tzdata (2025a-2) ... Current default time zone: 'Etc/UTC' -Local time is now: Mon Mar 24 06:58:52 UTC 2025. -Universal Time is now: Mon Mar 24 06:58:52 UTC 2025. +Local time is now: Sun Apr 26 13:24:02 UTC 2026. +Universal Time is now: Sun Apr 26 13:24:02 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... @@ -966,7 +998,11 @@ 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/4018767/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/4018767/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 @@ -1023,62 +1059,70 @@ [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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -[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 -mbranch-protection=standard -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 -[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 -mbranch-protection=standard -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 +[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 -mbranch-protection=standard -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 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-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 -mbranch-protection=standard -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 [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 -mbranch-protection=standard -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 [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 -mbranch-protection=standard -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 [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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -[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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 +[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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -MD -MQ src/libsider.a.p/abnormal.c.o -MF src/libsider.a.p/abnormal.c.o.d -o src/libsider.a.p/abnormal.c.o -c ../src/abnormal.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 -mbranch-protection=standard -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 -[14/70] cc -Isrc/libsider.a.p -Isrc -I../src -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall 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-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -MD -MQ src/libsider.a.p/abnormal.c.o -MF src/libsider.a.p/abnormal.c.o.d -o src/libsider.a.p/abnormal.c.o -c ../src/abnormal.c -[17/70] 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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -MD -MQ src/libsider.a.p/logger.c.o -MF 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-[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 -mbranch-protection=standard -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 -[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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -MD -MQ src/libsider.a.p/process_sample.c.o -MF src/libsider.a.p/process_sample.c.o.d -o src/libsider.a.p/process_sample.c.o -c ../src/process_sample.c -[34/70] 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 -mbranch-protection=standard -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 -[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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -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 -[37/70] 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 -mbranch-protection=standard -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 -[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 -mbranch-protection=standard -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 -[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 -mbranch-protection=standard -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 +[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 -mbranch-protection=standard -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 +[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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -MD -MQ src/libsider.a.p/hash.c.o -MF src/libsider.a.p/hash.c.o.d -o src/libsider.a.p/hash.c.o -c ../src/hash.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 -mbranch-protection=standard -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 +[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 -mbranch-protection=standard -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 +[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 -mbranch-protection=standard -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 +[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 -mbranch-protection=standard -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] 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 -mbranch-protection=standard -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 +[38/70] 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 +[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 -mbranch-protection=standard -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 [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 -mbranch-protection=standard -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 -[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 -mbranch-protection=standard -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 -[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 -mbranch-protection=standard -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 +[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 -mbranch-protection=standard -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 +[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 -mbranch-protection=standard -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 [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 -mbranch-protection=standard -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 -[44/70] 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 -[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 -mbranch-protection=standard -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 -[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 -mbranch-protection=standard -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 -[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 -mbranch-protection=standard -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 +[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 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../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 -mbranch-protection=standard -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 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-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 -mbranch-protection=standard -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 +[67/70] /usr/bin/sphinx-build -b man /build/reproducible-path/sideretro-1.1.6/docs /build/reproducible-path/sideretro-1.1.6/obj-aarch64-linux-gnu/docs Running Sphinx v8.1.3 WARNING: Invalid configuration value found: 'language = None'. Update your configuration to a valid language code. Falling back to 'en' (English). loading translations [en]... done @@ -1108,14 +1152,6 @@ build succeeded, 2 warnings. The manual pages are in docs. -[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 -mbranch-protection=standard -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 -[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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group src/libsider.a -pthread /usr/lib/aarch64-linux-gnu/libsqlite3.so /usr/lib/aarch64-linux-gnu/libhts.so /usr/lib/aarch64-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 -mbranch-protection=standard -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 -[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 -mbranch-protection=standard -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 -[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 -mbranch-protection=standard -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 -[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 -mbranch-protection=standard -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 -[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 -mbranch-protection=standard -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 -[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 -mbranch-protection=standard -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 [68/70] 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 -mbranch-protection=standard -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] @@ -1132,7 +1168,7 @@ ninja: Entering directory `/build/reproducible-path/sideretro-1.1.6/obj-aarch64-linux-gnu' [1/65] Generating config.h with a custom command 1/1 all RUNNING ->>> MESON_TEST_ITERATION=1 UBSAN_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 MALLOC_PERTURB_=150 MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 /build/reproducible-path/sideretro-1.1.6/obj-aarch64-linux-gnu/tests/check_sider +>>> 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 MALLOC_PERTURB_=94 MESON_TEST_ITERATION=1 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 /build/reproducible-path/sideretro-1.1.6/obj-aarch64-linux-gnu/tests/check_sider ――――――――――――――――――――――――――――――――――――― ✀ ――――――――――――――――――――――――――――――――――――― Running suite(s): ProcessSample ok 1 - ../tests/check_sider_process_sample.c:Core:test_sider: Passed @@ -1329,7 +1365,7 @@ 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.d4EVID' +[E::idx_find_and_load] Could not retrieve index file for '/tmp/ponga_unsorted.bam.WD6whG' ok 170 - ../tests/check_sider_genotype.c:Core:test_genotype: Passed FASTA ok 171 - ../tests/check_sider_fasta.c:Core:test_fasta_read: Passed @@ -1352,7 +1388,7 @@ 100%: Checks: 185, Failures: 0, Errors: 0 1..185 ―――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――― -1/1 all OK 2.42s +1/1 all OK 2.90s Ok: 1 @@ -1392,8 +1428,8 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'sideretro-dbgsym' in '../sideretro-dbgsym_1.1.6-2_arm64.deb'. dpkg-deb: building package 'sideretro' in '../sideretro_1.1.6-2_arm64.deb'. +dpkg-deb: building package 'sideretro-dbgsym' in '../sideretro-dbgsym_1.1.6-2_arm64.deb'. dpkg-genbuildinfo --build=binary -O../sideretro_1.1.6-2_arm64.buildinfo dpkg-genchanges --build=binary -O../sideretro_1.1.6-2_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1401,12 +1437,14 @@ 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/4018767/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/4018767/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/827 and its subdirectories -I: Current time: Sun Mar 23 18:59:55 -12 2025 -I: pbuilder-time-stamp: 1742799595 +I: removing directory /srv/workspace/pbuilder/4018767 and its subdirectories +I: Current time: Mon Apr 27 03:25:22 +14 2026 +I: pbuilder-time-stamp: 1777209922