Diff of the two buildlogs: -- --- b1/build.log 2024-12-09 20:28:27.380989819 +0000 +++ b2/build.log 2024-12-09 20:30:24.751688737 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Dec 9 08:26:44 -12 2024 -I: pbuilder-time-stamp: 1733776004 +I: Current time: Tue Dec 10 10:28:30 +14 2024 +I: pbuilder-time-stamp: 1733776110 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -28,52 +28,84 @@ dpkg-source: info: applying reproducible.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/11169/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3094873/tmp/hooks/D01_modify_environment starting +debug: Running on codethink04-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 Dec 9 20:28 /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/3094873/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3094873/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='unstable' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='f3c6b9fe5fd045b989b8b78a567bb562' - 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='11169' - PS1='# ' - PS2='> ' + INVOCATION_ID=f6e04cb2e71d4a559de00f0b77eb337c + 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=3094873 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.zhUSbakh/pbuilderrc_7VFQ --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.zhUSbakh/b1 --logfile b1/build.log samtools_1.20-3.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.zhUSbakh/pbuilderrc_dMXL --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.zhUSbakh/b2 --logfile b2/build.log samtools_1.20-3.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 codethink02-arm64 6.1.0-28-cloud-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-28-cloud-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/11169/tmp/hooks/D02_print_environment finished +I: user script /srv/workspace/pbuilder/3094873/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -225,7 +257,7 @@ Get: 92 http://deb.debian.org/debian unstable/main arm64 libncurses6 arm64 6.5-2+b1 [96.1 kB] Get: 93 http://deb.debian.org/debian unstable/main arm64 libncurses-dev arm64 6.5-2+b1 [338 kB] Get: 94 http://deb.debian.org/debian unstable/main arm64 tabix arm64 1.20+ds-2 [455 kB] -Fetched 38.7 MB in 0s (99.4 MB/s) +Fetched 38.7 MB in 0s (146 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package autoconf-archive. (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 ... 20083 files and directories currently installed.) @@ -616,7 +648,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/samtools-1.20/ && 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 > ../samtools_1.20-3_source.changes +I: user script /srv/workspace/pbuilder/3094873/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/3094873/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/samtools-1.20/ && 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 > ../samtools_1.20-3_source.changes dpkg-buildpackage: info: source package samtools dpkg-buildpackage: info: source version 1.20-3 dpkg-buildpackage: info: source distribution unstable @@ -725,31 +761,31 @@ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_plcmd.o bam_plcmd.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_view.o sam_view.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_fastq.o bam_fastq.c -cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_cat.o bam_cat.c +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_md.o bam_md.c +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_plbuf.o bam_plbuf.c cc1: warning: command-line option '-frelease' is valid for D but not for C cc1: warning: command-line option '-frelease' is valid for D but not for C cc1: warning: command-line option '-frelease' is valid for D but not for C cc1: warning: command-line option '-frelease' is valid for D but not for C -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_md.o bam_md.c cc1: warning: command-line option '-frelease' is valid for D but not for C -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_plbuf.o bam_plbuf.c cc1: warning: command-line option '-frelease' is valid for D but not for C -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_reheader.o bam_reheader.c cc1: warning: command-line option '-frelease' is valid for D but not for C +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_reheader.o bam_reheader.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_sort.o bam_sort.c +cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_rmdup.o bam_rmdup.c +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_rmdupse.o bam_rmdupse.c cc1: warning: command-line option '-frelease' is valid for D but not for C cc1: warning: command-line option '-frelease' is valid for D but not for C -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_rmdupse.o bam_rmdupse.c cc1: warning: command-line option '-frelease' is valid for D but not for C -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_mate.o bam_mate.c cc1: warning: command-line option '-frelease' is valid for D but not for C +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_mate.o bam_mate.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_stat.o bam_stat.c -cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_color.o bam_color.c cc1: warning: command-line option '-frelease' is valid for D but not for C +cc1: warning: command-line option '-frelease' is valid for D but not for C echo '#define SAMTOOLS_VERSION "1.20"' > version.h echo '#define SAMTOOLS_CC "gcc"' >> version.h echo '#define SAMTOOLS_CPPFLAGS "-frelease -Wdate-time -D_FORTIFY_SOURCE=2"' >> version.h @@ -762,18 +798,18 @@ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sample.o sample.c cc1: warning: command-line option '-frelease' is valid for D but not for C -cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cut_target.o cut_target.c -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o phase.o phase.c cc1: warning: command-line option '-frelease' is valid for D but not for C cc1: warning: command-line option '-frelease' is valid for D but not for C +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o phase.o phase.c +cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2depth.o bam2depth.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o coverage.o coverage.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o padding.o padding.c -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bedcov.o bedcov.c cc1: warning: command-line option '-frelease' is valid for D but not for C +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bedcov.o bedcov.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bamshuf.o bamshuf.c cc1: warning: command-line option '-frelease' is valid for D but not for C @@ -796,8 +832,8 @@ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_tview_html.o bam_tview_html.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_lpileup.o bam_lpileup.c -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_quickcheck.o bam_quickcheck.c cc1: warning: command-line option '-frelease' is valid for D but not for C +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_quickcheck.o bam_quickcheck.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_addrprg.o bam_addrprg.c cc1: warning: command-line option '-frelease' is valid for D but not for C cc1: warning: command-line option '-frelease' is valid for D but not for C @@ -808,19 +844,19 @@ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_ampliconclip.o bam_ampliconclip.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o amplicon_stats.o amplicon_stats.c +cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_import.o bam_import.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_samples.o bam_samples.c -cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_consensus.o bam_consensus.c cc1: warning: command-line option '-frelease' is valid for D but not for C cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o consensus_pileup.o consensus_pileup.c -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o reference.o reference.c -cc1: warning: command-line option '-frelease' is valid for D but not for C cc1: warning: command-line option '-frelease' is valid for D but not for C +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o reference.o reference.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o reset.o reset.c cc1: warning: command-line option '-frelease' is valid for D but not for C +cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram_size.o cram_size.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o lz4/lz4.o lz4/lz4.c @@ -828,11 +864,11 @@ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_opts.o sam_opts.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_utils.o sam_utils.c +cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bedidx.o bedidx.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam.o bam.c cc1: warning: command-line option '-frelease' is valid for D but not for C -cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/ace2sam.o misc/ace2sam.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DMAQ_LONGREADS -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/maq2sam-long.o misc/maq2sam.c @@ -840,17 +876,17 @@ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/maq2sam-short.o misc/maq2sam.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/md5fa.o misc/md5fa.c cc1: warning: command-line option '-frelease' is valid for D but not for C -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/md5sum-lite.o misc/md5sum-lite.c -cc1: warning: command-line option '-frelease' is valid for D but not for C cc1: warning: command-line option '-frelease' is valid for D but not for C +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/md5sum-lite.o misc/md5sum-lite.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/wgsim.o misc/wgsim.c cc1: warning: command-line option '-frelease' is valid for D but not for C -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test.o test/test.c cc1: warning: command-line option '-frelease' is valid for D but not for C +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test.o test/test.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_count_rg.o test/split/test_count_rg.c -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_expand_format_string.o test/split/test_expand_format_string.c cc1: warning: command-line option '-frelease' is valid for D but not for C cc1: warning: command-line option '-frelease' is valid for D but not for C +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_expand_format_string.o test/split/test_expand_format_string.c +cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_filter_header_rg.o test/split/test_filter_header_rg.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_parse_args.o test/split/test_parse_args.c @@ -859,18 +895,18 @@ cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bamtk.o bamtk.c cc1: warning: command-line option '-frelease' is valid for D but not for C +ar -rcs libst.a sam_opts.o sam_utils.o bedidx.o bam.o gcc -Wl,-z,relro -Wl,-z,now -o misc/maq2sam-long misc/maq2sam-long.o -lz gcc -Wl,-z,relro -Wl,-z,now -o misc/maq2sam-short misc/maq2sam-short.o -lz gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/md5fa misc/md5fa.o -lhts -lz gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/md5sum-lite misc/md5sum-lite.o -lhts -lz -gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/vcf-miniview test/vcf-miniview.o -lhts -lz -lpthread -ar -rcs libst.a sam_opts.o sam_utils.o bedidx.o bam.o -gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/split/test_filter_header_rg test/split/test_filter_header_rg.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/wgsim misc/wgsim.o -lm -lhts -lz +gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/split/test_filter_header_rg test/split/test_filter_header_rg.o test/test.o libst.a -lhts -lz -lpthread +gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/vcf-miniview test/vcf-miniview.o -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/ace2sam misc/ace2sam.o -lhts -lz +gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/split/test_count_rg test/split/test_count_rg.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/split/test_expand_format_string test/split/test_expand_format_string.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/split/test_parse_args test/split/test_parse_args.o test/test.o libst.a -lhts -lz -lpthread -gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/split/test_count_rg test/split/test_count_rg.o test/test.o libst.a -lhts -lz -lpthread gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_bam_translate.o test/merge/test_bam_translate.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_rtrans_build.o test/merge/test_rtrans_build.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_trans_tbl_init.o test/merge/test_trans_tbl_init.c @@ -926,75 +962,75 @@ /build/reproducible-path/samtools-1.20/samtools reference -@ 2 -r 17:1000-1500 -e test/reference/mpileup.1.tmp.cram .. ok -/usr/bin/bgzip -c -b 65272 -s 5 /tmp/hHNpOiA7TK/bgzip.dat.gz +/usr/bin/bgzip -c -b 65272 -s 5 /tmp/Lr0N7SjhXr/bgzip.dat.gz .. ok -/usr/bin/bgzip -c -b 979200 -s 6 /tmp/hHNpOiA7TK/bgzip.dat.gz +/usr/bin/bgzip -c -b 979200 -s 6 /tmp/Lr0N7SjhXr/bgzip.dat.gz .. ok -/usr/bin/bgzip -c -b 652804 -s 6 /tmp/hHNpOiA7TK/bgzip.dat.gz +/usr/bin/bgzip -c -b 652804 -s 6 /tmp/Lr0N7SjhXr/bgzip.dat.gz .. ok -/build/reproducible-path/samtools-1.20/samtools faidx /tmp/hHNpOiA7TK/faidx.fa 3:11-13 | grep -v '^>' +/build/reproducible-path/samtools-1.20/samtools faidx /tmp/Lr0N7SjhXr/faidx.fa 3:11-13 | grep -v '^>' .. ok -/build/reproducible-path/samtools-1.20/samtools faidx /tmp/hHNpOiA7TK/faidx.fa.gz 3:11-13 | grep -v '^>' +/build/reproducible-path/samtools-1.20/samtools faidx /tmp/Lr0N7SjhXr/faidx.fa.gz 3:11-13 | grep -v '^>' .. ok -/build/reproducible-path/samtools-1.20/samtools faidx /tmp/hHNpOiA7TK/faidx.fa 2:998-1003 | grep -v '^>' +/build/reproducible-path/samtools-1.20/samtools faidx /tmp/Lr0N7SjhXr/faidx.fa 2:998-1003 | grep -v '^>' .. ok -/build/reproducible-path/samtools-1.20/samtools faidx /tmp/hHNpOiA7TK/faidx.fa.gz 2:998-1003 | grep -v '^>' +/build/reproducible-path/samtools-1.20/samtools faidx /tmp/Lr0N7SjhXr/faidx.fa.gz 2:998-1003 | grep -v '^>' .. ok -/build/reproducible-path/samtools-1.20/samtools faidx /tmp/hHNpOiA7TK/faidx.fa 1:100-104 | grep -v '^>' +/build/reproducible-path/samtools-1.20/samtools faidx /tmp/Lr0N7SjhXr/faidx.fa 1:100-104 | grep -v '^>' .. ok -/build/reproducible-path/samtools-1.20/samtools faidx /tmp/hHNpOiA7TK/faidx.fa.gz 1:100-104 | grep -v '^>' +/build/reproducible-path/samtools-1.20/samtools faidx /tmp/Lr0N7SjhXr/faidx.fa.gz 1:100-104 | grep -v '^>' .. ok -/build/reproducible-path/samtools-1.20/samtools faidx /tmp/hHNpOiA7TK/faidx.fa 1:99998-100007 | grep -v '^>' +/build/reproducible-path/samtools-1.20/samtools faidx /tmp/Lr0N7SjhXr/faidx.fa 1:99998-100007 | grep -v '^>' .. ok -/build/reproducible-path/samtools-1.20/samtools faidx /tmp/hHNpOiA7TK/faidx.fa.gz 1:99998-100007 | grep -v '^>' +/build/reproducible-path/samtools-1.20/samtools faidx /tmp/Lr0N7SjhXr/faidx.fa.gz 1:99998-100007 | grep -v '^>' .. ok -/build/reproducible-path/samtools-1.20/samtools fqidx /tmp/hHNpOiA7TK/fqidx.fq 3:11-13 +/build/reproducible-path/samtools-1.20/samtools fqidx /tmp/Lr0N7SjhXr/fqidx.fq 3:11-13 .. ok .. ok -/build/reproducible-path/samtools-1.20/samtools fqidx /tmp/hHNpOiA7TK/fqidx.fq.gz 3:11-13 +/build/reproducible-path/samtools-1.20/samtools fqidx /tmp/Lr0N7SjhXr/fqidx.fq.gz 3:11-13 .. ok .. ok -/build/reproducible-path/samtools-1.20/samtools fqidx /tmp/hHNpOiA7TK/fqidx.fq 2:998-1003 +/build/reproducible-path/samtools-1.20/samtools fqidx /tmp/Lr0N7SjhXr/fqidx.fq 2:998-1003 .. ok .. ok -/build/reproducible-path/samtools-1.20/samtools fqidx /tmp/hHNpOiA7TK/fqidx.fq.gz 2:998-1003 +/build/reproducible-path/samtools-1.20/samtools fqidx /tmp/Lr0N7SjhXr/fqidx.fq.gz 2:998-1003 .. ok .. ok -/build/reproducible-path/samtools-1.20/samtools fqidx /tmp/hHNpOiA7TK/fqidx.fq 1:100-104 +/build/reproducible-path/samtools-1.20/samtools fqidx /tmp/Lr0N7SjhXr/fqidx.fq 1:100-104 .. ok .. ok -/build/reproducible-path/samtools-1.20/samtools fqidx /tmp/hHNpOiA7TK/fqidx.fq.gz 1:100-104 +/build/reproducible-path/samtools-1.20/samtools fqidx /tmp/Lr0N7SjhXr/fqidx.fq.gz 1:100-104 .. ok .. ok -/build/reproducible-path/samtools-1.20/samtools fqidx /tmp/hHNpOiA7TK/fqidx.fq 1:99998-100007 +/build/reproducible-path/samtools-1.20/samtools fqidx /tmp/Lr0N7SjhXr/fqidx.fq 1:99998-100007 .. ok .. ok -/build/reproducible-path/samtools-1.20/samtools fqidx /tmp/hHNpOiA7TK/fqidx.fq.gz 1:99998-100007 +/build/reproducible-path/samtools-1.20/samtools fqidx /tmp/Lr0N7SjhXr/fqidx.fq.gz 1:99998-100007 .. ok .. ok @@ -1004,7 +1040,7 @@ .. ok test_dict: - /build/reproducible-path/samtools-1.20/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /tmp/hHNpOiA7TK/dict.fa.gz + /build/reproducible-path/samtools-1.20/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /tmp/Lr0N7SjhXr/dict.fa.gz .. ok test_dict: @@ -1020,11 +1056,11 @@ .. ok test_index: - /build/reproducible-path/samtools-1.20/samtools view /tmp/hHNpOiA7TK/large_chrom.bam ref2 + /build/reproducible-path/samtools-1.20/samtools view /tmp/Lr0N7SjhXr/large_chrom.bam ref2 .. ok test_index: - /build/reproducible-path/samtools-1.20/samtools view /tmp/hHNpOiA7TK/large_chrom.bam ref2:1-541556283 + /build/reproducible-path/samtools-1.20/samtools view /tmp/Lr0N7SjhXr/large_chrom.bam ref2:1-541556283 .. ok test_index: @@ -1032,19 +1068,19 @@ .. ok test_index: - /build/reproducible-path/samtools-1.20/samtools view -X /build/reproducible-path/samtools-1.20/test/dat/test_input_1_b.bam /tmp/hHNpOiA7TK/test_input_1_b.bam.bai ref2 + /build/reproducible-path/samtools-1.20/samtools view -X /build/reproducible-path/samtools-1.20/test/dat/test_input_1_b.bam /tmp/Lr0N7SjhXr/test_input_1_b.bam.bai ref2 .. ok test_index: - /build/reproducible-path/samtools-1.20/samtools view -X /build/reproducible-path/samtools-1.20/test/dat/test_input_1_b.bam /tmp/hHNpOiA7TK/test_input_1_b.bam.bai + /build/reproducible-path/samtools-1.20/samtools view -X /build/reproducible-path/samtools-1.20/test/dat/test_input_1_b.bam /tmp/Lr0N7SjhXr/test_input_1_b.bam.bai .. ok test_index: - /build/reproducible-path/samtools-1.20/samtools merge -O sam - -X -cp -R ref2 /build/reproducible-path/samtools-1.20/test/dat/test_input_1_a.bam /build/reproducible-path/samtools-1.20/test/dat/test_input_1_b.bam /build/reproducible-path/samtools-1.20/test/dat/test_input_1_a.bam.bai /tmp/hHNpOiA7TK/test_input_1_b.bam.bai + /build/reproducible-path/samtools-1.20/samtools merge -O sam - -X -cp -R ref2 /build/reproducible-path/samtools-1.20/test/dat/test_input_1_a.bam /build/reproducible-path/samtools-1.20/test/dat/test_input_1_b.bam /build/reproducible-path/samtools-1.20/test/dat/test_input_1_a.bam.bai /tmp/Lr0N7SjhXr/test_input_1_b.bam.bai .. ok test_index: - /build/reproducible-path/samtools-1.20/samtools view -X /build/reproducible-path/samtools-1.20/test/dat/test_input_1_b.bam /tmp/hHNpOiA7TK/test_input_1_b_opt.bam.bai ref2 + /build/reproducible-path/samtools-1.20/samtools view -X /build/reproducible-path/samtools-1.20/test/dat/test_input_1_b.bam /tmp/Lr0N7SjhXr/test_input_1_b_opt.bam.bai ref2 .. ok test_index: @@ -1060,23 +1096,23 @@ .. ok test_index: - /build/reproducible-path/samtools-1.20/samtools index -c /build/reproducible-path/samtools-1.20/test/dat/auto_indexed.tmp.bam /tmp/hHNpOiA7TK/auto_indexed.csi && cat /tmp/hHNpOiA7TK/auto_indexed.csi + /build/reproducible-path/samtools-1.20/samtools index -c /build/reproducible-path/samtools-1.20/test/dat/auto_indexed.tmp.bam /tmp/Lr0N7SjhXr/auto_indexed.csi && cat /tmp/Lr0N7SjhXr/auto_indexed.csi .. ok test_index: - /build/reproducible-path/samtools-1.20/samtools index /build/reproducible-path/samtools-1.20/test/dat/auto_indexed.tmp.cram /tmp/hHNpOiA7TK/auto_indexed.crai && cat /tmp/hHNpOiA7TK/auto_indexed.crai + /build/reproducible-path/samtools-1.20/samtools index /build/reproducible-path/samtools-1.20/test/dat/auto_indexed.tmp.cram /tmp/Lr0N7SjhXr/auto_indexed.crai && cat /tmp/Lr0N7SjhXr/auto_indexed.crai .. ok test_index: - /build/reproducible-path/samtools-1.20/samtools index -c /build/reproducible-path/samtools-1.20/test/dat/auto_indexed.tmp.sam /tmp/hHNpOiA7TK/auto_indexed.csi && cat /tmp/hHNpOiA7TK/auto_indexed.csi + /build/reproducible-path/samtools-1.20/samtools index -c /build/reproducible-path/samtools-1.20/test/dat/auto_indexed.tmp.sam /tmp/Lr0N7SjhXr/auto_indexed.csi && cat /tmp/Lr0N7SjhXr/auto_indexed.csi .. ok test_index: - /build/reproducible-path/samtools-1.20/samtools view -@ 2 /tmp/hHNpOiA7TK/large_chrom.bam ref2 + /build/reproducible-path/samtools-1.20/samtools view -@ 2 /tmp/Lr0N7SjhXr/large_chrom.bam ref2 .. ok test_index: - /build/reproducible-path/samtools-1.20/samtools view -@ 2 /tmp/hHNpOiA7TK/large_chrom.bam ref2:1-541556283 + /build/reproducible-path/samtools-1.20/samtools view -@ 2 /tmp/Lr0N7SjhXr/large_chrom.bam ref2:1-541556283 .. ok test_index: @@ -1084,19 +1120,19 @@ .. ok test_index: - /build/reproducible-path/samtools-1.20/samtools view -@ 2 -X /build/reproducible-path/samtools-1.20/test/dat/test_input_1_b.bam /tmp/hHNpOiA7TK/test_input_1_b.bam.bai ref2 + /build/reproducible-path/samtools-1.20/samtools view -@ 2 -X /build/reproducible-path/samtools-1.20/test/dat/test_input_1_b.bam /tmp/Lr0N7SjhXr/test_input_1_b.bam.bai ref2 .. ok test_index: - /build/reproducible-path/samtools-1.20/samtools view -@ 2 -X /build/reproducible-path/samtools-1.20/test/dat/test_input_1_b.bam /tmp/hHNpOiA7TK/test_input_1_b.bam.bai + /build/reproducible-path/samtools-1.20/samtools view -@ 2 -X /build/reproducible-path/samtools-1.20/test/dat/test_input_1_b.bam /tmp/Lr0N7SjhXr/test_input_1_b.bam.bai .. ok test_index: - /build/reproducible-path/samtools-1.20/samtools merge -@ 2 -O sam - -X -cp -R ref2 /build/reproducible-path/samtools-1.20/test/dat/test_input_1_a.bam /build/reproducible-path/samtools-1.20/test/dat/test_input_1_b.bam /build/reproducible-path/samtools-1.20/test/dat/test_input_1_a.bam.bai /tmp/hHNpOiA7TK/test_input_1_b.bam.bai + /build/reproducible-path/samtools-1.20/samtools merge -@ 2 -O sam - -X -cp -R ref2 /build/reproducible-path/samtools-1.20/test/dat/test_input_1_a.bam /build/reproducible-path/samtools-1.20/test/dat/test_input_1_b.bam /build/reproducible-path/samtools-1.20/test/dat/test_input_1_a.bam.bai /tmp/Lr0N7SjhXr/test_input_1_b.bam.bai .. ok test_index: - /build/reproducible-path/samtools-1.20/samtools view -@ 2 -X /build/reproducible-path/samtools-1.20/test/dat/test_input_1_b.bam /tmp/hHNpOiA7TK/test_input_1_b_opt.bam.bai ref2 + /build/reproducible-path/samtools-1.20/samtools view -@ 2 -X /build/reproducible-path/samtools-1.20/test/dat/test_input_1_b.bam /tmp/Lr0N7SjhXr/test_input_1_b_opt.bam.bai ref2 .. ok test_index: @@ -1112,39 +1148,39 @@ .. ok test_index: - /build/reproducible-path/samtools-1.20/samtools index -@ 2 -c /build/reproducible-path/samtools-1.20/test/dat/auto_indexed.tmp.bam /tmp/hHNpOiA7TK/auto_indexed.csi && cat /tmp/hHNpOiA7TK/auto_indexed.csi + /build/reproducible-path/samtools-1.20/samtools index -@ 2 -c /build/reproducible-path/samtools-1.20/test/dat/auto_indexed.tmp.bam /tmp/Lr0N7SjhXr/auto_indexed.csi && cat /tmp/Lr0N7SjhXr/auto_indexed.csi .. ok test_index: - /build/reproducible-path/samtools-1.20/samtools index -@ 2 /build/reproducible-path/samtools-1.20/test/dat/auto_indexed.tmp.cram /tmp/hHNpOiA7TK/auto_indexed.crai && cat /tmp/hHNpOiA7TK/auto_indexed.crai + /build/reproducible-path/samtools-1.20/samtools index -@ 2 /build/reproducible-path/samtools-1.20/test/dat/auto_indexed.tmp.cram /tmp/Lr0N7SjhXr/auto_indexed.crai && cat /tmp/Lr0N7SjhXr/auto_indexed.crai .. ok test_index: - /build/reproducible-path/samtools-1.20/samtools index -@ 2 -c /build/reproducible-path/samtools-1.20/test/dat/auto_indexed.tmp.sam /tmp/hHNpOiA7TK/auto_indexed.csi && cat /tmp/hHNpOiA7TK/auto_indexed.csi + /build/reproducible-path/samtools-1.20/samtools index -@ 2 -c /build/reproducible-path/samtools-1.20/test/dat/auto_indexed.tmp.sam /tmp/Lr0N7SjhXr/auto_indexed.csi && cat /tmp/Lr0N7SjhXr/auto_indexed.csi .. ok test_mpileup: - /build/reproducible-path/samtools-1.20/samtools mpileup -b /tmp/hHNpOiA7TK/mpileup.bam.list -f /tmp/hHNpOiA7TK/mpileup.ref.fa.gz -r17:100-150 + /build/reproducible-path/samtools-1.20/samtools mpileup -b /tmp/Lr0N7SjhXr/mpileup.bam.list -f /tmp/Lr0N7SjhXr/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: - /build/reproducible-path/samtools-1.20/samtools mpileup -b /tmp/hHNpOiA7TK/mpileup.cram.list -f /tmp/hHNpOiA7TK/mpileup.ref.fa.gz -r17:100-150 + /build/reproducible-path/samtools-1.20/samtools mpileup -b /tmp/Lr0N7SjhXr/mpileup.cram.list -f /tmp/Lr0N7SjhXr/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: - /build/reproducible-path/samtools-1.20/samtools mpileup -b /tmp/hHNpOiA7TK/mpileup.bam.urllist -f /tmp/hHNpOiA7TK/mpileup.ref.fa.gz -r17:100-150 + /build/reproducible-path/samtools-1.20/samtools mpileup -b /tmp/Lr0N7SjhXr/mpileup.bam.urllist -f /tmp/Lr0N7SjhXr/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: - /build/reproducible-path/samtools-1.20/samtools mpileup -b /tmp/hHNpOiA7TK/mpileup.cram.urllist -f /tmp/hHNpOiA7TK/mpileup.ref.fa.gz -r17:100-150 + /build/reproducible-path/samtools-1.20/samtools mpileup -b /tmp/Lr0N7SjhXr/mpileup.cram.urllist -f /tmp/Lr0N7SjhXr/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: - /build/reproducible-path/samtools-1.20/samtools mpileup -B --ff 0x14 -f /tmp/hHNpOiA7TK/mpileup.ref.fa.gz -r17:1050-1060 /tmp/hHNpOiA7TK/mpileup.1.bam | grep -v mpileup + /build/reproducible-path/samtools-1.20/samtools mpileup -B --ff 0x14 -f /tmp/Lr0N7SjhXr/mpileup.ref.fa.gz -r17:1050-1060 /tmp/Lr0N7SjhXr/mpileup.1.bam | grep -v mpileup .. ok test_mpileup: - /build/reproducible-path/samtools-1.20/samtools mpileup -B --ff 0x14 -f /tmp/hHNpOiA7TK/mpileup.ref.fa.gz -r17:1050-1060 /tmp/hHNpOiA7TK/mpileup.1.cram | grep -v mpileup + /build/reproducible-path/samtools-1.20/samtools mpileup -B --ff 0x14 -f /tmp/Lr0N7SjhXr/mpileup.ref.fa.gz -r17:1050-1060 /tmp/Lr0N7SjhXr/mpileup.1.cram | grep -v mpileup .. ok test_mpileup: @@ -1432,53 +1468,53 @@ 48: Count -r grp2 (CRAM input) .. ok - 49: Filter -R /tmp/hHNpOiA7TK/view.001.fogn (SAM input) .. ok + 49: Filter -R /tmp/Lr0N7SjhXr/view.001.fogn (SAM input) .. ok - 50: Count -R /tmp/hHNpOiA7TK/view.001.fogn (SAM input) .. ok + 50: Count -R /tmp/Lr0N7SjhXr/view.001.fogn (SAM input) .. ok - 51: Filter -R /tmp/hHNpOiA7TK/view.001.fogn (BAM input) .. ok + 51: Filter -R /tmp/Lr0N7SjhXr/view.001.fogn (BAM input) .. ok - 52: Count -R /tmp/hHNpOiA7TK/view.001.fogn (BAM input) .. ok + 52: Count -R /tmp/Lr0N7SjhXr/view.001.fogn (BAM input) .. ok - 53: Filter -R /tmp/hHNpOiA7TK/view.001.fogn (CRAM input) .. ok + 53: Filter -R /tmp/Lr0N7SjhXr/view.001.fogn (CRAM input) .. ok - 54: Count -R /tmp/hHNpOiA7TK/view.001.fogn (CRAM input) .. ok + 54: Count -R /tmp/Lr0N7SjhXr/view.001.fogn (CRAM input) .. ok - 55: Filter -R /tmp/hHNpOiA7TK/view.001.fogn -r grp2 (SAM input).. ok + 55: Filter -R /tmp/Lr0N7SjhXr/view.001.fogn -r grp2 (SAM input).. ok - 56: Count -R /tmp/hHNpOiA7TK/view.001.fogn -r grp2 (SAM input).. ok + 56: Count -R /tmp/Lr0N7SjhXr/view.001.fogn -r grp2 (SAM input).. ok - 57: Filter -R /tmp/hHNpOiA7TK/view.001.fogn -r grp2 (BAM input).. ok + 57: Filter -R /tmp/Lr0N7SjhXr/view.001.fogn -r grp2 (BAM input).. ok - 58: Count -R /tmp/hHNpOiA7TK/view.001.fogn -r grp2 (BAM input).. ok + 58: Count -R /tmp/Lr0N7SjhXr/view.001.fogn -r grp2 (BAM input).. ok - 59: Filter -R /tmp/hHNpOiA7TK/view.001.fogn -r grp2 (CRAM input).. ok + 59: Filter -R /tmp/Lr0N7SjhXr/view.001.fogn -r grp2 (CRAM input).. ok - 60: Count -R /tmp/hHNpOiA7TK/view.001.fogn -r grp2 (CRAM input).. ok + 60: Count -R /tmp/Lr0N7SjhXr/view.001.fogn -r grp2 (CRAM input).. ok - 61: Filter -r grp2 -R /tmp/hHNpOiA7TK/view.001.fogn (SAM input).. ok + 61: Filter -r grp2 -R /tmp/Lr0N7SjhXr/view.001.fogn (SAM input).. ok - 62: Count -r grp2 -R /tmp/hHNpOiA7TK/view.001.fogn (SAM input).. ok + 62: Count -r grp2 -R /tmp/Lr0N7SjhXr/view.001.fogn (SAM input).. ok - 63: Filter -r grp2 -R /tmp/hHNpOiA7TK/view.001.fogn (BAM input).. ok + 63: Filter -r grp2 -R /tmp/Lr0N7SjhXr/view.001.fogn (BAM input).. ok - 64: Count -r grp2 -R /tmp/hHNpOiA7TK/view.001.fogn (BAM input).. ok + 64: Count -r grp2 -R /tmp/Lr0N7SjhXr/view.001.fogn (BAM input).. ok - 65: Filter -r grp2 -R /tmp/hHNpOiA7TK/view.001.fogn (CRAM input).. ok + 65: Filter -r grp2 -R /tmp/Lr0N7SjhXr/view.001.fogn (CRAM input).. ok - 66: Count -r grp2 -R /tmp/hHNpOiA7TK/view.001.fogn (CRAM input).. ok + 66: Count -r grp2 -R /tmp/Lr0N7SjhXr/view.001.fogn (CRAM input).. ok - 67: Filter -N /tmp/hHNpOiA7TK/view.001.forn (SAM input) .. ok + 67: Filter -N /tmp/Lr0N7SjhXr/view.001.forn (SAM input) .. ok - 68: Count -N /tmp/hHNpOiA7TK/view.001.forn (SAM input) .. ok + 68: Count -N /tmp/Lr0N7SjhXr/view.001.forn (SAM input) .. ok - 69: Filter -N /tmp/hHNpOiA7TK/view.001.forn (BAM input) .. ok + 69: Filter -N /tmp/Lr0N7SjhXr/view.001.forn (BAM input) .. ok - 70: Count -N /tmp/hHNpOiA7TK/view.001.forn (BAM input) .. ok + 70: Count -N /tmp/Lr0N7SjhXr/view.001.forn (BAM input) .. ok - 71: Filter -N /tmp/hHNpOiA7TK/view.001.forn (CRAM input) .. ok + 71: Filter -N /tmp/Lr0N7SjhXr/view.001.forn (CRAM input) .. ok - 72: Count -N /tmp/hHNpOiA7TK/view.001.forn (CRAM input) .. ok + 72: Count -N /tmp/Lr0N7SjhXr/view.001.forn (CRAM input) .. ok 73: Filter -d BC (SAM input) .. ok @@ -1504,53 +1540,53 @@ 84: Count -d BC:TGCA (CRAM input) .. ok - 85: Filter -D BC:/tmp/hHNpOiA7TK/view.001.fobc (SAM input) .. ok + 85: Filter -D BC:/tmp/Lr0N7SjhXr/view.001.fobc (SAM input) .. ok - 86: Count -D BC:/tmp/hHNpOiA7TK/view.001.fobc (SAM input) .. ok + 86: Count -D BC:/tmp/Lr0N7SjhXr/view.001.fobc (SAM input) .. ok - 87: Filter -D BC:/tmp/hHNpOiA7TK/view.001.fobc (BAM input) .. ok + 87: Filter -D BC:/tmp/Lr0N7SjhXr/view.001.fobc (BAM input) .. ok - 88: Count -D BC:/tmp/hHNpOiA7TK/view.001.fobc (BAM input) .. ok + 88: Count -D BC:/tmp/Lr0N7SjhXr/view.001.fobc (BAM input) .. ok - 89: Filter -D BC:/tmp/hHNpOiA7TK/view.001.fobc (CRAM input) .. ok + 89: Filter -D BC:/tmp/Lr0N7SjhXr/view.001.fobc (CRAM input) .. ok - 90: Count -D BC:/tmp/hHNpOiA7TK/view.001.fobc (CRAM input) .. ok + 90: Count -D BC:/tmp/Lr0N7SjhXr/view.001.fobc (CRAM input) .. ok - 91: Filter -D BC:/tmp/hHNpOiA7TK/view.001.fobc -d BC:TGCA (SAM input).. ok + 91: Filter -D BC:/tmp/Lr0N7SjhXr/view.001.fobc -d BC:TGCA (SAM input).. ok - 92: Count -D BC:/tmp/hHNpOiA7TK/view.001.fobc -d BC:TGCA (SAM input).. ok + 92: Count -D BC:/tmp/Lr0N7SjhXr/view.001.fobc -d BC:TGCA (SAM input).. ok - 93: Filter -D BC:/tmp/hHNpOiA7TK/view.001.fobc -d BC:TGCA (BAM input).. ok + 93: Filter -D BC:/tmp/Lr0N7SjhXr/view.001.fobc -d BC:TGCA (BAM input).. ok - 94: Count -D BC:/tmp/hHNpOiA7TK/view.001.fobc -d BC:TGCA (BAM input).. ok + 94: Count -D BC:/tmp/Lr0N7SjhXr/view.001.fobc -d BC:TGCA (BAM input).. ok - 95: Filter -D BC:/tmp/hHNpOiA7TK/view.001.fobc -d BC:TGCA (CRAM input).. ok + 95: Filter -D BC:/tmp/Lr0N7SjhXr/view.001.fobc -d BC:TGCA (CRAM input).. ok - 96: Count -D BC:/tmp/hHNpOiA7TK/view.001.fobc -d BC:TGCA (CRAM input).. ok + 96: Count -D BC:/tmp/Lr0N7SjhXr/view.001.fobc -d BC:TGCA (CRAM input).. ok - 97: Filter -d BC:TGCA -D BC:/tmp/hHNpOiA7TK/view.001.fobc (SAM input).. ok + 97: Filter -d BC:TGCA -D BC:/tmp/Lr0N7SjhXr/view.001.fobc (SAM input).. ok - 98: Count -d BC:TGCA -D BC:/tmp/hHNpOiA7TK/view.001.fobc (SAM input).. ok + 98: Count -d BC:TGCA -D BC:/tmp/Lr0N7SjhXr/view.001.fobc (SAM input).. ok - 99: Filter -d BC:TGCA -D BC:/tmp/hHNpOiA7TK/view.001.fobc (BAM input).. ok + 99: Filter -d BC:TGCA -D BC:/tmp/Lr0N7SjhXr/view.001.fobc (BAM input).. ok - 100: Count -d BC:TGCA -D BC:/tmp/hHNpOiA7TK/view.001.fobc (BAM input).. ok + 100: Count -d BC:TGCA -D BC:/tmp/Lr0N7SjhXr/view.001.fobc (BAM input).. ok - 101: Filter -d BC:TGCA -D BC:/tmp/hHNpOiA7TK/view.001.fobc (CRAM input).. ok + 101: Filter -d BC:TGCA -D BC:/tmp/Lr0N7SjhXr/view.001.fobc (CRAM input).. ok - 102: Count -d BC:TGCA -D BC:/tmp/hHNpOiA7TK/view.001.fobc (CRAM input).. ok + 102: Count -d BC:TGCA -D BC:/tmp/Lr0N7SjhXr/view.001.fobc (CRAM input).. ok - 103: Filter -D RG:/tmp/hHNpOiA7TK/view.001.fogn (SAM input) .. ok + 103: Filter -D RG:/tmp/Lr0N7SjhXr/view.001.fogn (SAM input) .. ok - 104: Count -D RG:/tmp/hHNpOiA7TK/view.001.fogn (SAM input) .. ok + 104: Count -D RG:/tmp/Lr0N7SjhXr/view.001.fogn (SAM input) .. ok - 105: Filter -D RG:/tmp/hHNpOiA7TK/view.001.fogn (BAM input) .. ok + 105: Filter -D RG:/tmp/Lr0N7SjhXr/view.001.fogn (BAM input) .. ok - 106: Count -D RG:/tmp/hHNpOiA7TK/view.001.fogn (BAM input) .. ok + 106: Count -D RG:/tmp/Lr0N7SjhXr/view.001.fogn (BAM input) .. ok - 107: Filter -D RG:/tmp/hHNpOiA7TK/view.001.fogn (CRAM input).. ok + 107: Filter -D RG:/tmp/Lr0N7SjhXr/view.001.fogn (CRAM input).. ok - 108: Count -D RG:/tmp/hHNpOiA7TK/view.001.fogn (CRAM input) .. ok + 108: Count -D RG:/tmp/Lr0N7SjhXr/view.001.fogn (CRAM input) .. ok 109: Filter -d NE:TGCA (SAM input) .. ok @@ -1566,126 +1602,126 @@ 115: Filter -d TGCA (SAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: - /build/reproducible-path/samtools-1.20/samtools view -o /tmp/hHNpOiA7TK/view.test115.sam -h -d TGCA /tmp/hHNpOiA7TK/view.001.sam --no-PG + /build/reproducible-path/samtools-1.20/samtools view -o /tmp/Lr0N7SjhXr/view.test115.sam -h -d TGCA /tmp/Lr0N7SjhXr/view.001.sam --no-PG .. expected failure 116: Count -d TGCA (SAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: - /build/reproducible-path/samtools-1.20/samtools view -c -d TGCA /tmp/hHNpOiA7TK/view.001.sam --no-PG + /build/reproducible-path/samtools-1.20/samtools view -c -d TGCA /tmp/Lr0N7SjhXr/view.001.sam --no-PG .. expected failure 117: Filter -d TGCA (BAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: - /build/reproducible-path/samtools-1.20/samtools view -o /tmp/hHNpOiA7TK/view.test117.sam -h -d TGCA /tmp/hHNpOiA7TK/view.test001.bam --no-PG + /build/reproducible-path/samtools-1.20/samtools view -o /tmp/Lr0N7SjhXr/view.test117.sam -h -d TGCA /tmp/Lr0N7SjhXr/view.test001.bam --no-PG .. expected failure 118: Count -d TGCA (BAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: - /build/reproducible-path/samtools-1.20/samtools view -c -d TGCA /tmp/hHNpOiA7TK/view.test001.bam --no-PG + /build/reproducible-path/samtools-1.20/samtools view -c -d TGCA /tmp/Lr0N7SjhXr/view.test001.bam --no-PG .. expected failure 119: Filter -d TGCA (CRAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: - /build/reproducible-path/samtools-1.20/samtools view -o /tmp/hHNpOiA7TK/view.test119.sam -h -d TGCA /tmp/hHNpOiA7TK/view.test006.cram --no-PG + /build/reproducible-path/samtools-1.20/samtools view -o /tmp/Lr0N7SjhXr/view.test119.sam -h -d TGCA /tmp/Lr0N7SjhXr/view.test006.cram --no-PG .. expected failure 120: Count -d TGCA (CRAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: - /build/reproducible-path/samtools-1.20/samtools view -c -d TGCA /tmp/hHNpOiA7TK/view.test006.cram --no-PG + /build/reproducible-path/samtools-1.20/samtools view -c -d TGCA /tmp/Lr0N7SjhXr/view.test006.cram --no-PG .. expected failure - 121: Filter -D BClong:/tmp/hHNpOiA7TK/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/hHNpOiA7TK/view.001.fobc" + 121: Filter -D BClong:/tmp/Lr0N7SjhXr/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/Lr0N7SjhXr/view.001.fobc" Failed command: - /build/reproducible-path/samtools-1.20/samtools view -o /tmp/hHNpOiA7TK/view.test121.sam -h -D BClong:/tmp/hHNpOiA7TK/view.001.fobc /tmp/hHNpOiA7TK/view.001.sam --no-PG + /build/reproducible-path/samtools-1.20/samtools view -o /tmp/Lr0N7SjhXr/view.test121.sam -h -D BClong:/tmp/Lr0N7SjhXr/view.001.fobc /tmp/Lr0N7SjhXr/view.001.sam --no-PG .. expected failure - 122: Count -D BClong:/tmp/hHNpOiA7TK/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/hHNpOiA7TK/view.001.fobc" + 122: Count -D BClong:/tmp/Lr0N7SjhXr/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/Lr0N7SjhXr/view.001.fobc" Failed command: - /build/reproducible-path/samtools-1.20/samtools view -c -D BClong:/tmp/hHNpOiA7TK/view.001.fobc /tmp/hHNpOiA7TK/view.001.sam --no-PG + /build/reproducible-path/samtools-1.20/samtools view -c -D BClong:/tmp/Lr0N7SjhXr/view.001.fobc /tmp/Lr0N7SjhXr/view.001.sam --no-PG .. expected failure - 123: Filter -D BClong:/tmp/hHNpOiA7TK/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/hHNpOiA7TK/view.001.fobc" + 123: Filter -D BClong:/tmp/Lr0N7SjhXr/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/Lr0N7SjhXr/view.001.fobc" Failed command: - /build/reproducible-path/samtools-1.20/samtools view -o /tmp/hHNpOiA7TK/view.test123.sam -h -D BClong:/tmp/hHNpOiA7TK/view.001.fobc /tmp/hHNpOiA7TK/view.test001.bam --no-PG + /build/reproducible-path/samtools-1.20/samtools view -o /tmp/Lr0N7SjhXr/view.test123.sam -h -D BClong:/tmp/Lr0N7SjhXr/view.001.fobc /tmp/Lr0N7SjhXr/view.test001.bam --no-PG .. expected failure - 124: Count -D BClong:/tmp/hHNpOiA7TK/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/hHNpOiA7TK/view.001.fobc" + 124: Count -D BClong:/tmp/Lr0N7SjhXr/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/Lr0N7SjhXr/view.001.fobc" Failed command: - /build/reproducible-path/samtools-1.20/samtools view -c -D BClong:/tmp/hHNpOiA7TK/view.001.fobc /tmp/hHNpOiA7TK/view.test001.bam --no-PG + /build/reproducible-path/samtools-1.20/samtools view -c -D BClong:/tmp/Lr0N7SjhXr/view.001.fobc /tmp/Lr0N7SjhXr/view.test001.bam --no-PG .. expected failure - 125: Filter -D BClong:/tmp/hHNpOiA7TK/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/hHNpOiA7TK/view.001.fobc" + 125: Filter -D BClong:/tmp/Lr0N7SjhXr/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/Lr0N7SjhXr/view.001.fobc" Failed command: - /build/reproducible-path/samtools-1.20/samtools view -o /tmp/hHNpOiA7TK/view.test125.sam -h -D BClong:/tmp/hHNpOiA7TK/view.001.fobc /tmp/hHNpOiA7TK/view.test006.cram --no-PG + /build/reproducible-path/samtools-1.20/samtools view -o /tmp/Lr0N7SjhXr/view.test125.sam -h -D BClong:/tmp/Lr0N7SjhXr/view.001.fobc /tmp/Lr0N7SjhXr/view.test006.cram --no-PG .. expected failure - 126: Count -D BClong:/tmp/hHNpOiA7TK/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/hHNpOiA7TK/view.001.fobc" + 126: Count -D BClong:/tmp/Lr0N7SjhXr/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/Lr0N7SjhXr/view.001.fobc" Failed command: - /build/reproducible-path/samtools-1.20/samtools view -c -D BClong:/tmp/hHNpOiA7TK/view.001.fobc /tmp/hHNpOiA7TK/view.test006.cram --no-PG + /build/reproducible-path/samtools-1.20/samtools view -c -D BClong:/tmp/Lr0N7SjhXr/view.001.fobc /tmp/Lr0N7SjhXr/view.test006.cram --no-PG .. expected failure 127: Filter -d BC:ACGT -d RG:grp2 (SAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: - /build/reproducible-path/samtools-1.20/samtools view -o /tmp/hHNpOiA7TK/view.test127.sam -h -d BC:ACGT -d RG:grp2 /tmp/hHNpOiA7TK/view.001.sam --no-PG + /build/reproducible-path/samtools-1.20/samtools view -o /tmp/Lr0N7SjhXr/view.test127.sam -h -d BC:ACGT -d RG:grp2 /tmp/Lr0N7SjhXr/view.001.sam --no-PG .. expected failure 128: Count -d BC:ACGT -d RG:grp2 (SAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: - /build/reproducible-path/samtools-1.20/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/hHNpOiA7TK/view.001.sam --no-PG + /build/reproducible-path/samtools-1.20/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/Lr0N7SjhXr/view.001.sam --no-PG .. expected failure 129: Filter -d BC:ACGT -d RG:grp2 (BAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: - /build/reproducible-path/samtools-1.20/samtools view -o /tmp/hHNpOiA7TK/view.test129.sam -h -d BC:ACGT -d RG:grp2 /tmp/hHNpOiA7TK/view.test001.bam --no-PG + /build/reproducible-path/samtools-1.20/samtools view -o /tmp/Lr0N7SjhXr/view.test129.sam -h -d BC:ACGT -d RG:grp2 /tmp/Lr0N7SjhXr/view.test001.bam --no-PG .. expected failure 130: Count -d BC:ACGT -d RG:grp2 (BAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: - /build/reproducible-path/samtools-1.20/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/hHNpOiA7TK/view.test001.bam --no-PG + /build/reproducible-path/samtools-1.20/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/Lr0N7SjhXr/view.test001.bam --no-PG .. expected failure 131: Filter -d BC:ACGT -d RG:grp2 (CRAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: - /build/reproducible-path/samtools-1.20/samtools view -o /tmp/hHNpOiA7TK/view.test131.sam -h -d BC:ACGT -d RG:grp2 /tmp/hHNpOiA7TK/view.test006.cram --no-PG + /build/reproducible-path/samtools-1.20/samtools view -o /tmp/Lr0N7SjhXr/view.test131.sam -h -d BC:ACGT -d RG:grp2 /tmp/Lr0N7SjhXr/view.test006.cram --no-PG .. expected failure 132: Count -d BC:ACGT -d RG:grp2 (CRAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: - /build/reproducible-path/samtools-1.20/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/hHNpOiA7TK/view.test006.cram --no-PG + /build/reproducible-path/samtools-1.20/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/Lr0N7SjhXr/view.test006.cram --no-PG .. expected failure @@ -2567,7 +2603,7 @@ .. ok test_bam2fq: - /build/reproducible-path/samtools-1.20/samtools fastq -N -s /tmp/hHNpOiA7TK/bam2fq.discard.s.fq -0 /tmp/hHNpOiA7TK/bam2fq.discard.0.fq /build/reproducible-path/samtools-1.20/test/dat/bam2fq.001.sam + /build/reproducible-path/samtools-1.20/samtools fastq -N -s /tmp/Lr0N7SjhXr/bam2fq.discard.s.fq -0 /tmp/Lr0N7SjhXr/bam2fq.discard.0.fq /build/reproducible-path/samtools-1.20/test/dat/bam2fq.001.sam .. ok test_bam2fq: @@ -2708,7 +2744,7 @@ .. ok test_bam2fq: - /build/reproducible-path/samtools-1.20/samtools fastq -@ 2 -N -s /tmp/hHNpOiA7TK/bam2fq.discard.s.fq -0 /tmp/hHNpOiA7TK/bam2fq.discard.0.fq /build/reproducible-path/samtools-1.20/test/dat/bam2fq.001.sam + /build/reproducible-path/samtools-1.20/samtools fastq -@ 2 -N -s /tmp/Lr0N7SjhXr/bam2fq.discard.s.fq -0 /tmp/Lr0N7SjhXr/bam2fq.discard.0.fq /build/reproducible-path/samtools-1.20/test/dat/bam2fq.001.sam .. ok test_bam2fq: @@ -2925,7 +2961,7 @@ .. ok test_merge: - /build/reproducible-path/samtools-1.20/samtools merge -s 1 -O sam -b /tmp/76JiaoqGfV - /build/reproducible-path/samtools-1.20/test/dat/test_input_1_a.bam + /build/reproducible-path/samtools-1.20/samtools merge -s 1 -O sam -b /tmp/XaELrlBdP5 - /build/reproducible-path/samtools-1.20/test/dat/test_input_1_a.bam .. ok test_merge: @@ -2949,11 +2985,11 @@ .. ok test_merge: - /build/reproducible-path/samtools-1.20/samtools merge -s 1 -p -c -t PG -O SAM - /tmp/hHNpOiA7TK/merge.tag.1.bam /tmp/hHNpOiA7TK/merge.tag.2.bam + /build/reproducible-path/samtools-1.20/samtools merge -s 1 -p -c -t PG -O SAM - /tmp/Lr0N7SjhXr/merge.tag.1.bam /tmp/Lr0N7SjhXr/merge.tag.2.bam .. ok test_merge: - /build/reproducible-path/samtools-1.20/samtools merge -s 1 -p -c -n -t PG -O SAM - /tmp/hHNpOiA7TK/merge.tag.3.bam /tmp/hHNpOiA7TK/merge.tag.4.bam + /build/reproducible-path/samtools-1.20/samtools merge -s 1 -p -c -n -t PG -O SAM - /tmp/Lr0N7SjhXr/merge.tag.3.bam /tmp/Lr0N7SjhXr/merge.tag.4.bam .. ok test_merge: @@ -2961,7 +2997,7 @@ .. ok test_merge: - /build/reproducible-path/samtools-1.20/samtools merge --no-PG -O SAM -L /build/reproducible-path/samtools-1.20/test/merge/merge.bed - /tmp/hHNpOiA7TK/merge.bed.1.bam /tmp/hHNpOiA7TK/merge.bed.2.bam + /build/reproducible-path/samtools-1.20/samtools merge --no-PG -O SAM -L /build/reproducible-path/samtools-1.20/test/merge/merge.bed - /tmp/Lr0N7SjhXr/merge.bed.1.bam /tmp/Lr0N7SjhXr/merge.bed.2.bam .. ok test_merge: @@ -2977,7 +3013,7 @@ .. ok test_merge: - /build/reproducible-path/samtools-1.20/samtools merge -@ 2 -s 1 -O sam -b /tmp/ramzZ0Pb2V - /build/reproducible-path/samtools-1.20/test/dat/test_input_1_a.bam + /build/reproducible-path/samtools-1.20/samtools merge -@ 2 -s 1 -O sam -b /tmp/FiZawOg3Dn - /build/reproducible-path/samtools-1.20/test/dat/test_input_1_a.bam .. ok test_merge: @@ -3001,11 +3037,11 @@ .. ok test_merge: - /build/reproducible-path/samtools-1.20/samtools merge -@ 2 -s 1 -p -c -t PG -O SAM - /tmp/hHNpOiA7TK/merge.tag.1.bam /tmp/hHNpOiA7TK/merge.tag.2.bam + /build/reproducible-path/samtools-1.20/samtools merge -@ 2 -s 1 -p -c -t PG -O SAM - /tmp/Lr0N7SjhXr/merge.tag.1.bam /tmp/Lr0N7SjhXr/merge.tag.2.bam .. ok test_merge: - /build/reproducible-path/samtools-1.20/samtools merge -@ 2 -s 1 -p -c -n -t PG -O SAM - /tmp/hHNpOiA7TK/merge.tag.3.bam /tmp/hHNpOiA7TK/merge.tag.4.bam + /build/reproducible-path/samtools-1.20/samtools merge -@ 2 -s 1 -p -c -n -t PG -O SAM - /tmp/Lr0N7SjhXr/merge.tag.3.bam /tmp/Lr0N7SjhXr/merge.tag.4.bam .. ok test_merge: @@ -3013,7 +3049,7 @@ .. ok test_merge: - /build/reproducible-path/samtools-1.20/samtools merge -@ 2 --no-PG -O SAM -L /build/reproducible-path/samtools-1.20/test/merge/merge.bed - /tmp/hHNpOiA7TK/merge.bed.1.bam /tmp/hHNpOiA7TK/merge.bed.2.bam + /build/reproducible-path/samtools-1.20/samtools merge -@ 2 --no-PG -O SAM -L /build/reproducible-path/samtools-1.20/test/merge/merge.bed - /tmp/Lr0N7SjhXr/merge.bed.1.bam /tmp/Lr0N7SjhXr/merge.bed.2.bam .. ok test_merge: @@ -3021,15 +3057,15 @@ .. ok test_sort: - /build/reproducible-path/samtools-1.20/samtools sort /build/reproducible-path/samtools-1.20/test/dat/test_input_1_a.bam /tmp/hHNpOiA7TK/sortout + /build/reproducible-path/samtools-1.20/samtools sort /build/reproducible-path/samtools-1.20/test/dat/test_input_1_a.bam /tmp/Lr0N7SjhXr/sortout .. ok test_sort: - /build/reproducible-path/samtools-1.20/samtools sort -f /build/reproducible-path/samtools-1.20/test/dat/test_input_1_a.bam /tmp/hHNpOiA7TK/sortout.bam + /build/reproducible-path/samtools-1.20/samtools sort -f /build/reproducible-path/samtools-1.20/test/dat/test_input_1_a.bam /tmp/Lr0N7SjhXr/sortout.bam .. ok test_sort: - /build/reproducible-path/samtools-1.20/samtools sort -o /build/reproducible-path/samtools-1.20/test/dat/test_input_1_a.bam /tmp/hHNpOiA7TK/sorttmp + /build/reproducible-path/samtools-1.20/samtools sort -o /build/reproducible-path/samtools-1.20/test/dat/test_input_1_a.bam /tmp/Lr0N7SjhXr/sorttmp .. ok test_sort: @@ -3081,15 +3117,15 @@ .. ok test_sort: - /build/reproducible-path/samtools-1.20/samtools sort -@ 2 /build/reproducible-path/samtools-1.20/test/dat/test_input_1_a.bam /tmp/hHNpOiA7TK/sortout + /build/reproducible-path/samtools-1.20/samtools sort -@ 2 /build/reproducible-path/samtools-1.20/test/dat/test_input_1_a.bam /tmp/Lr0N7SjhXr/sortout .. ok test_sort: - /build/reproducible-path/samtools-1.20/samtools sort -@ 2 -f /build/reproducible-path/samtools-1.20/test/dat/test_input_1_a.bam /tmp/hHNpOiA7TK/sortout.bam + /build/reproducible-path/samtools-1.20/samtools sort -@ 2 -f /build/reproducible-path/samtools-1.20/test/dat/test_input_1_a.bam /tmp/Lr0N7SjhXr/sortout.bam .. ok test_sort: - /build/reproducible-path/samtools-1.20/samtools sort -@ 2 -o /build/reproducible-path/samtools-1.20/test/dat/test_input_1_a.bam /tmp/hHNpOiA7TK/sorttmp + /build/reproducible-path/samtools-1.20/samtools sort -@ 2 -o /build/reproducible-path/samtools-1.20/test/dat/test_input_1_a.bam /tmp/Lr0N7SjhXr/sorttmp .. ok test_sort: @@ -3793,15 +3829,15 @@ .. ok test_large_positions: - /build/reproducible-path/samtools-1.20/samtools view -h --no-PG /tmp/hHNpOiA7TK/longref.sam.gz + /build/reproducible-path/samtools-1.20/samtools view -h --no-PG /tmp/Lr0N7SjhXr/longref.sam.gz .. ok test_large_positions: - /build/reproducible-path/samtools-1.20/samtools view -h --no-PG /tmp/hHNpOiA7TK/longref.sam.gz CHROMOSOME_I:10000000114-10000000168 + /build/reproducible-path/samtools-1.20/samtools view -h --no-PG /tmp/Lr0N7SjhXr/longref.sam.gz CHROMOSOME_I:10000000114-10000000168 .. ok test_large_positions: - /build/reproducible-path/samtools-1.20/samtools view -h --no-PG -L /build/reproducible-path/samtools-1.20/test/large_pos/test.bed /tmp/hHNpOiA7TK/longref.sam.gz + /build/reproducible-path/samtools-1.20/samtools view -h --no-PG -L /build/reproducible-path/samtools-1.20/test/large_pos/test.bed /tmp/Lr0N7SjhXr/longref.sam.gz .. ok test_large_positions: @@ -3821,7 +3857,7 @@ .. ok test_large_positions: - /build/reproducible-path/samtools-1.20/samtools tview -d T -p CHROMOSOME_I:10000000000 /tmp/hHNpOiA7TK/longref.sam.gz + /build/reproducible-path/samtools-1.20/samtools tview -d T -p CHROMOSOME_I:10000000000 /tmp/Lr0N7SjhXr/longref.sam.gz .. ok test_large_positions: @@ -4049,7 +4085,7 @@ Unexpected failures: 0 => PASS make[2]: Leaving directory '/build/reproducible-path/samtools-1.20' - rm -fr -- /tmp/dh-xdg-rundir-IiR25Ihy + rm -fr -- /tmp/dh-xdg-rundir-ukEkKe2P make[1]: Leaving directory '/build/reproducible-path/samtools-1.20' create-stamp debian/debhelper-build-stamp dh_prep @@ -4119,12 +4155,12 @@ debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/reproducible-path/samtools-1.20' dh_installchangelogs NEWS.md - install -m0755 -d debian/samtools-test/usr/share/doc/samtools-test - install -p -m0644 debian/.debhelper/generated/samtools-test/dh_installchangelogs.dch.trimmed debian/samtools-test/usr/share/doc/samtools-test/changelog.Debian - install -p -m0644 NEWS.md debian/samtools-test/usr/share/doc/samtools-test/changelog install -m0755 -d debian/samtools/usr/share/doc/samtools install -p -m0644 debian/.debhelper/generated/samtools/dh_installchangelogs.dch.trimmed debian/samtools/usr/share/doc/samtools/changelog.Debian install -p -m0644 NEWS.md debian/samtools/usr/share/doc/samtools/changelog + install -m0755 -d debian/samtools-test/usr/share/doc/samtools-test + install -p -m0644 debian/.debhelper/generated/samtools-test/dh_installchangelogs.dch.trimmed debian/samtools-test/usr/share/doc/samtools-test/changelog.Debian + install -p -m0644 NEWS.md debian/samtools-test/usr/share/doc/samtools-test/changelog make[1]: Leaving directory '/build/reproducible-path/samtools-1.20' dh_installexamples install -m0755 -d debian/samtools/usr/share/doc/samtools/examples @@ -4155,8 +4191,13 @@ man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-markdup.1 debian/samtools/usr/share/man/man1/samtools-merge.1 debian/samtools/usr/share/man/man1/samtools-mpileup.1 debian/samtools/usr/share/man/man1/samtools-phase.1 man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-quickcheck.1 debian/samtools/usr/share/man/man1/samtools-reference.1 debian/samtools/usr/share/man/man1/samtools-reheader.1 debian/samtools/usr/share/man/man1/samtools-reset.1 man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-rmdup.1 debian/samtools/usr/share/man/man1/samtools-samples.1 debian/samtools/usr/share/man/man1/samtools-sort.1 debian/samtools/usr/share/man/man1/samtools-split.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-stats.1 debian/samtools/usr/share/man/man1/samtools-targetcut.1 debian/samtools/usr/share/man/man1/samtools-tview.1 debian/samtools/usr/share/man/man1/samtools-view.1 man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools.1 debian/samtools/usr/share/man/man1/samtools.pl.1 debian/samtools/usr/share/man/man1/wgsim.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-stats.1 debian/samtools/usr/share/man/man1/samtools-targetcut.1 debian/samtools/usr/share/man/man1/samtools-tview.1 debian/samtools/usr/share/man/man1/samtools-view.1 + mv debian/samtools/usr/share/man/man1/ace2sam.1.dh-new debian/samtools/usr/share/man/man1/ace2sam.1 + mv debian/samtools/usr/share/man/man1/samtools-addreplacerg.1.dh-new debian/samtools/usr/share/man/man1/samtools-addreplacerg.1 + mv debian/samtools/usr/share/man/man1/samtools-ampliconclip.1.dh-new debian/samtools/usr/share/man/man1/samtools-ampliconclip.1 + mv debian/samtools/usr/share/man/man1/samtools-ampliconstats.1.dh-new debian/samtools/usr/share/man/man1/samtools-ampliconstats.1 + chmod 0644 -- debian/samtools/usr/share/man/man1/ace2sam.1 debian/samtools/usr/share/man/man1/samtools-addreplacerg.1 debian/samtools/usr/share/man/man1/samtools-ampliconclip.1 debian/samtools/usr/share/man/man1/samtools-ampliconstats.1 mv debian/samtools/usr/share/man/man1/samtools-bedcov.1.dh-new debian/samtools/usr/share/man/man1/samtools-bedcov.1 mv debian/samtools/usr/share/man/man1/samtools-calmd.1.dh-new debian/samtools/usr/share/man/man1/samtools-calmd.1 mv debian/samtools/usr/share/man/man1/samtools-cat.1.dh-new debian/samtools/usr/share/man/man1/samtools-cat.1 @@ -4167,31 +4208,6 @@ mv debian/samtools/usr/share/man/man1/samtools-import.1.dh-new debian/samtools/usr/share/man/man1/samtools-import.1 mv debian/samtools/usr/share/man/man1/samtools-index.1.dh-new debian/samtools/usr/share/man/man1/samtools-index.1 chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-head.1 debian/samtools/usr/share/man/man1/samtools-idxstats.1 debian/samtools/usr/share/man/man1/samtools-import.1 debian/samtools/usr/share/man/man1/samtools-index.1 - mv debian/samtools/usr/share/man/man1/samtools-depth.1.dh-new debian/samtools/usr/share/man/man1/samtools-depth.1 - mv debian/samtools/usr/share/man/man1/samtools-dict.1.dh-new debian/samtools/usr/share/man/man1/samtools-dict.1 - mv debian/samtools/usr/share/man/man1/samtools-faidx.1.dh-new debian/samtools/usr/share/man/man1/samtools-faidx.1 - mv debian/samtools/usr/share/man/man1/samtools-fasta.1.dh-new debian/samtools/usr/share/man/man1/samtools-fasta.1 - chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-depth.1 debian/samtools/usr/share/man/man1/samtools-dict.1 debian/samtools/usr/share/man/man1/samtools-faidx.1 debian/samtools/usr/share/man/man1/samtools-fasta.1 - mv debian/samtools/usr/share/man/man1/ace2sam.1.dh-new debian/samtools/usr/share/man/man1/ace2sam.1 - mv debian/samtools/usr/share/man/man1/samtools-addreplacerg.1.dh-new debian/samtools/usr/share/man/man1/samtools-addreplacerg.1 - mv debian/samtools/usr/share/man/man1/samtools-ampliconclip.1.dh-new debian/samtools/usr/share/man/man1/samtools-ampliconclip.1 - mv debian/samtools/usr/share/man/man1/samtools-ampliconstats.1.dh-new debian/samtools/usr/share/man/man1/samtools-ampliconstats.1 - chmod 0644 -- debian/samtools/usr/share/man/man1/ace2sam.1 debian/samtools/usr/share/man/man1/samtools-addreplacerg.1 debian/samtools/usr/share/man/man1/samtools-ampliconclip.1 debian/samtools/usr/share/man/man1/samtools-ampliconstats.1 - mv debian/samtools/usr/share/man/man1/samtools-rmdup.1.dh-new debian/samtools/usr/share/man/man1/samtools-rmdup.1 - mv debian/samtools/usr/share/man/man1/samtools-samples.1.dh-new debian/samtools/usr/share/man/man1/samtools-samples.1 - mv debian/samtools/usr/share/man/man1/samtools-sort.1.dh-new debian/samtools/usr/share/man/man1/samtools-sort.1 - mv debian/samtools/usr/share/man/man1/samtools-split.1.dh-new debian/samtools/usr/share/man/man1/samtools-split.1 - chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-rmdup.1 debian/samtools/usr/share/man/man1/samtools-samples.1 debian/samtools/usr/share/man/man1/samtools-sort.1 debian/samtools/usr/share/man/man1/samtools-split.1 - mv debian/samtools/usr/share/man/man1/samtools-fixmate.1.dh-new debian/samtools/usr/share/man/man1/samtools-fixmate.1 - mv debian/samtools/usr/share/man/man1/samtools-flags.1.dh-new debian/samtools/usr/share/man/man1/samtools-flags.1 - mv debian/samtools/usr/share/man/man1/samtools-flagstat.1.dh-new debian/samtools/usr/share/man/man1/samtools-flagstat.1 - mv debian/samtools/usr/share/man/man1/samtools-fqidx.1.dh-new debian/samtools/usr/share/man/man1/samtools-fqidx.1 - chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-fixmate.1 debian/samtools/usr/share/man/man1/samtools-flags.1 debian/samtools/usr/share/man/man1/samtools-flagstat.1 debian/samtools/usr/share/man/man1/samtools-fqidx.1 - mv debian/samtools/usr/share/man/man1/samtools-stats.1.dh-new debian/samtools/usr/share/man/man1/samtools-stats.1 - mv debian/samtools/usr/share/man/man1/samtools-targetcut.1.dh-new debian/samtools/usr/share/man/man1/samtools-targetcut.1 - mv debian/samtools/usr/share/man/man1/samtools-tview.1.dh-new debian/samtools/usr/share/man/man1/samtools-tview.1 - mv debian/samtools/usr/share/man/man1/samtools-view.1.dh-new debian/samtools/usr/share/man/man1/samtools-view.1 - chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-stats.1 debian/samtools/usr/share/man/man1/samtools-targetcut.1 debian/samtools/usr/share/man/man1/samtools-tview.1 debian/samtools/usr/share/man/man1/samtools-view.1 mv debian/samtools/usr/share/man/man1/samtools-markdup.1.dh-new debian/samtools/usr/share/man/man1/samtools-markdup.1 mv debian/samtools/usr/share/man/man1/samtools-merge.1.dh-new debian/samtools/usr/share/man/man1/samtools-merge.1 mv debian/samtools/usr/share/man/man1/samtools-mpileup.1.dh-new debian/samtools/usr/share/man/man1/samtools-mpileup.1 @@ -4206,11 +4222,31 @@ mv debian/samtools/usr/share/man/man1/samtools-cram-size.1.dh-new debian/samtools/usr/share/man/man1/samtools-cram-size.1 mv debian/samtools/usr/share/man/man1/samtools-depad.1.dh-new debian/samtools/usr/share/man/man1/samtools-depad.1 chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-consensus.1 debian/samtools/usr/share/man/man1/samtools-coverage.1 debian/samtools/usr/share/man/man1/samtools-cram-size.1 debian/samtools/usr/share/man/man1/samtools-depad.1 + mv debian/samtools/usr/share/man/man1/samtools-fixmate.1.dh-new debian/samtools/usr/share/man/man1/samtools-fixmate.1 + mv debian/samtools/usr/share/man/man1/samtools-flags.1.dh-new debian/samtools/usr/share/man/man1/samtools-flags.1 + mv debian/samtools/usr/share/man/man1/samtools-flagstat.1.dh-new debian/samtools/usr/share/man/man1/samtools-flagstat.1 + mv debian/samtools/usr/share/man/man1/samtools-fqidx.1.dh-new debian/samtools/usr/share/man/man1/samtools-fqidx.1 + chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-fixmate.1 debian/samtools/usr/share/man/man1/samtools-flags.1 debian/samtools/usr/share/man/man1/samtools-flagstat.1 debian/samtools/usr/share/man/man1/samtools-fqidx.1 mv debian/samtools/usr/share/man/man1/samtools-quickcheck.1.dh-new debian/samtools/usr/share/man/man1/samtools-quickcheck.1 mv debian/samtools/usr/share/man/man1/samtools-reference.1.dh-new debian/samtools/usr/share/man/man1/samtools-reference.1 mv debian/samtools/usr/share/man/man1/samtools-reheader.1.dh-new debian/samtools/usr/share/man/man1/samtools-reheader.1 mv debian/samtools/usr/share/man/man1/samtools-reset.1.dh-new debian/samtools/usr/share/man/man1/samtools-reset.1 chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-quickcheck.1 debian/samtools/usr/share/man/man1/samtools-reference.1 debian/samtools/usr/share/man/man1/samtools-reheader.1 debian/samtools/usr/share/man/man1/samtools-reset.1 + mv debian/samtools/usr/share/man/man1/samtools-depth.1.dh-new debian/samtools/usr/share/man/man1/samtools-depth.1 + mv debian/samtools/usr/share/man/man1/samtools-dict.1.dh-new debian/samtools/usr/share/man/man1/samtools-dict.1 + mv debian/samtools/usr/share/man/man1/samtools-faidx.1.dh-new debian/samtools/usr/share/man/man1/samtools-faidx.1 + mv debian/samtools/usr/share/man/man1/samtools-fasta.1.dh-new debian/samtools/usr/share/man/man1/samtools-fasta.1 + chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-depth.1 debian/samtools/usr/share/man/man1/samtools-dict.1 debian/samtools/usr/share/man/man1/samtools-faidx.1 debian/samtools/usr/share/man/man1/samtools-fasta.1 + mv debian/samtools/usr/share/man/man1/samtools-rmdup.1.dh-new debian/samtools/usr/share/man/man1/samtools-rmdup.1 + mv debian/samtools/usr/share/man/man1/samtools-samples.1.dh-new debian/samtools/usr/share/man/man1/samtools-samples.1 + mv debian/samtools/usr/share/man/man1/samtools-sort.1.dh-new debian/samtools/usr/share/man/man1/samtools-sort.1 + mv debian/samtools/usr/share/man/man1/samtools-split.1.dh-new debian/samtools/usr/share/man/man1/samtools-split.1 + chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-rmdup.1 debian/samtools/usr/share/man/man1/samtools-samples.1 debian/samtools/usr/share/man/man1/samtools-sort.1 debian/samtools/usr/share/man/man1/samtools-split.1 + mv debian/samtools/usr/share/man/man1/samtools-stats.1.dh-new debian/samtools/usr/share/man/man1/samtools-stats.1 + mv debian/samtools/usr/share/man/man1/samtools-targetcut.1.dh-new debian/samtools/usr/share/man/man1/samtools-targetcut.1 + mv debian/samtools/usr/share/man/man1/samtools-tview.1.dh-new debian/samtools/usr/share/man/man1/samtools-tview.1 + mv debian/samtools/usr/share/man/man1/samtools-view.1.dh-new debian/samtools/usr/share/man/man1/samtools-view.1 + chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-stats.1 debian/samtools/usr/share/man/man1/samtools-targetcut.1 debian/samtools/usr/share/man/man1/samtools-tview.1 debian/samtools/usr/share/man/man1/samtools-view.1 dh_lintian install -m0755 -d debian/samtools/usr/share/lintian/overrides install -p -m0644 debian/samtools.lintian-overrides debian/samtools/usr/share/lintian/overrides/samtools @@ -4269,11 +4305,6 @@ chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ed/b8f2ac8a83f1dcb15779a53f4802e278304186.debug strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/ace2sam objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ed/b8f2ac8a83f1dcb15779a53f4802e278304186.debug debian/samtools/usr/bin/ace2sam - install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/4d - objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-long debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/4d/88af8d8aed3fc3b15403625a03dd7507517efd.debug - chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/4d/88af8d8aed3fc3b15403625a03dd7507517efd.debug - strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/maq2sam-long - objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/4d/88af8d8aed3fc3b15403625a03dd7507517efd.debug debian/samtools/usr/bin/maq2sam-long install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/cd objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5fa debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/cd/4a06f86057da5253e70a5ca9862de98b5e5482.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/cd/4a06f86057da5253e70a5ca9862de98b5e5482.debug @@ -4284,6 +4315,11 @@ chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/63/2726a8ed868fd89d569b668791cff6675d7fc9.debug strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/maq2sam-short objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/63/2726a8ed868fd89d569b668791cff6675d7fc9.debug debian/samtools/usr/bin/maq2sam-short + install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/4d + objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-long debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/4d/88af8d8aed3fc3b15403625a03dd7507517efd.debug + chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/4d/88af8d8aed3fc3b15403625a03dd7507517efd.debug + strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/maq2sam-long + objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/4d/88af8d8aed3fc3b15403625a03dd7507517efd.debug debian/samtools/usr/bin/maq2sam-long install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/d4 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5sum-lite debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/d4/b4f6166d68191c16298844b686228f205a63b2.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/d4/b4f6166d68191c16298844b686228f205a63b2.debug @@ -4305,7 +4341,7 @@ rm -f debian/samtools/DEBIAN/shlibs dh_shlibdeps -a install -m0755 -d debian/samtools/DEBIAN - dpkg-shlibdeps -Tdebian/samtools.substvars debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/samtools + dpkg-shlibdeps -Tdebian/samtools.substvars debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/samtools dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect @@ -4323,11 +4359,11 @@ echo misc:Pre-Depends= >> debian/samtools.substvars install -m0755 -d debian/.debhelper/samtools/dbgsym-root/DEBIAN dpkg-gencontrol -psamtools -ldebian/changelog -Tdebian/samtools.substvars -cdebian/control -Pdebian/.debhelper/samtools/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -UProtected -UBuilt-Using -UStatic-Built-Using -DPackage=samtools-dbgsym "-DDepends=samtools (= \${binary:Version})" "-DDescription=debug symbols for samtools" "-DBuild-Ids=424e6ff5e40eaf8210cf28c522423589d1fdb537 4d88af8d8aed3fc3b15403625a03dd7507517efd 5542c727b55ba0724947fc6b5ecab22ca84da473 632726a8ed868fd89d569b668791cff6675d7fc9 cd4a06f86057da5253e70a5ca9862de98b5e5482 d4b4f6166d68191c16298844b686228f205a63b2 edb8f2ac8a83f1dcb15779a53f4802e278304186" -DSection=debug -UMulti-Arch -UReplaces -UBreaks -dpkg-gencontrol: warning: package samtools-test: substitution variable ${perl:Depends} unused, but is defined - chmod 0644 -- debian/samtools-test/DEBIAN/control dpkg-gencontrol: warning: package samtools: substitution variable ${perl:Depends} unused, but is defined chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/DEBIAN/control dpkg-gencontrol -psamtools -ldebian/changelog -Tdebian/samtools.substvars -cdebian/control -Pdebian/samtools +dpkg-gencontrol: warning: package samtools-test: substitution variable ${perl:Depends} unused, but is defined + chmod 0644 -- debian/samtools-test/DEBIAN/control dpkg-gencontrol: warning: package samtools: substitution variable ${perl:Depends} unused, but is defined chmod 0644 -- debian/samtools/DEBIAN/control dh_md5sums @@ -4355,12 +4391,14 @@ 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/3094873/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3094873/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/11169 and its subdirectories -I: Current time: Mon Dec 9 08:28:26 -12 2024 -I: pbuilder-time-stamp: 1733776106 +I: removing directory /srv/workspace/pbuilder/3094873 and its subdirectories +I: Current time: Tue Dec 10 10:30:23 +14 2024 +I: pbuilder-time-stamp: 1733776223