Diff of the two buildlogs: -- --- b1/build.log 2025-01-10 17:31:33.490111724 +0000 +++ b2/build.log 2025-01-10 17:33:17.809346644 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Jan 10 05:28:06 -12 2025 -I: pbuilder-time-stamp: 1736530086 +I: Current time: Fri Feb 13 13:54:36 +14 2026 +I: pbuilder-time-stamp: 1770940476 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -24,52 +24,84 @@ dpkg-source: info: applying reproducible.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1563099/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1803923/tmp/hooks/D01_modify_environment starting +debug: Running on ionos5-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Feb 12 23:54 /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/1803923/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1803923/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='35e61bf386534819910567054d3c4610' - 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='1563099' - PS1='# ' - PS2='> ' + INVOCATION_ID=aebd2663c5b94e55b6629d5ff3238b9f + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=1803923 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.gOTZXUkp/pbuilderrc_NumS --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.gOTZXUkp/b1 --logfile b1/build.log samtools_1.20-3.dsc' - SUDO_GID='110' - SUDO_UID='105' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://46.16.76.132:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.gOTZXUkp/pbuilderrc_Inhm --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.gOTZXUkp/b2 --logfile b2/build.log samtools_1.20-3.dsc' + SUDO_GID=110 + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos1-amd64 6.1.0-28-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.119-1 (2024-11-22) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.11.10+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.10-1~bpo12+1 (2024-12-19) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1563099/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1803923/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -227,7 +259,7 @@ Get: 98 http://deb.debian.org/debian trixie/main amd64 libncurses6 amd64 6.5-2+b1 [105 kB] Get: 99 http://deb.debian.org/debian trixie/main amd64 libncurses-dev amd64 6.5-2+b1 [351 kB] Get: 100 http://deb.debian.org/debian trixie/main amd64 tabix amd64 1.20+ds-2 [486 kB] -Fetched 41.7 MB in 1s (36.2 MB/s) +Fetched 41.7 MB in 3s (12.1 MB/s) Preconfiguring packages ... 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 ... 19853 files and directories currently installed.) @@ -642,7 +674,11 @@ 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/1803923/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/1803923/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 @@ -657,7 +693,7 @@ rm -f config.mk touch config.mk dh_auto_clean -- - make -j20 distclean + make -j42 distclean make[2]: Entering directory '/build/reproducible-path/samtools-1.20' rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp test/*/*.tmp.* cd test/dat && rm -f test_input_*.bam.bai view.*.bam.bai @@ -744,7 +780,7 @@ CFLAGS="$(dpkg-buildflags --get CFLAGS)" \ CPPFLAGS="\$(DFLAGS) \$(INCLUDES) $(dpkg-buildflags --get CPPFLAGS)" \ LDFLAGS="$(dpkg-buildflags --get LDFLAGS)" - make -j20 "CFLAGS=-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 -fcf-protection" "CPPFLAGS=\$(DFLAGS) \$(INCLUDES) -Wdate-time -D_FORTIFY_SOURCE=2" "LDFLAGS=-Wl,-z,relro -Wl,-z,now" + make -j42 "CFLAGS=-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 -fcf-protection" "CPPFLAGS=\$(DFLAGS) \$(INCLUDES) -Wdate-time -D_FORTIFY_SOURCE=2" "LDFLAGS=-Wl,-z,relro -Wl,-z,now" make[2]: Entering directory '/build/reproducible-path/samtools-1.20' 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 -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_aux.o bam_aux.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 -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_index.o bam_index.c @@ -754,106 +790,106 @@ 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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_plbuf.o bam_plbuf.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 -fcf-protection -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 -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_sort.o bam_sort.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 -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_rmdup.o bam_rmdup.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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 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 -fcf-protection -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 -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_rmdupse.o bam_rmdupse.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 -fcf-protection -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 -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 -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_stat.o bam_stat.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 -fcf-protection -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 cc1: warning: command-line option '-frelease' is valid for D but not for C echo '#define SAMTOOLS_VERSION "1.20"' > version.h -cc1: warning: command-line option '-frelease' is valid for D but not for C -echo '#define SAMTOOLS_CC "gcc"' >> version.h -echo '#define SAMTOOLS_CPPFLAGS "-frelease -Wdate-time -D_FORTIFY_SOURCE=2"' >> version.h -echo '#define SAMTOOLS_CFLAGS "-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 -fcf-protection"' >> version.h -echo '#define SAMTOOLS_LDFLAGS "-Wl,-z,relro -Wl,-z,now"' >> version.h -echo '#define SAMTOOLS_HTSDIR ""' >> version.h -echo '#define SAMTOOLS_LIBS ""' >> version.h -echo '#define SAMTOOLS_CURSES_LIB "-lcurses"' >> version.h -sed -i -e 's@/build/reproducible-path/samtools-1.20@«BUILDPATH»@g' version.h 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 -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.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 -fcf-protection -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 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 -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cut_target.o cut_target.c +echo '#define SAMTOOLS_CC "gcc"' >> version.h 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 -fcf-protection -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 -fcf-protection -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 +echo '#define SAMTOOLS_CPPFLAGS "-frelease -Wdate-time -D_FORTIFY_SOURCE=2"' >> version.h 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 -fcf-protection -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 +echo '#define SAMTOOLS_CFLAGS "-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 -fcf-protection"' >> version.h 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 -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o padding.o padding.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 -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bedcov.o bedcov.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 -fcf-protection -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 cc1: warning: command-line option '-frelease' is valid for D but not for C +echo '#define SAMTOOLS_LDFLAGS "-Wl,-z,relro -Wl,-z,now"' >> version.h +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 -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bamshuf.o bamshuf.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 -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o faidx.o faidx.c cc1: warning: command-line option '-frelease' is valid for D but not for C +echo '#define SAMTOOLS_HTSDIR ""' >> version.h 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 -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o dict.o dict.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 -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stats.o 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 -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stats_isize.o stats_isize.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 -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_flags.o bam_flags.c +echo '#define SAMTOOLS_LIBS ""' >> version.h 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 -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_split.o bam_split.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 -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_tview.o bam_tview.c -cc1: warning: command-line option '-frelease' is valid for D but not for C +echo '#define SAMTOOLS_CURSES_LIB "-lcurses"' >> version.h 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 -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_tview_curses.o bam_tview_curses.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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 +sed -i -e 's@/build/reproducible-path/samtools-1.20@«BUILDPATH»@g' version.h 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 -fcf-protection -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 -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_addrprg.o bam_addrprg.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 -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_markdup.o bam_markdup.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 -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_markdup.o bam_markdup.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 -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tmp_file.o tmp_file.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 -fcf-protection -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 +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 -fcf-protection -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 +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 -fcf-protection -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 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 -fcf-protection -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 +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 -fcf-protection -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 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 -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o consensus_pileup.o consensus_pileup.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 -fcf-protection -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 -fcf-protection -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 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 -fcf-protection -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 -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o lz4/lz4.o lz4/lz4.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 -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_opts.o sam_opts.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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 @@ -868,35 +904,35 @@ 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 -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/md5fa.o misc/md5fa.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 -fcf-protection -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 -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_parse_args.o test/split/test_parse_args.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 -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/vcf-miniview.o test/vcf-miniview.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 -fcf-protection -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 -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 +cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/md5sum-lite misc/md5sum-lite.o -lhts -lz gcc -Wl,-z,relro -Wl,-z,now -o misc/maq2sam-long misc/maq2sam-long.o -lz 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/md5fa misc/md5fa.o -lhts -lz +gcc -Wl,-z,relro -Wl,-z,now -o misc/maq2sam-short misc/maq2sam-short.o -lz +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 -fcf-protection -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 -fcf-protection -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 +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 -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_parse_args.o test/split/test_parse_args.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 -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 misc/ace2sam misc/ace2sam.o -lhts -lz 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_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_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/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 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 samtools bam_aux.o bam_index.o bam_plcmd.o sam_view.o bam_fastq.o bam_cat.o bam_md.o bam_plbuf.o bam_reheader.o bam_sort.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o bam2bcf.o sample.o cut_target.o phase.o bam2depth.o coverage.o padding.o bedcov.o bamshuf.o faidx.o dict.o stats.o stats_isize.o bam_flags.o bam_split.o bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o bam_quickcheck.o bam_addrprg.o bam_markdup.o tmp_file.o bam_ampliconclip.o amplicon_stats.o bam_import.o bam_samples.o bam_consensus.o consensus_pileup.o reference.o reset.o cram_size.o ./lz4/lz4.o libst.a -lhts -lcurses -lm -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 -fcf-protection -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 -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_rtrans_build.o test/merge/test_rtrans_build.c @@ -913,7 +949,7 @@ debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/samtools-1.20' dh_auto_test -- BGZIP=/usr/bin/bgzip - make -j20 test "TESTSUITEFLAGS=-j20 --verbose" VERBOSE=1 BGZIP=/usr/bin/bgzip + make -j42 test "TESTSUITEFLAGS=-j42 --verbose" VERBOSE=1 BGZIP=/usr/bin/bgzip make[2]: Entering directory '/build/reproducible-path/samtools-1.20' test/split/test_count_rg test/split/test_expand_format_string @@ -952,75 +988,75 @@ /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/NPo_S5Sm_0/bgzip.dat.gz +/usr/bin/bgzip -c -b 65272 -s 5 /tmp/5nYwRZjWOG/bgzip.dat.gz .. ok -/usr/bin/bgzip -c -b 979200 -s 6 /tmp/NPo_S5Sm_0/bgzip.dat.gz +/usr/bin/bgzip -c -b 979200 -s 6 /tmp/5nYwRZjWOG/bgzip.dat.gz .. ok -/usr/bin/bgzip -c -b 652804 -s 6 /tmp/NPo_S5Sm_0/bgzip.dat.gz +/usr/bin/bgzip -c -b 652804 -s 6 /tmp/5nYwRZjWOG/bgzip.dat.gz .. ok -/build/reproducible-path/samtools-1.20/samtools faidx /tmp/NPo_S5Sm_0/faidx.fa 3:11-13 | grep -v '^>' +/build/reproducible-path/samtools-1.20/samtools faidx /tmp/5nYwRZjWOG/faidx.fa 3:11-13 | grep -v '^>' .. ok -/build/reproducible-path/samtools-1.20/samtools faidx /tmp/NPo_S5Sm_0/faidx.fa.gz 3:11-13 | grep -v '^>' +/build/reproducible-path/samtools-1.20/samtools faidx /tmp/5nYwRZjWOG/faidx.fa.gz 3:11-13 | grep -v '^>' .. ok -/build/reproducible-path/samtools-1.20/samtools faidx /tmp/NPo_S5Sm_0/faidx.fa 2:998-1003 | grep -v '^>' +/build/reproducible-path/samtools-1.20/samtools faidx /tmp/5nYwRZjWOG/faidx.fa 2:998-1003 | grep -v '^>' .. ok -/build/reproducible-path/samtools-1.20/samtools faidx /tmp/NPo_S5Sm_0/faidx.fa.gz 2:998-1003 | grep -v '^>' +/build/reproducible-path/samtools-1.20/samtools faidx /tmp/5nYwRZjWOG/faidx.fa.gz 2:998-1003 | grep -v '^>' .. ok -/build/reproducible-path/samtools-1.20/samtools faidx /tmp/NPo_S5Sm_0/faidx.fa 1:100-104 | grep -v '^>' +/build/reproducible-path/samtools-1.20/samtools faidx /tmp/5nYwRZjWOG/faidx.fa 1:100-104 | grep -v '^>' .. ok -/build/reproducible-path/samtools-1.20/samtools faidx /tmp/NPo_S5Sm_0/faidx.fa.gz 1:100-104 | grep -v '^>' +/build/reproducible-path/samtools-1.20/samtools faidx /tmp/5nYwRZjWOG/faidx.fa.gz 1:100-104 | grep -v '^>' .. ok -/build/reproducible-path/samtools-1.20/samtools faidx /tmp/NPo_S5Sm_0/faidx.fa 1:99998-100007 | grep -v '^>' +/build/reproducible-path/samtools-1.20/samtools faidx /tmp/5nYwRZjWOG/faidx.fa 1:99998-100007 | grep -v '^>' .. ok -/build/reproducible-path/samtools-1.20/samtools faidx /tmp/NPo_S5Sm_0/faidx.fa.gz 1:99998-100007 | grep -v '^>' +/build/reproducible-path/samtools-1.20/samtools faidx /tmp/5nYwRZjWOG/faidx.fa.gz 1:99998-100007 | grep -v '^>' .. ok -/build/reproducible-path/samtools-1.20/samtools fqidx /tmp/NPo_S5Sm_0/fqidx.fq 3:11-13 +/build/reproducible-path/samtools-1.20/samtools fqidx /tmp/5nYwRZjWOG/fqidx.fq 3:11-13 .. ok .. ok -/build/reproducible-path/samtools-1.20/samtools fqidx /tmp/NPo_S5Sm_0/fqidx.fq.gz 3:11-13 +/build/reproducible-path/samtools-1.20/samtools fqidx /tmp/5nYwRZjWOG/fqidx.fq.gz 3:11-13 .. ok .. ok -/build/reproducible-path/samtools-1.20/samtools fqidx /tmp/NPo_S5Sm_0/fqidx.fq 2:998-1003 +/build/reproducible-path/samtools-1.20/samtools fqidx /tmp/5nYwRZjWOG/fqidx.fq 2:998-1003 .. ok .. ok -/build/reproducible-path/samtools-1.20/samtools fqidx /tmp/NPo_S5Sm_0/fqidx.fq.gz 2:998-1003 +/build/reproducible-path/samtools-1.20/samtools fqidx /tmp/5nYwRZjWOG/fqidx.fq.gz 2:998-1003 .. ok .. ok -/build/reproducible-path/samtools-1.20/samtools fqidx /tmp/NPo_S5Sm_0/fqidx.fq 1:100-104 +/build/reproducible-path/samtools-1.20/samtools fqidx /tmp/5nYwRZjWOG/fqidx.fq 1:100-104 .. ok .. ok -/build/reproducible-path/samtools-1.20/samtools fqidx /tmp/NPo_S5Sm_0/fqidx.fq.gz 1:100-104 +/build/reproducible-path/samtools-1.20/samtools fqidx /tmp/5nYwRZjWOG/fqidx.fq.gz 1:100-104 .. ok .. ok -/build/reproducible-path/samtools-1.20/samtools fqidx /tmp/NPo_S5Sm_0/fqidx.fq 1:99998-100007 +/build/reproducible-path/samtools-1.20/samtools fqidx /tmp/5nYwRZjWOG/fqidx.fq 1:99998-100007 .. ok .. ok -/build/reproducible-path/samtools-1.20/samtools fqidx /tmp/NPo_S5Sm_0/fqidx.fq.gz 1:99998-100007 +/build/reproducible-path/samtools-1.20/samtools fqidx /tmp/5nYwRZjWOG/fqidx.fq.gz 1:99998-100007 .. ok .. ok @@ -1030,7 +1066,7 @@ .. ok test_dict: - /build/reproducible-path/samtools-1.20/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /tmp/NPo_S5Sm_0/dict.fa.gz + /build/reproducible-path/samtools-1.20/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /tmp/5nYwRZjWOG/dict.fa.gz .. ok test_dict: @@ -1046,11 +1082,11 @@ .. ok test_index: - /build/reproducible-path/samtools-1.20/samtools view /tmp/NPo_S5Sm_0/large_chrom.bam ref2 + /build/reproducible-path/samtools-1.20/samtools view /tmp/5nYwRZjWOG/large_chrom.bam ref2 .. ok test_index: - /build/reproducible-path/samtools-1.20/samtools view /tmp/NPo_S5Sm_0/large_chrom.bam ref2:1-541556283 + /build/reproducible-path/samtools-1.20/samtools view /tmp/5nYwRZjWOG/large_chrom.bam ref2:1-541556283 .. ok test_index: @@ -1058,19 +1094,19 @@ .. 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/NPo_S5Sm_0/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/5nYwRZjWOG/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/NPo_S5Sm_0/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/5nYwRZjWOG/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/NPo_S5Sm_0/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/5nYwRZjWOG/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/NPo_S5Sm_0/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/5nYwRZjWOG/test_input_1_b_opt.bam.bai ref2 .. ok test_index: @@ -1086,23 +1122,23 @@ .. 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/NPo_S5Sm_0/auto_indexed.csi && cat /tmp/NPo_S5Sm_0/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/5nYwRZjWOG/auto_indexed.csi && cat /tmp/5nYwRZjWOG/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/NPo_S5Sm_0/auto_indexed.crai && cat /tmp/NPo_S5Sm_0/auto_indexed.crai + /build/reproducible-path/samtools-1.20/samtools index /build/reproducible-path/samtools-1.20/test/dat/auto_indexed.tmp.cram /tmp/5nYwRZjWOG/auto_indexed.crai && cat /tmp/5nYwRZjWOG/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/NPo_S5Sm_0/auto_indexed.csi && cat /tmp/NPo_S5Sm_0/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/5nYwRZjWOG/auto_indexed.csi && cat /tmp/5nYwRZjWOG/auto_indexed.csi .. ok test_index: - /build/reproducible-path/samtools-1.20/samtools view -@ 2 /tmp/NPo_S5Sm_0/large_chrom.bam ref2 + /build/reproducible-path/samtools-1.20/samtools view -@ 2 /tmp/5nYwRZjWOG/large_chrom.bam ref2 .. ok test_index: - /build/reproducible-path/samtools-1.20/samtools view -@ 2 /tmp/NPo_S5Sm_0/large_chrom.bam ref2:1-541556283 + /build/reproducible-path/samtools-1.20/samtools view -@ 2 /tmp/5nYwRZjWOG/large_chrom.bam ref2:1-541556283 .. ok test_index: @@ -1110,19 +1146,19 @@ .. 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/NPo_S5Sm_0/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/5nYwRZjWOG/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/NPo_S5Sm_0/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/5nYwRZjWOG/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/NPo_S5Sm_0/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/5nYwRZjWOG/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/NPo_S5Sm_0/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/5nYwRZjWOG/test_input_1_b_opt.bam.bai ref2 .. ok test_index: @@ -1138,39 +1174,39 @@ .. 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/NPo_S5Sm_0/auto_indexed.csi && cat /tmp/NPo_S5Sm_0/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/5nYwRZjWOG/auto_indexed.csi && cat /tmp/5nYwRZjWOG/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/NPo_S5Sm_0/auto_indexed.crai && cat /tmp/NPo_S5Sm_0/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/5nYwRZjWOG/auto_indexed.crai && cat /tmp/5nYwRZjWOG/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/NPo_S5Sm_0/auto_indexed.csi && cat /tmp/NPo_S5Sm_0/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/5nYwRZjWOG/auto_indexed.csi && cat /tmp/5nYwRZjWOG/auto_indexed.csi .. ok test_mpileup: - /build/reproducible-path/samtools-1.20/samtools mpileup -b /tmp/NPo_S5Sm_0/mpileup.bam.list -f /tmp/NPo_S5Sm_0/mpileup.ref.fa.gz -r17:100-150 + /build/reproducible-path/samtools-1.20/samtools mpileup -b /tmp/5nYwRZjWOG/mpileup.bam.list -f /tmp/5nYwRZjWOG/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: - /build/reproducible-path/samtools-1.20/samtools mpileup -b /tmp/NPo_S5Sm_0/mpileup.cram.list -f /tmp/NPo_S5Sm_0/mpileup.ref.fa.gz -r17:100-150 + /build/reproducible-path/samtools-1.20/samtools mpileup -b /tmp/5nYwRZjWOG/mpileup.cram.list -f /tmp/5nYwRZjWOG/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: - /build/reproducible-path/samtools-1.20/samtools mpileup -b /tmp/NPo_S5Sm_0/mpileup.bam.urllist -f /tmp/NPo_S5Sm_0/mpileup.ref.fa.gz -r17:100-150 + /build/reproducible-path/samtools-1.20/samtools mpileup -b /tmp/5nYwRZjWOG/mpileup.bam.urllist -f /tmp/5nYwRZjWOG/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: - /build/reproducible-path/samtools-1.20/samtools mpileup -b /tmp/NPo_S5Sm_0/mpileup.cram.urllist -f /tmp/NPo_S5Sm_0/mpileup.ref.fa.gz -r17:100-150 + /build/reproducible-path/samtools-1.20/samtools mpileup -b /tmp/5nYwRZjWOG/mpileup.cram.urllist -f /tmp/5nYwRZjWOG/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: - /build/reproducible-path/samtools-1.20/samtools mpileup -B --ff 0x14 -f /tmp/NPo_S5Sm_0/mpileup.ref.fa.gz -r17:1050-1060 /tmp/NPo_S5Sm_0/mpileup.1.bam | grep -v mpileup + /build/reproducible-path/samtools-1.20/samtools mpileup -B --ff 0x14 -f /tmp/5nYwRZjWOG/mpileup.ref.fa.gz -r17:1050-1060 /tmp/5nYwRZjWOG/mpileup.1.bam | grep -v mpileup .. ok test_mpileup: - /build/reproducible-path/samtools-1.20/samtools mpileup -B --ff 0x14 -f /tmp/NPo_S5Sm_0/mpileup.ref.fa.gz -r17:1050-1060 /tmp/NPo_S5Sm_0/mpileup.1.cram | grep -v mpileup + /build/reproducible-path/samtools-1.20/samtools mpileup -B --ff 0x14 -f /tmp/5nYwRZjWOG/mpileup.ref.fa.gz -r17:1050-1060 /tmp/5nYwRZjWOG/mpileup.1.cram | grep -v mpileup .. ok test_mpileup: @@ -1458,53 +1494,53 @@ 48: Count -r grp2 (CRAM input) .. ok - 49: Filter -R /tmp/NPo_S5Sm_0/view.001.fogn (SAM input) .. ok + 49: Filter -R /tmp/5nYwRZjWOG/view.001.fogn (SAM input) .. ok - 50: Count -R /tmp/NPo_S5Sm_0/view.001.fogn (SAM input) .. ok + 50: Count -R /tmp/5nYwRZjWOG/view.001.fogn (SAM input) .. ok - 51: Filter -R /tmp/NPo_S5Sm_0/view.001.fogn (BAM input) .. ok + 51: Filter -R /tmp/5nYwRZjWOG/view.001.fogn (BAM input) .. ok - 52: Count -R /tmp/NPo_S5Sm_0/view.001.fogn (BAM input) .. ok + 52: Count -R /tmp/5nYwRZjWOG/view.001.fogn (BAM input) .. ok - 53: Filter -R /tmp/NPo_S5Sm_0/view.001.fogn (CRAM input) .. ok + 53: Filter -R /tmp/5nYwRZjWOG/view.001.fogn (CRAM input) .. ok - 54: Count -R /tmp/NPo_S5Sm_0/view.001.fogn (CRAM input) .. ok + 54: Count -R /tmp/5nYwRZjWOG/view.001.fogn (CRAM input) .. ok - 55: Filter -R /tmp/NPo_S5Sm_0/view.001.fogn -r grp2 (SAM input).. ok + 55: Filter -R /tmp/5nYwRZjWOG/view.001.fogn -r grp2 (SAM input).. ok - 56: Count -R /tmp/NPo_S5Sm_0/view.001.fogn -r grp2 (SAM input).. ok + 56: Count -R /tmp/5nYwRZjWOG/view.001.fogn -r grp2 (SAM input).. ok - 57: Filter -R /tmp/NPo_S5Sm_0/view.001.fogn -r grp2 (BAM input).. ok + 57: Filter -R /tmp/5nYwRZjWOG/view.001.fogn -r grp2 (BAM input).. ok - 58: Count -R /tmp/NPo_S5Sm_0/view.001.fogn -r grp2 (BAM input).. ok + 58: Count -R /tmp/5nYwRZjWOG/view.001.fogn -r grp2 (BAM input).. ok - 59: Filter -R /tmp/NPo_S5Sm_0/view.001.fogn -r grp2 (CRAM input).. ok + 59: Filter -R /tmp/5nYwRZjWOG/view.001.fogn -r grp2 (CRAM input).. ok - 60: Count -R /tmp/NPo_S5Sm_0/view.001.fogn -r grp2 (CRAM input).. ok + 60: Count -R /tmp/5nYwRZjWOG/view.001.fogn -r grp2 (CRAM input).. ok - 61: Filter -r grp2 -R /tmp/NPo_S5Sm_0/view.001.fogn (SAM input).. ok + 61: Filter -r grp2 -R /tmp/5nYwRZjWOG/view.001.fogn (SAM input).. ok - 62: Count -r grp2 -R /tmp/NPo_S5Sm_0/view.001.fogn (SAM input).. ok + 62: Count -r grp2 -R /tmp/5nYwRZjWOG/view.001.fogn (SAM input).. ok - 63: Filter -r grp2 -R /tmp/NPo_S5Sm_0/view.001.fogn (BAM input).. ok + 63: Filter -r grp2 -R /tmp/5nYwRZjWOG/view.001.fogn (BAM input).. ok - 64: Count -r grp2 -R /tmp/NPo_S5Sm_0/view.001.fogn (BAM input).. ok + 64: Count -r grp2 -R /tmp/5nYwRZjWOG/view.001.fogn (BAM input).. ok - 65: Filter -r grp2 -R /tmp/NPo_S5Sm_0/view.001.fogn (CRAM input).. ok + 65: Filter -r grp2 -R /tmp/5nYwRZjWOG/view.001.fogn (CRAM input).. ok - 66: Count -r grp2 -R /tmp/NPo_S5Sm_0/view.001.fogn (CRAM input).. ok + 66: Count -r grp2 -R /tmp/5nYwRZjWOG/view.001.fogn (CRAM input).. ok - 67: Filter -N /tmp/NPo_S5Sm_0/view.001.forn (SAM input) .. ok + 67: Filter -N /tmp/5nYwRZjWOG/view.001.forn (SAM input) .. ok - 68: Count -N /tmp/NPo_S5Sm_0/view.001.forn (SAM input) .. ok + 68: Count -N /tmp/5nYwRZjWOG/view.001.forn (SAM input) .. ok - 69: Filter -N /tmp/NPo_S5Sm_0/view.001.forn (BAM input) .. ok + 69: Filter -N /tmp/5nYwRZjWOG/view.001.forn (BAM input) .. ok - 70: Count -N /tmp/NPo_S5Sm_0/view.001.forn (BAM input) .. ok + 70: Count -N /tmp/5nYwRZjWOG/view.001.forn (BAM input) .. ok - 71: Filter -N /tmp/NPo_S5Sm_0/view.001.forn (CRAM input) .. ok + 71: Filter -N /tmp/5nYwRZjWOG/view.001.forn (CRAM input) .. ok - 72: Count -N /tmp/NPo_S5Sm_0/view.001.forn (CRAM input) .. ok + 72: Count -N /tmp/5nYwRZjWOG/view.001.forn (CRAM input) .. ok 73: Filter -d BC (SAM input) .. ok @@ -1530,53 +1566,53 @@ 84: Count -d BC:TGCA (CRAM input) .. ok - 85: Filter -D BC:/tmp/NPo_S5Sm_0/view.001.fobc (SAM input) .. ok + 85: Filter -D BC:/tmp/5nYwRZjWOG/view.001.fobc (SAM input) .. ok - 86: Count -D BC:/tmp/NPo_S5Sm_0/view.001.fobc (SAM input) .. ok + 86: Count -D BC:/tmp/5nYwRZjWOG/view.001.fobc (SAM input) .. ok - 87: Filter -D BC:/tmp/NPo_S5Sm_0/view.001.fobc (BAM input) .. ok + 87: Filter -D BC:/tmp/5nYwRZjWOG/view.001.fobc (BAM input) .. ok - 88: Count -D BC:/tmp/NPo_S5Sm_0/view.001.fobc (BAM input) .. ok + 88: Count -D BC:/tmp/5nYwRZjWOG/view.001.fobc (BAM input) .. ok - 89: Filter -D BC:/tmp/NPo_S5Sm_0/view.001.fobc (CRAM input) .. ok + 89: Filter -D BC:/tmp/5nYwRZjWOG/view.001.fobc (CRAM input) .. ok - 90: Count -D BC:/tmp/NPo_S5Sm_0/view.001.fobc (CRAM input) .. ok + 90: Count -D BC:/tmp/5nYwRZjWOG/view.001.fobc (CRAM input) .. ok - 91: Filter -D BC:/tmp/NPo_S5Sm_0/view.001.fobc -d BC:TGCA (SAM input).. ok + 91: Filter -D BC:/tmp/5nYwRZjWOG/view.001.fobc -d BC:TGCA (SAM input).. ok - 92: Count -D BC:/tmp/NPo_S5Sm_0/view.001.fobc -d BC:TGCA (SAM input).. ok + 92: Count -D BC:/tmp/5nYwRZjWOG/view.001.fobc -d BC:TGCA (SAM input).. ok - 93: Filter -D BC:/tmp/NPo_S5Sm_0/view.001.fobc -d BC:TGCA (BAM input).. ok + 93: Filter -D BC:/tmp/5nYwRZjWOG/view.001.fobc -d BC:TGCA (BAM input).. ok - 94: Count -D BC:/tmp/NPo_S5Sm_0/view.001.fobc -d BC:TGCA (BAM input).. ok + 94: Count -D BC:/tmp/5nYwRZjWOG/view.001.fobc -d BC:TGCA (BAM input).. ok - 95: Filter -D BC:/tmp/NPo_S5Sm_0/view.001.fobc -d BC:TGCA (CRAM input).. ok + 95: Filter -D BC:/tmp/5nYwRZjWOG/view.001.fobc -d BC:TGCA (CRAM input).. ok - 96: Count -D BC:/tmp/NPo_S5Sm_0/view.001.fobc -d BC:TGCA (CRAM input).. ok + 96: Count -D BC:/tmp/5nYwRZjWOG/view.001.fobc -d BC:TGCA (CRAM input).. ok - 97: Filter -d BC:TGCA -D BC:/tmp/NPo_S5Sm_0/view.001.fobc (SAM input).. ok + 97: Filter -d BC:TGCA -D BC:/tmp/5nYwRZjWOG/view.001.fobc (SAM input).. ok - 98: Count -d BC:TGCA -D BC:/tmp/NPo_S5Sm_0/view.001.fobc (SAM input).. ok + 98: Count -d BC:TGCA -D BC:/tmp/5nYwRZjWOG/view.001.fobc (SAM input).. ok - 99: Filter -d BC:TGCA -D BC:/tmp/NPo_S5Sm_0/view.001.fobc (BAM input).. ok + 99: Filter -d BC:TGCA -D BC:/tmp/5nYwRZjWOG/view.001.fobc (BAM input).. ok - 100: Count -d BC:TGCA -D BC:/tmp/NPo_S5Sm_0/view.001.fobc (BAM input).. ok + 100: Count -d BC:TGCA -D BC:/tmp/5nYwRZjWOG/view.001.fobc (BAM input).. ok - 101: Filter -d BC:TGCA -D BC:/tmp/NPo_S5Sm_0/view.001.fobc (CRAM input).. ok + 101: Filter -d BC:TGCA -D BC:/tmp/5nYwRZjWOG/view.001.fobc (CRAM input).. ok - 102: Count -d BC:TGCA -D BC:/tmp/NPo_S5Sm_0/view.001.fobc (CRAM input).. ok + 102: Count -d BC:TGCA -D BC:/tmp/5nYwRZjWOG/view.001.fobc (CRAM input).. ok - 103: Filter -D RG:/tmp/NPo_S5Sm_0/view.001.fogn (SAM input) .. ok + 103: Filter -D RG:/tmp/5nYwRZjWOG/view.001.fogn (SAM input) .. ok - 104: Count -D RG:/tmp/NPo_S5Sm_0/view.001.fogn (SAM input) .. ok + 104: Count -D RG:/tmp/5nYwRZjWOG/view.001.fogn (SAM input) .. ok - 105: Filter -D RG:/tmp/NPo_S5Sm_0/view.001.fogn (BAM input) .. ok + 105: Filter -D RG:/tmp/5nYwRZjWOG/view.001.fogn (BAM input) .. ok - 106: Count -D RG:/tmp/NPo_S5Sm_0/view.001.fogn (BAM input) .. ok + 106: Count -D RG:/tmp/5nYwRZjWOG/view.001.fogn (BAM input) .. ok - 107: Filter -D RG:/tmp/NPo_S5Sm_0/view.001.fogn (CRAM input).. ok + 107: Filter -D RG:/tmp/5nYwRZjWOG/view.001.fogn (CRAM input).. ok - 108: Count -D RG:/tmp/NPo_S5Sm_0/view.001.fogn (CRAM input) .. ok + 108: Count -D RG:/tmp/5nYwRZjWOG/view.001.fogn (CRAM input) .. ok 109: Filter -d NE:TGCA (SAM input) .. ok @@ -1592,126 +1628,126 @@ 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/NPo_S5Sm_0/view.test115.sam -h -d TGCA /tmp/NPo_S5Sm_0/view.001.sam --no-PG + /build/reproducible-path/samtools-1.20/samtools view -o /tmp/5nYwRZjWOG/view.test115.sam -h -d TGCA /tmp/5nYwRZjWOG/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/NPo_S5Sm_0/view.001.sam --no-PG + /build/reproducible-path/samtools-1.20/samtools view -c -d TGCA /tmp/5nYwRZjWOG/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/NPo_S5Sm_0/view.test117.sam -h -d TGCA /tmp/NPo_S5Sm_0/view.test001.bam --no-PG + /build/reproducible-path/samtools-1.20/samtools view -o /tmp/5nYwRZjWOG/view.test117.sam -h -d TGCA /tmp/5nYwRZjWOG/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/NPo_S5Sm_0/view.test001.bam --no-PG + /build/reproducible-path/samtools-1.20/samtools view -c -d TGCA /tmp/5nYwRZjWOG/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/NPo_S5Sm_0/view.test119.sam -h -d TGCA /tmp/NPo_S5Sm_0/view.test006.cram --no-PG + /build/reproducible-path/samtools-1.20/samtools view -o /tmp/5nYwRZjWOG/view.test119.sam -h -d TGCA /tmp/5nYwRZjWOG/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/NPo_S5Sm_0/view.test006.cram --no-PG + /build/reproducible-path/samtools-1.20/samtools view -c -d TGCA /tmp/5nYwRZjWOG/view.test006.cram --no-PG .. expected failure - 121: Filter -D BClong:/tmp/NPo_S5Sm_0/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/NPo_S5Sm_0/view.001.fobc" + 121: Filter -D BClong:/tmp/5nYwRZjWOG/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/5nYwRZjWOG/view.001.fobc" Failed command: - /build/reproducible-path/samtools-1.20/samtools view -o /tmp/NPo_S5Sm_0/view.test121.sam -h -D BClong:/tmp/NPo_S5Sm_0/view.001.fobc /tmp/NPo_S5Sm_0/view.001.sam --no-PG + /build/reproducible-path/samtools-1.20/samtools view -o /tmp/5nYwRZjWOG/view.test121.sam -h -D BClong:/tmp/5nYwRZjWOG/view.001.fobc /tmp/5nYwRZjWOG/view.001.sam --no-PG .. expected failure - 122: Count -D BClong:/tmp/NPo_S5Sm_0/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/NPo_S5Sm_0/view.001.fobc" + 122: Count -D BClong:/tmp/5nYwRZjWOG/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/5nYwRZjWOG/view.001.fobc" Failed command: - /build/reproducible-path/samtools-1.20/samtools view -c -D BClong:/tmp/NPo_S5Sm_0/view.001.fobc /tmp/NPo_S5Sm_0/view.001.sam --no-PG + /build/reproducible-path/samtools-1.20/samtools view -c -D BClong:/tmp/5nYwRZjWOG/view.001.fobc /tmp/5nYwRZjWOG/view.001.sam --no-PG .. expected failure - 123: Filter -D BClong:/tmp/NPo_S5Sm_0/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/NPo_S5Sm_0/view.001.fobc" + 123: Filter -D BClong:/tmp/5nYwRZjWOG/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/5nYwRZjWOG/view.001.fobc" Failed command: - /build/reproducible-path/samtools-1.20/samtools view -o /tmp/NPo_S5Sm_0/view.test123.sam -h -D BClong:/tmp/NPo_S5Sm_0/view.001.fobc /tmp/NPo_S5Sm_0/view.test001.bam --no-PG + /build/reproducible-path/samtools-1.20/samtools view -o /tmp/5nYwRZjWOG/view.test123.sam -h -D BClong:/tmp/5nYwRZjWOG/view.001.fobc /tmp/5nYwRZjWOG/view.test001.bam --no-PG .. expected failure - 124: Count -D BClong:/tmp/NPo_S5Sm_0/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/NPo_S5Sm_0/view.001.fobc" + 124: Count -D BClong:/tmp/5nYwRZjWOG/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/5nYwRZjWOG/view.001.fobc" Failed command: - /build/reproducible-path/samtools-1.20/samtools view -c -D BClong:/tmp/NPo_S5Sm_0/view.001.fobc /tmp/NPo_S5Sm_0/view.test001.bam --no-PG + /build/reproducible-path/samtools-1.20/samtools view -c -D BClong:/tmp/5nYwRZjWOG/view.001.fobc /tmp/5nYwRZjWOG/view.test001.bam --no-PG .. expected failure - 125: Filter -D BClong:/tmp/NPo_S5Sm_0/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/NPo_S5Sm_0/view.001.fobc" + 125: Filter -D BClong:/tmp/5nYwRZjWOG/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/5nYwRZjWOG/view.001.fobc" Failed command: - /build/reproducible-path/samtools-1.20/samtools view -o /tmp/NPo_S5Sm_0/view.test125.sam -h -D BClong:/tmp/NPo_S5Sm_0/view.001.fobc /tmp/NPo_S5Sm_0/view.test006.cram --no-PG + /build/reproducible-path/samtools-1.20/samtools view -o /tmp/5nYwRZjWOG/view.test125.sam -h -D BClong:/tmp/5nYwRZjWOG/view.001.fobc /tmp/5nYwRZjWOG/view.test006.cram --no-PG .. expected failure - 126: Count -D BClong:/tmp/NPo_S5Sm_0/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/NPo_S5Sm_0/view.001.fobc" + 126: Count -D BClong:/tmp/5nYwRZjWOG/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/5nYwRZjWOG/view.001.fobc" Failed command: - /build/reproducible-path/samtools-1.20/samtools view -c -D BClong:/tmp/NPo_S5Sm_0/view.001.fobc /tmp/NPo_S5Sm_0/view.test006.cram --no-PG + /build/reproducible-path/samtools-1.20/samtools view -c -D BClong:/tmp/5nYwRZjWOG/view.001.fobc /tmp/5nYwRZjWOG/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/NPo_S5Sm_0/view.test127.sam -h -d BC:ACGT -d RG:grp2 /tmp/NPo_S5Sm_0/view.001.sam --no-PG + /build/reproducible-path/samtools-1.20/samtools view -o /tmp/5nYwRZjWOG/view.test127.sam -h -d BC:ACGT -d RG:grp2 /tmp/5nYwRZjWOG/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/NPo_S5Sm_0/view.001.sam --no-PG + /build/reproducible-path/samtools-1.20/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/5nYwRZjWOG/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/NPo_S5Sm_0/view.test129.sam -h -d BC:ACGT -d RG:grp2 /tmp/NPo_S5Sm_0/view.test001.bam --no-PG + /build/reproducible-path/samtools-1.20/samtools view -o /tmp/5nYwRZjWOG/view.test129.sam -h -d BC:ACGT -d RG:grp2 /tmp/5nYwRZjWOG/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/NPo_S5Sm_0/view.test001.bam --no-PG + /build/reproducible-path/samtools-1.20/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/5nYwRZjWOG/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/NPo_S5Sm_0/view.test131.sam -h -d BC:ACGT -d RG:grp2 /tmp/NPo_S5Sm_0/view.test006.cram --no-PG + /build/reproducible-path/samtools-1.20/samtools view -o /tmp/5nYwRZjWOG/view.test131.sam -h -d BC:ACGT -d RG:grp2 /tmp/5nYwRZjWOG/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/NPo_S5Sm_0/view.test006.cram --no-PG + /build/reproducible-path/samtools-1.20/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/5nYwRZjWOG/view.test006.cram --no-PG .. expected failure @@ -2593,7 +2629,7 @@ .. ok test_bam2fq: - /build/reproducible-path/samtools-1.20/samtools fastq -N -s /tmp/NPo_S5Sm_0/bam2fq.discard.s.fq -0 /tmp/NPo_S5Sm_0/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/5nYwRZjWOG/bam2fq.discard.s.fq -0 /tmp/5nYwRZjWOG/bam2fq.discard.0.fq /build/reproducible-path/samtools-1.20/test/dat/bam2fq.001.sam .. ok test_bam2fq: @@ -2734,7 +2770,7 @@ .. ok test_bam2fq: - /build/reproducible-path/samtools-1.20/samtools fastq -@ 2 -N -s /tmp/NPo_S5Sm_0/bam2fq.discard.s.fq -0 /tmp/NPo_S5Sm_0/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/5nYwRZjWOG/bam2fq.discard.s.fq -0 /tmp/5nYwRZjWOG/bam2fq.discard.0.fq /build/reproducible-path/samtools-1.20/test/dat/bam2fq.001.sam .. ok test_bam2fq: @@ -2951,7 +2987,7 @@ .. ok test_merge: - /build/reproducible-path/samtools-1.20/samtools merge -s 1 -O sam -b /tmp/_j2leMGeh7 - /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/WisgFW9pyk - /build/reproducible-path/samtools-1.20/test/dat/test_input_1_a.bam .. ok test_merge: @@ -2975,11 +3011,11 @@ .. ok test_merge: - /build/reproducible-path/samtools-1.20/samtools merge -s 1 -p -c -t PG -O SAM - /tmp/NPo_S5Sm_0/merge.tag.1.bam /tmp/NPo_S5Sm_0/merge.tag.2.bam + /build/reproducible-path/samtools-1.20/samtools merge -s 1 -p -c -t PG -O SAM - /tmp/5nYwRZjWOG/merge.tag.1.bam /tmp/5nYwRZjWOG/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/NPo_S5Sm_0/merge.tag.3.bam /tmp/NPo_S5Sm_0/merge.tag.4.bam + /build/reproducible-path/samtools-1.20/samtools merge -s 1 -p -c -n -t PG -O SAM - /tmp/5nYwRZjWOG/merge.tag.3.bam /tmp/5nYwRZjWOG/merge.tag.4.bam .. ok test_merge: @@ -2987,7 +3023,7 @@ .. 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/NPo_S5Sm_0/merge.bed.1.bam /tmp/NPo_S5Sm_0/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/5nYwRZjWOG/merge.bed.1.bam /tmp/5nYwRZjWOG/merge.bed.2.bam .. ok test_merge: @@ -3003,7 +3039,7 @@ .. ok test_merge: - /build/reproducible-path/samtools-1.20/samtools merge -@ 2 -s 1 -O sam -b /tmp/65eQvsO6BL - /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/YNVuHX98HX - /build/reproducible-path/samtools-1.20/test/dat/test_input_1_a.bam .. ok test_merge: @@ -3027,11 +3063,11 @@ .. ok test_merge: - /build/reproducible-path/samtools-1.20/samtools merge -@ 2 -s 1 -p -c -t PG -O SAM - /tmp/NPo_S5Sm_0/merge.tag.1.bam /tmp/NPo_S5Sm_0/merge.tag.2.bam + /build/reproducible-path/samtools-1.20/samtools merge -@ 2 -s 1 -p -c -t PG -O SAM - /tmp/5nYwRZjWOG/merge.tag.1.bam /tmp/5nYwRZjWOG/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/NPo_S5Sm_0/merge.tag.3.bam /tmp/NPo_S5Sm_0/merge.tag.4.bam + /build/reproducible-path/samtools-1.20/samtools merge -@ 2 -s 1 -p -c -n -t PG -O SAM - /tmp/5nYwRZjWOG/merge.tag.3.bam /tmp/5nYwRZjWOG/merge.tag.4.bam .. ok test_merge: @@ -3039,7 +3075,7 @@ .. 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/NPo_S5Sm_0/merge.bed.1.bam /tmp/NPo_S5Sm_0/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/5nYwRZjWOG/merge.bed.1.bam /tmp/5nYwRZjWOG/merge.bed.2.bam .. ok test_merge: @@ -3047,15 +3083,15 @@ .. 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/NPo_S5Sm_0/sortout + /build/reproducible-path/samtools-1.20/samtools sort /build/reproducible-path/samtools-1.20/test/dat/test_input_1_a.bam /tmp/5nYwRZjWOG/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/NPo_S5Sm_0/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/5nYwRZjWOG/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/NPo_S5Sm_0/sorttmp + /build/reproducible-path/samtools-1.20/samtools sort -o /build/reproducible-path/samtools-1.20/test/dat/test_input_1_a.bam /tmp/5nYwRZjWOG/sorttmp .. ok test_sort: @@ -3107,15 +3143,15 @@ .. 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/NPo_S5Sm_0/sortout + /build/reproducible-path/samtools-1.20/samtools sort -@ 2 /build/reproducible-path/samtools-1.20/test/dat/test_input_1_a.bam /tmp/5nYwRZjWOG/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/NPo_S5Sm_0/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/5nYwRZjWOG/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/NPo_S5Sm_0/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/5nYwRZjWOG/sorttmp .. ok test_sort: @@ -3819,15 +3855,15 @@ .. ok test_large_positions: - /build/reproducible-path/samtools-1.20/samtools view -h --no-PG /tmp/NPo_S5Sm_0/longref.sam.gz + /build/reproducible-path/samtools-1.20/samtools view -h --no-PG /tmp/5nYwRZjWOG/longref.sam.gz .. ok test_large_positions: - /build/reproducible-path/samtools-1.20/samtools view -h --no-PG /tmp/NPo_S5Sm_0/longref.sam.gz CHROMOSOME_I:10000000114-10000000168 + /build/reproducible-path/samtools-1.20/samtools view -h --no-PG /tmp/5nYwRZjWOG/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/NPo_S5Sm_0/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/5nYwRZjWOG/longref.sam.gz .. ok test_large_positions: @@ -3847,7 +3883,7 @@ .. ok test_large_positions: - /build/reproducible-path/samtools-1.20/samtools tview -d T -p CHROMOSOME_I:10000000000 /tmp/NPo_S5Sm_0/longref.sam.gz + /build/reproducible-path/samtools-1.20/samtools tview -d T -p CHROMOSOME_I:10000000000 /tmp/5nYwRZjWOG/longref.sam.gz .. ok test_large_positions: @@ -4075,7 +4111,7 @@ Unexpected failures: 0 => PASS make[2]: Leaving directory '/build/reproducible-path/samtools-1.20' - rm -fr -- /tmp/dh-xdg-rundir-ni_7TdE2 + rm -fr -- /tmp/dh-xdg-rundir-ry7JAqr_ make[1]: Leaving directory '/build/reproducible-path/samtools-1.20' create-stamp debian/debhelper-build-stamp dh_prep @@ -4087,7 +4123,7 @@ dh_auto_install -- \ prefix=/usr install -m0755 -d /build/reproducible-path/samtools-1.20/debian/tmp - make -j20 install DESTDIR=/build/reproducible-path/samtools-1.20/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr + make -j42 install DESTDIR=/build/reproducible-path/samtools-1.20/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr make[2]: Entering directory '/build/reproducible-path/samtools-1.20' mkdir -p -m 755 /build/reproducible-path/samtools-1.20/debian/tmp/usr/bin /build/reproducible-path/samtools-1.20/debian/tmp/usr/bin /build/reproducible-path/samtools-1.20/debian/tmp/usr/share/man/man1 install -p samtools /build/reproducible-path/samtools-1.20/debian/tmp/usr/bin @@ -4172,79 +4208,93 @@ dh_installman rm -f debian/samtools/usr/share/man/man1/samtools-fastq.1 ln -s samtools-fasta.1 debian/samtools/usr/share/man/man1/samtools-fastq.1 - man-recode --to-code UTF-8 --suffix .dh-new 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 - man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-ampliconstats.1 debian/samtools/usr/share/man/man1/samtools-bedcov.1 debian/samtools/usr/share/man/man1/samtools-calmd.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-cat.1 debian/samtools/usr/share/man/man1/samtools-collate.1 debian/samtools/usr/share/man/man1/samtools-consensus.1 - man-recode --to-code UTF-8 --suffix .dh-new 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 - man-recode --to-code UTF-8 --suffix .dh-new 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 - man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-fasta.1 debian/samtools/usr/share/man/man1/samtools-fixmate.1 debian/samtools/usr/share/man/man1/samtools-flags.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-flagstat.1 debian/samtools/usr/share/man/man1/samtools-fqidx.1 debian/samtools/usr/share/man/man1/samtools-head.1 - man-recode --to-code UTF-8 --suffix .dh-new 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 - 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 - man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-phase.1 debian/samtools/usr/share/man/man1/samtools-quickcheck.1 debian/samtools/usr/share/man/man1/samtools-reference.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-reheader.1 debian/samtools/usr/share/man/man1/samtools-reset.1 debian/samtools/usr/share/man/man1/samtools-rmdup.1 - man-recode --to-code UTF-8 --suffix .dh-new 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 - man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-view.1 debian/samtools/usr/share/man/man1/samtools.1 debian/samtools/usr/share/man/man1/samtools.pl.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/ace2sam.1 debian/samtools/usr/share/man/man1/samtools-addreplacerg.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-ampliconclip.1 debian/samtools/usr/share/man/man1/samtools-ampliconstats.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-bedcov.1 debian/samtools/usr/share/man/man1/samtools-calmd.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-cat.1 debian/samtools/usr/share/man/man1/samtools-collate.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-consensus.1 debian/samtools/usr/share/man/man1/samtools-coverage.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-cram-size.1 debian/samtools/usr/share/man/man1/samtools-depad.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-depth.1 debian/samtools/usr/share/man/man1/samtools-dict.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-faidx.1 debian/samtools/usr/share/man/man1/samtools-fasta.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-fixmate.1 debian/samtools/usr/share/man/man1/samtools-flags.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-flagstat.1 debian/samtools/usr/share/man/man1/samtools-fqidx.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-head.1 debian/samtools/usr/share/man/man1/samtools-idxstats.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-import.1 debian/samtools/usr/share/man/man1/samtools-index.1 + 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 + man-recode --to-code UTF-8 --suffix .dh-new 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 + man-recode --to-code UTF-8 --suffix .dh-new 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 + man-recode --to-code UTF-8 --suffix .dh-new 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 + man-recode --to-code UTF-8 --suffix .dh-new 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 man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/wgsim.1 - mv debian/samtools/usr/share/man/man1/wgsim.1.dh-new debian/samtools/usr/share/man/man1/wgsim.1 - chmod 0644 -- debian/samtools/usr/share/man/man1/wgsim.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 - 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 - 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 - mv debian/samtools/usr/share/man/man1/samtools-head.1.dh-new debian/samtools/usr/share/man/man1/samtools-head.1 - chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-flagstat.1 debian/samtools/usr/share/man/man1/samtools-fqidx.1 debian/samtools/usr/share/man/man1/samtools-head.1 + chmod 0644 -- debian/samtools/usr/share/man/man1/ace2sam.1 debian/samtools/usr/share/man/man1/samtools-addreplacerg.1 + mv debian/samtools/usr/share/man/man1/samtools-cat.1.dh-new debian/samtools/usr/share/man/man1/samtools-cat.1 + mv debian/samtools/usr/share/man/man1/samtools-collate.1.dh-new debian/samtools/usr/share/man/man1/samtools-collate.1 + chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-cat.1 debian/samtools/usr/share/man/man1/samtools-collate.1 + mv debian/samtools/usr/share/man/man1/samtools-consensus.1.dh-new debian/samtools/usr/share/man/man1/samtools-consensus.1 mv debian/samtools/usr/share/man/man1/samtools-coverage.1.dh-new debian/samtools/usr/share/man/man1/samtools-coverage.1 + chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-consensus.1 debian/samtools/usr/share/man/man1/samtools-coverage.1 + mv debian/samtools/usr/share/man/man1/wgsim.1.dh-new debian/samtools/usr/share/man/man1/wgsim.1 + chmod 0644 -- debian/samtools/usr/share/man/man1/wgsim.1 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-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-fasta.1.dh-new debian/samtools/usr/share/man/man1/samtools-fasta.1 + chmod 0644 -- 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 - chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-fasta.1 debian/samtools/usr/share/man/man1/samtools-fixmate.1 debian/samtools/usr/share/man/man1/samtools-flags.1 - mv debian/samtools/usr/share/man/man1/samtools-cat.1.dh-new debian/samtools/usr/share/man/man1/samtools-cat.1 - mv debian/samtools/usr/share/man/man1/samtools-collate.1.dh-new debian/samtools/usr/share/man/man1/samtools-collate.1 - mv debian/samtools/usr/share/man/man1/samtools-consensus.1.dh-new debian/samtools/usr/share/man/man1/samtools-consensus.1 - chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-cat.1 debian/samtools/usr/share/man/man1/samtools-collate.1 debian/samtools/usr/share/man/man1/samtools-consensus.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 - mv debian/samtools/usr/share/man/man1/samtools-rmdup.1.dh-new debian/samtools/usr/share/man/man1/samtools-rmdup.1 - chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-reheader.1 debian/samtools/usr/share/man/man1/samtools-reset.1 debian/samtools/usr/share/man/man1/samtools-rmdup.1 + chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-fixmate.1 debian/samtools/usr/share/man/man1/samtools-flags.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 + chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-bedcov.1 debian/samtools/usr/share/man/man1/samtools-calmd.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/samtools-ampliconclip.1 debian/samtools/usr/share/man/man1/samtools-ampliconstats.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-faidx.1 debian/samtools/usr/share/man/man1/samtools-fasta.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 - chmod 0644 -- 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 - 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-samples.1 debian/samtools/usr/share/man/man1/samtools-sort.1 debian/samtools/usr/share/man/man1/samtools-split.1 + chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-markdup.1 debian/samtools/usr/share/man/man1/samtools-merge.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-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 + chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-quickcheck.1 debian/samtools/usr/share/man/man1/samtools-reference.1 + mv debian/samtools/usr/share/man/man1/samtools-head.1.dh-new debian/samtools/usr/share/man/man1/samtools-head.1 mv debian/samtools/usr/share/man/man1/samtools-idxstats.1.dh-new debian/samtools/usr/share/man/man1/samtools-idxstats.1 + chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-head.1 debian/samtools/usr/share/man/man1/samtools-idxstats.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 + chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-rmdup.1 debian/samtools/usr/share/man/man1/samtools-samples.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 + chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-depth.1 debian/samtools/usr/share/man/man1/samtools-dict.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-reheader.1 debian/samtools/usr/share/man/man1/samtools-reset.1 + mv debian/samtools/usr/share/man/man1/samtools-mpileup.1.dh-new debian/samtools/usr/share/man/man1/samtools-mpileup.1 + mv debian/samtools/usr/share/man/man1/samtools-phase.1.dh-new debian/samtools/usr/share/man/man1/samtools-phase.1 + chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-mpileup.1 debian/samtools/usr/share/man/man1/samtools-phase.1 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-idxstats.1 debian/samtools/usr/share/man/man1/samtools-import.1 debian/samtools/usr/share/man/man1/samtools-index.1 + chmod 0644 -- 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-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-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 + chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-stats.1 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 - 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 - mv debian/samtools/usr/share/man/man1/samtools-ampliconstats.1.dh-new 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 - chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-ampliconstats.1 debian/samtools/usr/share/man/man1/samtools-bedcov.1 debian/samtools/usr/share/man/man1/samtools-calmd.1 - mv debian/samtools/usr/share/man/man1/samtools-phase.1.dh-new debian/samtools/usr/share/man/man1/samtools-phase.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 - chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-phase.1 debian/samtools/usr/share/man/man1/samtools-quickcheck.1 debian/samtools/usr/share/man/man1/samtools-reference.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 - 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 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-tview.1 debian/samtools/usr/share/man/man1/samtools-view.1 mv debian/samtools/usr/share/man/man1/samtools.1.dh-new debian/samtools/usr/share/man/man1/samtools.1 mv debian/samtools/usr/share/man/man1/samtools.pl.1.dh-new debian/samtools/usr/share/man/man1/samtools.pl.1 - chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-view.1 debian/samtools/usr/share/man/man1/samtools.1 debian/samtools/usr/share/man/man1/samtools.pl.1 + chmod 0644 -- debian/samtools/usr/share/man/man1/samtools.1 debian/samtools/usr/share/man/man1/samtools.pl.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 @@ -4274,12 +4324,12 @@ find debian/samtools ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/samtools-test ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/samtools/usr/share/doc -type f -a -true -a ! -regex 'debian/samtools/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 - find debian/samtools-test/usr/share/doc -type f -a -true -a ! -regex 'debian/samtools-test/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/samtools/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 - find debian/samtools-test/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 + find debian/samtools-test/usr/share/doc -type f -a -true -a ! -regex 'debian/samtools-test/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/samtools/usr/share/man debian/samtools/usr/share/lintian/overrides -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 - find debian/samtools-test -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 + find debian/samtools-test/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/samtools -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 + find debian/samtools-test -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/samtools/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x debian/rules execute_after_dh_fixperms-indep make[1]: Entering directory '/build/reproducible-path/samtools-1.20' @@ -4293,11 +4343,16 @@ objcopy --compress-debug-sections debian/samtools/usr/lib/debug/.dwz/x86_64-linux-gnu/samtools.debug chmod 0644 -- debian/samtools/usr/lib/debug/.dwz/x86_64-linux-gnu/samtools.debug dh_strip -a - install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/e7 - objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/wgsim debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/e7/fbd3eb37736f2d6957a0d2f98bf459390b525c.debug - chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/e7/fbd3eb37736f2d6957a0d2f98bf459390b525c.debug - strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/wgsim - objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/e7/fbd3eb37736f2d6957a0d2f98bf459390b525c.debug debian/samtools/usr/bin/wgsim + install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/6e + objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5fa debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/6e/bb408818b3178673942d10e5d72f99570327fd.debug + chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/6e/bb408818b3178673942d10e5d72f99570327fd.debug + strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/md5fa + objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/6e/bb408818b3178673942d10e5d72f99570327fd.debug debian/samtools/usr/bin/md5fa + install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/52 + objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5sum-lite debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/52/aae5257e154835835de2d6daeae5897b064c84.debug + chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/52/aae5257e154835835de2d6daeae5897b064c84.debug + strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/md5sum-lite + objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/52/aae5257e154835835de2d6daeae5897b064c84.debug debian/samtools/usr/bin/md5sum-lite install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/22 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-long debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/22/955db446ee53e042d333a8903a0a83ea66277c.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/22/955db446ee53e042d333a8903a0a83ea66277c.debug @@ -4308,16 +4363,11 @@ chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/b7/3b8e178cbbf221ff545d49679df7f6b4bec335.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/b7/3b8e178cbbf221ff545d49679df7f6b4bec335.debug debian/samtools/usr/bin/ace2sam - install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/52 - objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5sum-lite debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/52/aae5257e154835835de2d6daeae5897b064c84.debug - chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/52/aae5257e154835835de2d6daeae5897b064c84.debug - strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/md5sum-lite - objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/52/aae5257e154835835de2d6daeae5897b064c84.debug debian/samtools/usr/bin/md5sum-lite - install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/6e - objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5fa debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/6e/bb408818b3178673942d10e5d72f99570327fd.debug - chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/6e/bb408818b3178673942d10e5d72f99570327fd.debug - strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/md5fa - objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/6e/bb408818b3178673942d10e5d72f99570327fd.debug debian/samtools/usr/bin/md5fa + install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/e7 + objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/wgsim debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/e7/fbd3eb37736f2d6957a0d2f98bf459390b525c.debug + chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/e7/fbd3eb37736f2d6957a0d2f98bf459390b525c.debug + strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/wgsim + objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/e7/fbd3eb37736f2d6957a0d2f98bf459390b525c.debug debian/samtools/usr/bin/wgsim install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/34 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/samtools debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/34/8e1ba851d840ff0dacf4208c541c29d107d2a4.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/34/8e1ba851d840ff0dacf4208c541c29d107d2a4.debug @@ -4339,31 +4389,31 @@ 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/maq2sam-long debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/samtools debian/samtools/usr/bin/maq2sam-short + dpkg-shlibdeps -Tdebian/samtools.substvars debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/samtools debian/samtools/usr/bin/maq2sam-short dh_installdeb install -m0755 -d debian/samtools/DEBIAN install -m0755 -d debian/samtools-test/DEBIAN dh_gencontrol + install -m0755 -d debian/samtools-test/DEBIAN + echo misc:Depends= >> debian/samtools-test.substvars + echo misc:Pre-Depends= >> debian/samtools-test.substvars + dpkg-gencontrol -psamtools-test -ldebian/changelog -Tdebian/samtools-test.substvars -cdebian/control -Pdebian/samtools-test install -m0755 -d debian/samtools/DEBIAN echo misc:Depends= >> debian/samtools.substvars 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=22955db446ee53e042d333a8903a0a83ea66277c 27a2fbd3003c116789d7c1310d90eb3a0b239c36 348e1ba851d840ff0dacf4208c541c29d107d2a4 52aae5257e154835835de2d6daeae5897b064c84 6ebb408818b3178673942d10e5d72f99570327fd b73b8e178cbbf221ff545d49679df7f6b4bec335 e7fbd3eb37736f2d6957a0d2f98bf459390b525c" -DSection=debug -UMulti-Arch -UReplaces -UBreaks - install -m0755 -d debian/samtools-test/DEBIAN - echo misc:Depends= >> debian/samtools-test.substvars - echo misc:Pre-Depends= >> debian/samtools-test.substvars - dpkg-gencontrol -psamtools-test -ldebian/changelog -Tdebian/samtools-test.substvars -cdebian/control -Pdebian/samtools-test -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 +dpkg-gencontrol: warning: package samtools-test: 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 + 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 install -m0755 -d debian/samtools/DEBIAN - cd debian/samtools >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums install -m0755 -d debian/samtools-test/DEBIAN + cd debian/samtools >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/samtools-test >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/samtools/DEBIAN/md5sums install -m0755 -d debian/.debhelper/samtools/dbgsym-root/DEBIAN @@ -4385,12 +4435,14 @@ 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/1803923/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1803923/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/1563099 and its subdirectories -I: Current time: Fri Jan 10 05:31:32 -12 2025 -I: pbuilder-time-stamp: 1736530292 +I: removing directory /srv/workspace/pbuilder/1803923 and its subdirectories +I: Current time: Fri Feb 13 13:56:17 +14 2026 +I: pbuilder-time-stamp: 1770940577