Diff of the two buildlogs: -- --- b1/build.log 2024-05-11 10:57:49.619244548 +0000 +++ b2/build.log 2024-05-11 11:00:14.753062740 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri May 10 22:52:20 -12 2024 -I: pbuilder-time-stamp: 1715424740 +I: Current time: Sat Jun 14 07:20:52 +14 2025 +I: pbuilder-time-stamp: 1749835252 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -28,52 +28,84 @@ dpkg-source: info: applying reproducible.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2682622/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/323021/tmp/hooks/D01_modify_environment starting +debug: Running on ionos5-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Jun 13 17:21 /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/323021/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/323021/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]="21" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.21(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' + DIRSTACK=() + DISTRIBUTION=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='fad62b2d284840a58249793d7f87c28e' - 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='2682622' - PS1='# ' - PS2='> ' + INVOCATION_ID=4575d1b85f634b97b022339282847a95 + 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=323021 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.RDOKlOdX/pbuilderrc_q3CF --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.RDOKlOdX/b1 --logfile b1/build.log samtools_1.19.2-1.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://46.16.76.132:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.RDOKlOdX/pbuilderrc_lFmJ --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.RDOKlOdX/b2 --logfile b2/build.log samtools_1.19.2-1.dsc' + SUDO_GID=110 + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos11-amd64 6.1.0-21-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.6.13+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.6.13-1~bpo12+1 (2024-02-15) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 10 11:25 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2682622/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Jun 10 17:46 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/323021/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -194,7 +226,7 @@ Get: 61 http://deb.debian.org/debian trixie/main amd64 pkgconf-bin amd64 1.8.1-1+b2 [29.7 kB] Get: 62 http://deb.debian.org/debian trixie/main amd64 pkgconf amd64 1.8.1-1+b2 [26.2 kB] Get: 63 http://deb.debian.org/debian trixie/main amd64 tabix amd64 1.19+ds-1.1+b1 [476 kB] -Fetched 27.3 MB in 1s (27.0 MB/s) +Fetched 27.3 MB in 0s (72.2 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package autoconf-archive. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19699 files and directories currently installed.) @@ -461,7 +493,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/samtools-1.19.2/ && 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_1.19.2-1_source.changes +I: user script /srv/workspace/pbuilder/323021/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/323021/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/samtools-1.19.2/ && 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_1.19.2-1_source.changes dpkg-buildpackage: info: source package samtools dpkg-buildpackage: info: source version 1.19.2-1 dpkg-buildpackage: info: source distribution unstable @@ -476,7 +512,7 @@ rm -f config.mk touch config.mk dh_auto_clean -- - make -j20 distclean + make -j42 distclean make[2]: Entering directory '/build/reproducible-path/samtools-1.19.2' rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp test/*/*.tmp.* cd test/dat && rm -f test_input_*.bam.bai view.*.bam.bai @@ -564,118 +600,118 @@ 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-1.19.2=. -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-1.19.2=. -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-1.19.2' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -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-1.19.2=. -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 -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-1.19.2=. -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_plcmd.o bam_plcmd.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -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_view.o sam_view.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -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_fastq.o bam_fastq.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -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 -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-1.19.2=. -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 -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-1.19.2=. -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 -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-1.19.2=. -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-1.19.2=. -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-1.19.2=. -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -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-1.19.2=. -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-1.19.2=. -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-1.19.2=. -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-1.19.2=. -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 -echo '#define SAMTOOLS_VERSION "1.19.2"' > version.h 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_CC "gcc"' >> version.h +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 "1.19.2"' > 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-1.19.2=. -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 -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-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection"' >> version.h 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-1.19.2=. -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -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 -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -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 -echo '#define SAMTOOLS_HTSDIR ""' >> version.h 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_CC "gcc"' >> 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-1.19.2=. -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 -echo '#define SAMTOOLS_LIBS ""' >> version.h -echo '#define SAMTOOLS_CURSES_LIB "-lcurses"' >> version.h -sed -i -e 's@/build/reproducible-path/samtools-1.19.2@«BUILDPATH»@g' version.h gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -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 -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-1.19.2=. -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 -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -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 -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-1.19.2=. -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-1.19.2=. -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 -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -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 +echo '#define SAMTOOLS_CFLAGS "-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection"' >> 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-1.19.2=. -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -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-1.19.2=. -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 +echo '#define SAMTOOLS_LDFLAGS "-Wl,-z,relro -Wl,-z,now"' >> 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-1.19.2=. -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -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 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-1.19.2=. -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 +echo '#define SAMTOOLS_HTSDIR ""' >> version.h gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -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 -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -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 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-1.19.2=. -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-1.19.2=. -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 +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_LIBS ""' >> version.h gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -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 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-1.19.2=. -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -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 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_CURSES_LIB "-lcurses"' >> version.h gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -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 -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -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 +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -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 +sed -i -e 's@/build/reproducible-path/samtools-1.19.2@«BUILDPATH»@g' version.h gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -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 +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-1.19.2=. -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -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-1.19.2=. -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -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-1.19.2=. -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 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-1.19.2=. -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-1.19.2=. -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 +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-1.19.2=. -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 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-1.19.2=. -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-1.19.2=. -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 -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -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 +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -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.o bam.c cc1: warning: command-line option '-frelease' is valid for D but not for C @@ -686,54 +722,54 @@ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -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/maq2sam-short.o misc/maq2sam.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-1.19.2=. -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 -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-1.19.2=. -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 +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-1.19.2=. -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-1.19.2=. -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 +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -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 +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -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 +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -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 +gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/md5sum-lite misc/md5sum-lite.o -lhts -lz 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-1.19.2=. -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 -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-1.19.2=. -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-1.19.2=. -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 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 -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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -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-1.19.2=. -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-1.19.2=. -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 -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -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 -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -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-long misc/maq2sam-long.o -lz -gcc -Wl,-z,relro -Wl,-z,now -o misc/maq2sam-short misc/maq2sam-short.o -lz 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/md5fa misc/md5fa.o -lhts -lz -gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/md5sum-lite misc/md5sum-lite.o -lhts -lz +gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/wgsim misc/wgsim.o -lm -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_filter_header_rg test/split/test_filter_header_rg.o test/test.o libst.a -lhts -lz -lpthread -gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/vcf-miniview test/vcf-miniview.o -lhts -lz -lpthread -gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/wgsim misc/wgsim.o -lm -lhts -lz 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_parse_args test/split/test_parse_args.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/split/test_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-1.19.2=. -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-1.19.2=. -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.19.2=. -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_trans_tbl_init.o test/merge/test_trans_tbl_init.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 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 -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/merge/test_rtrans_build test/merge/test_rtrans_build.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/merge/test_trans_tbl_init test/merge/test_trans_tbl_init.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/merge/test_bam_translate test/merge/test_bam_translate.o test/test.o libst.a -lhts -lz -lpthread -gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/merge/test_rtrans_build test/merge/test_rtrans_build.o test/test.o libst.a -lhts -lz -lpthread make[2]: Leaving directory '/build/reproducible-path/samtools-1.19.2' make[1]: Leaving directory '/build/reproducible-path/samtools-1.19.2' rm -f debian/samtools-test.debhelper.log debian/samtools.debhelper.log debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/samtools-1.19.2' 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-1.19.2' test/split/test_count_rg test/split/test_expand_format_string @@ -772,75 +808,75 @@ /build/reproducible-path/samtools-1.19.2/samtools reference -@ 2 -r 17:1000-1500 -e test/reference/mpileup.1.tmp.cram .. ok -/usr/bin/bgzip -c -b 65272 -s 5 /tmp/vGdHfQK99f/bgzip.dat.gz +/usr/bin/bgzip -c -b 65272 -s 5 /tmp/s3TWm1fqcD/bgzip.dat.gz .. ok -/usr/bin/bgzip -c -b 979200 -s 6 /tmp/vGdHfQK99f/bgzip.dat.gz +/usr/bin/bgzip -c -b 979200 -s 6 /tmp/s3TWm1fqcD/bgzip.dat.gz .. ok -/usr/bin/bgzip -c -b 652804 -s 6 /tmp/vGdHfQK99f/bgzip.dat.gz +/usr/bin/bgzip -c -b 652804 -s 6 /tmp/s3TWm1fqcD/bgzip.dat.gz .. ok -/build/reproducible-path/samtools-1.19.2/samtools faidx /tmp/vGdHfQK99f/faidx.fa 3:11-13 | grep -v '^>' +/build/reproducible-path/samtools-1.19.2/samtools faidx /tmp/s3TWm1fqcD/faidx.fa 3:11-13 | grep -v '^>' .. ok -/build/reproducible-path/samtools-1.19.2/samtools faidx /tmp/vGdHfQK99f/faidx.fa.gz 3:11-13 | grep -v '^>' +/build/reproducible-path/samtools-1.19.2/samtools faidx /tmp/s3TWm1fqcD/faidx.fa.gz 3:11-13 | grep -v '^>' .. ok -/build/reproducible-path/samtools-1.19.2/samtools faidx /tmp/vGdHfQK99f/faidx.fa 2:998-1003 | grep -v '^>' +/build/reproducible-path/samtools-1.19.2/samtools faidx /tmp/s3TWm1fqcD/faidx.fa 2:998-1003 | grep -v '^>' .. ok -/build/reproducible-path/samtools-1.19.2/samtools faidx /tmp/vGdHfQK99f/faidx.fa.gz 2:998-1003 | grep -v '^>' +/build/reproducible-path/samtools-1.19.2/samtools faidx /tmp/s3TWm1fqcD/faidx.fa.gz 2:998-1003 | grep -v '^>' .. ok -/build/reproducible-path/samtools-1.19.2/samtools faidx /tmp/vGdHfQK99f/faidx.fa 1:100-104 | grep -v '^>' +/build/reproducible-path/samtools-1.19.2/samtools faidx /tmp/s3TWm1fqcD/faidx.fa 1:100-104 | grep -v '^>' .. ok -/build/reproducible-path/samtools-1.19.2/samtools faidx /tmp/vGdHfQK99f/faidx.fa.gz 1:100-104 | grep -v '^>' +/build/reproducible-path/samtools-1.19.2/samtools faidx /tmp/s3TWm1fqcD/faidx.fa.gz 1:100-104 | grep -v '^>' .. ok -/build/reproducible-path/samtools-1.19.2/samtools faidx /tmp/vGdHfQK99f/faidx.fa 1:99998-100007 | grep -v '^>' +/build/reproducible-path/samtools-1.19.2/samtools faidx /tmp/s3TWm1fqcD/faidx.fa 1:99998-100007 | grep -v '^>' .. ok -/build/reproducible-path/samtools-1.19.2/samtools faidx /tmp/vGdHfQK99f/faidx.fa.gz 1:99998-100007 | grep -v '^>' +/build/reproducible-path/samtools-1.19.2/samtools faidx /tmp/s3TWm1fqcD/faidx.fa.gz 1:99998-100007 | grep -v '^>' .. ok -/build/reproducible-path/samtools-1.19.2/samtools fqidx /tmp/vGdHfQK99f/fqidx.fq 3:11-13 +/build/reproducible-path/samtools-1.19.2/samtools fqidx /tmp/s3TWm1fqcD/fqidx.fq 3:11-13 .. ok .. ok -/build/reproducible-path/samtools-1.19.2/samtools fqidx /tmp/vGdHfQK99f/fqidx.fq.gz 3:11-13 +/build/reproducible-path/samtools-1.19.2/samtools fqidx /tmp/s3TWm1fqcD/fqidx.fq.gz 3:11-13 .. ok .. ok -/build/reproducible-path/samtools-1.19.2/samtools fqidx /tmp/vGdHfQK99f/fqidx.fq 2:998-1003 +/build/reproducible-path/samtools-1.19.2/samtools fqidx /tmp/s3TWm1fqcD/fqidx.fq 2:998-1003 .. ok .. ok -/build/reproducible-path/samtools-1.19.2/samtools fqidx /tmp/vGdHfQK99f/fqidx.fq.gz 2:998-1003 +/build/reproducible-path/samtools-1.19.2/samtools fqidx /tmp/s3TWm1fqcD/fqidx.fq.gz 2:998-1003 .. ok .. ok -/build/reproducible-path/samtools-1.19.2/samtools fqidx /tmp/vGdHfQK99f/fqidx.fq 1:100-104 +/build/reproducible-path/samtools-1.19.2/samtools fqidx /tmp/s3TWm1fqcD/fqidx.fq 1:100-104 .. ok .. ok -/build/reproducible-path/samtools-1.19.2/samtools fqidx /tmp/vGdHfQK99f/fqidx.fq.gz 1:100-104 +/build/reproducible-path/samtools-1.19.2/samtools fqidx /tmp/s3TWm1fqcD/fqidx.fq.gz 1:100-104 .. ok .. ok -/build/reproducible-path/samtools-1.19.2/samtools fqidx /tmp/vGdHfQK99f/fqidx.fq 1:99998-100007 +/build/reproducible-path/samtools-1.19.2/samtools fqidx /tmp/s3TWm1fqcD/fqidx.fq 1:99998-100007 .. ok .. ok -/build/reproducible-path/samtools-1.19.2/samtools fqidx /tmp/vGdHfQK99f/fqidx.fq.gz 1:99998-100007 +/build/reproducible-path/samtools-1.19.2/samtools fqidx /tmp/s3TWm1fqcD/fqidx.fq.gz 1:99998-100007 .. ok .. ok @@ -850,7 +886,7 @@ .. ok test_dict: - /build/reproducible-path/samtools-1.19.2/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /tmp/vGdHfQK99f/dict.fa.gz + /build/reproducible-path/samtools-1.19.2/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /tmp/s3TWm1fqcD/dict.fa.gz .. ok test_dict: @@ -866,11 +902,11 @@ .. ok test_index: - /build/reproducible-path/samtools-1.19.2/samtools view /tmp/vGdHfQK99f/large_chrom.bam ref2 + /build/reproducible-path/samtools-1.19.2/samtools view /tmp/s3TWm1fqcD/large_chrom.bam ref2 .. ok test_index: - /build/reproducible-path/samtools-1.19.2/samtools view /tmp/vGdHfQK99f/large_chrom.bam ref2:1-541556283 + /build/reproducible-path/samtools-1.19.2/samtools view /tmp/s3TWm1fqcD/large_chrom.bam ref2:1-541556283 .. ok test_index: @@ -878,19 +914,19 @@ .. ok test_index: - /build/reproducible-path/samtools-1.19.2/samtools view -X /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_b.bam /tmp/vGdHfQK99f/test_input_1_b.bam.bai ref2 + /build/reproducible-path/samtools-1.19.2/samtools view -X /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_b.bam /tmp/s3TWm1fqcD/test_input_1_b.bam.bai ref2 .. ok test_index: - /build/reproducible-path/samtools-1.19.2/samtools view -X /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_b.bam /tmp/vGdHfQK99f/test_input_1_b.bam.bai + /build/reproducible-path/samtools-1.19.2/samtools view -X /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_b.bam /tmp/s3TWm1fqcD/test_input_1_b.bam.bai .. ok test_index: - /build/reproducible-path/samtools-1.19.2/samtools merge -O sam - -X -cp -R ref2 /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.bam /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_b.bam /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.bam.bai /tmp/vGdHfQK99f/test_input_1_b.bam.bai + /build/reproducible-path/samtools-1.19.2/samtools merge -O sam - -X -cp -R ref2 /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.bam /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_b.bam /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.bam.bai /tmp/s3TWm1fqcD/test_input_1_b.bam.bai .. ok test_index: - /build/reproducible-path/samtools-1.19.2/samtools view -X /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_b.bam /tmp/vGdHfQK99f/test_input_1_b_opt.bam.bai ref2 + /build/reproducible-path/samtools-1.19.2/samtools view -X /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_b.bam /tmp/s3TWm1fqcD/test_input_1_b_opt.bam.bai ref2 .. ok test_index: @@ -906,23 +942,23 @@ .. ok test_index: - /build/reproducible-path/samtools-1.19.2/samtools index -c /build/reproducible-path/samtools-1.19.2/test/dat/auto_indexed.tmp.bam /tmp/vGdHfQK99f/auto_indexed.csi && cat /tmp/vGdHfQK99f/auto_indexed.csi + /build/reproducible-path/samtools-1.19.2/samtools index -c /build/reproducible-path/samtools-1.19.2/test/dat/auto_indexed.tmp.bam /tmp/s3TWm1fqcD/auto_indexed.csi && cat /tmp/s3TWm1fqcD/auto_indexed.csi .. ok test_index: - /build/reproducible-path/samtools-1.19.2/samtools index /build/reproducible-path/samtools-1.19.2/test/dat/auto_indexed.tmp.cram /tmp/vGdHfQK99f/auto_indexed.crai && cat /tmp/vGdHfQK99f/auto_indexed.crai + /build/reproducible-path/samtools-1.19.2/samtools index /build/reproducible-path/samtools-1.19.2/test/dat/auto_indexed.tmp.cram /tmp/s3TWm1fqcD/auto_indexed.crai && cat /tmp/s3TWm1fqcD/auto_indexed.crai .. ok test_index: - /build/reproducible-path/samtools-1.19.2/samtools index -c /build/reproducible-path/samtools-1.19.2/test/dat/auto_indexed.tmp.sam /tmp/vGdHfQK99f/auto_indexed.csi && cat /tmp/vGdHfQK99f/auto_indexed.csi + /build/reproducible-path/samtools-1.19.2/samtools index -c /build/reproducible-path/samtools-1.19.2/test/dat/auto_indexed.tmp.sam /tmp/s3TWm1fqcD/auto_indexed.csi && cat /tmp/s3TWm1fqcD/auto_indexed.csi .. ok test_index: - /build/reproducible-path/samtools-1.19.2/samtools view -@ 2 /tmp/vGdHfQK99f/large_chrom.bam ref2 + /build/reproducible-path/samtools-1.19.2/samtools view -@ 2 /tmp/s3TWm1fqcD/large_chrom.bam ref2 .. ok test_index: - /build/reproducible-path/samtools-1.19.2/samtools view -@ 2 /tmp/vGdHfQK99f/large_chrom.bam ref2:1-541556283 + /build/reproducible-path/samtools-1.19.2/samtools view -@ 2 /tmp/s3TWm1fqcD/large_chrom.bam ref2:1-541556283 .. ok test_index: @@ -930,19 +966,19 @@ .. ok test_index: - /build/reproducible-path/samtools-1.19.2/samtools view -@ 2 -X /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_b.bam /tmp/vGdHfQK99f/test_input_1_b.bam.bai ref2 + /build/reproducible-path/samtools-1.19.2/samtools view -@ 2 -X /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_b.bam /tmp/s3TWm1fqcD/test_input_1_b.bam.bai ref2 .. ok test_index: - /build/reproducible-path/samtools-1.19.2/samtools view -@ 2 -X /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_b.bam /tmp/vGdHfQK99f/test_input_1_b.bam.bai + /build/reproducible-path/samtools-1.19.2/samtools view -@ 2 -X /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_b.bam /tmp/s3TWm1fqcD/test_input_1_b.bam.bai .. ok test_index: - /build/reproducible-path/samtools-1.19.2/samtools merge -@ 2 -O sam - -X -cp -R ref2 /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.bam /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_b.bam /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.bam.bai /tmp/vGdHfQK99f/test_input_1_b.bam.bai + /build/reproducible-path/samtools-1.19.2/samtools merge -@ 2 -O sam - -X -cp -R ref2 /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.bam /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_b.bam /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.bam.bai /tmp/s3TWm1fqcD/test_input_1_b.bam.bai .. ok test_index: - /build/reproducible-path/samtools-1.19.2/samtools view -@ 2 -X /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_b.bam /tmp/vGdHfQK99f/test_input_1_b_opt.bam.bai ref2 + /build/reproducible-path/samtools-1.19.2/samtools view -@ 2 -X /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_b.bam /tmp/s3TWm1fqcD/test_input_1_b_opt.bam.bai ref2 .. ok test_index: @@ -958,39 +994,39 @@ .. ok test_index: - /build/reproducible-path/samtools-1.19.2/samtools index -@ 2 -c /build/reproducible-path/samtools-1.19.2/test/dat/auto_indexed.tmp.bam /tmp/vGdHfQK99f/auto_indexed.csi && cat /tmp/vGdHfQK99f/auto_indexed.csi + /build/reproducible-path/samtools-1.19.2/samtools index -@ 2 -c /build/reproducible-path/samtools-1.19.2/test/dat/auto_indexed.tmp.bam /tmp/s3TWm1fqcD/auto_indexed.csi && cat /tmp/s3TWm1fqcD/auto_indexed.csi .. ok test_index: - /build/reproducible-path/samtools-1.19.2/samtools index -@ 2 /build/reproducible-path/samtools-1.19.2/test/dat/auto_indexed.tmp.cram /tmp/vGdHfQK99f/auto_indexed.crai && cat /tmp/vGdHfQK99f/auto_indexed.crai + /build/reproducible-path/samtools-1.19.2/samtools index -@ 2 /build/reproducible-path/samtools-1.19.2/test/dat/auto_indexed.tmp.cram /tmp/s3TWm1fqcD/auto_indexed.crai && cat /tmp/s3TWm1fqcD/auto_indexed.crai .. ok test_index: - /build/reproducible-path/samtools-1.19.2/samtools index -@ 2 -c /build/reproducible-path/samtools-1.19.2/test/dat/auto_indexed.tmp.sam /tmp/vGdHfQK99f/auto_indexed.csi && cat /tmp/vGdHfQK99f/auto_indexed.csi + /build/reproducible-path/samtools-1.19.2/samtools index -@ 2 -c /build/reproducible-path/samtools-1.19.2/test/dat/auto_indexed.tmp.sam /tmp/s3TWm1fqcD/auto_indexed.csi && cat /tmp/s3TWm1fqcD/auto_indexed.csi .. ok test_mpileup: - /build/reproducible-path/samtools-1.19.2/samtools mpileup -b /tmp/vGdHfQK99f/mpileup.bam.list -f /tmp/vGdHfQK99f/mpileup.ref.fa.gz -r17:100-150 + /build/reproducible-path/samtools-1.19.2/samtools mpileup -b /tmp/s3TWm1fqcD/mpileup.bam.list -f /tmp/s3TWm1fqcD/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: - /build/reproducible-path/samtools-1.19.2/samtools mpileup -b /tmp/vGdHfQK99f/mpileup.cram.list -f /tmp/vGdHfQK99f/mpileup.ref.fa.gz -r17:100-150 + /build/reproducible-path/samtools-1.19.2/samtools mpileup -b /tmp/s3TWm1fqcD/mpileup.cram.list -f /tmp/s3TWm1fqcD/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: - /build/reproducible-path/samtools-1.19.2/samtools mpileup -b /tmp/vGdHfQK99f/mpileup.bam.urllist -f /tmp/vGdHfQK99f/mpileup.ref.fa.gz -r17:100-150 + /build/reproducible-path/samtools-1.19.2/samtools mpileup -b /tmp/s3TWm1fqcD/mpileup.bam.urllist -f /tmp/s3TWm1fqcD/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: - /build/reproducible-path/samtools-1.19.2/samtools mpileup -b /tmp/vGdHfQK99f/mpileup.cram.urllist -f /tmp/vGdHfQK99f/mpileup.ref.fa.gz -r17:100-150 + /build/reproducible-path/samtools-1.19.2/samtools mpileup -b /tmp/s3TWm1fqcD/mpileup.cram.urllist -f /tmp/s3TWm1fqcD/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: - /build/reproducible-path/samtools-1.19.2/samtools mpileup -B --ff 0x14 -f /tmp/vGdHfQK99f/mpileup.ref.fa.gz -r17:1050-1060 /tmp/vGdHfQK99f/mpileup.1.bam | grep -v mpileup + /build/reproducible-path/samtools-1.19.2/samtools mpileup -B --ff 0x14 -f /tmp/s3TWm1fqcD/mpileup.ref.fa.gz -r17:1050-1060 /tmp/s3TWm1fqcD/mpileup.1.bam | grep -v mpileup .. ok test_mpileup: - /build/reproducible-path/samtools-1.19.2/samtools mpileup -B --ff 0x14 -f /tmp/vGdHfQK99f/mpileup.ref.fa.gz -r17:1050-1060 /tmp/vGdHfQK99f/mpileup.1.cram | grep -v mpileup + /build/reproducible-path/samtools-1.19.2/samtools mpileup -B --ff 0x14 -f /tmp/s3TWm1fqcD/mpileup.ref.fa.gz -r17:1050-1060 /tmp/s3TWm1fqcD/mpileup.1.cram | grep -v mpileup .. ok test_mpileup: @@ -1278,53 +1314,53 @@ 48: Count -r grp2 (CRAM input) .. ok - 49: Filter -R /tmp/vGdHfQK99f/view.001.fogn (SAM input) .. ok + 49: Filter -R /tmp/s3TWm1fqcD/view.001.fogn (SAM input) .. ok - 50: Count -R /tmp/vGdHfQK99f/view.001.fogn (SAM input) .. ok + 50: Count -R /tmp/s3TWm1fqcD/view.001.fogn (SAM input) .. ok - 51: Filter -R /tmp/vGdHfQK99f/view.001.fogn (BAM input) .. ok + 51: Filter -R /tmp/s3TWm1fqcD/view.001.fogn (BAM input) .. ok - 52: Count -R /tmp/vGdHfQK99f/view.001.fogn (BAM input) .. ok + 52: Count -R /tmp/s3TWm1fqcD/view.001.fogn (BAM input) .. ok - 53: Filter -R /tmp/vGdHfQK99f/view.001.fogn (CRAM input) .. ok + 53: Filter -R /tmp/s3TWm1fqcD/view.001.fogn (CRAM input) .. ok - 54: Count -R /tmp/vGdHfQK99f/view.001.fogn (CRAM input) .. ok + 54: Count -R /tmp/s3TWm1fqcD/view.001.fogn (CRAM input) .. ok - 55: Filter -R /tmp/vGdHfQK99f/view.001.fogn -r grp2 (SAM input).. ok + 55: Filter -R /tmp/s3TWm1fqcD/view.001.fogn -r grp2 (SAM input).. ok - 56: Count -R /tmp/vGdHfQK99f/view.001.fogn -r grp2 (SAM input).. ok + 56: Count -R /tmp/s3TWm1fqcD/view.001.fogn -r grp2 (SAM input).. ok - 57: Filter -R /tmp/vGdHfQK99f/view.001.fogn -r grp2 (BAM input).. ok + 57: Filter -R /tmp/s3TWm1fqcD/view.001.fogn -r grp2 (BAM input).. ok - 58: Count -R /tmp/vGdHfQK99f/view.001.fogn -r grp2 (BAM input).. ok + 58: Count -R /tmp/s3TWm1fqcD/view.001.fogn -r grp2 (BAM input).. ok - 59: Filter -R /tmp/vGdHfQK99f/view.001.fogn -r grp2 (CRAM input).. ok + 59: Filter -R /tmp/s3TWm1fqcD/view.001.fogn -r grp2 (CRAM input).. ok - 60: Count -R /tmp/vGdHfQK99f/view.001.fogn -r grp2 (CRAM input).. ok + 60: Count -R /tmp/s3TWm1fqcD/view.001.fogn -r grp2 (CRAM input).. ok - 61: Filter -r grp2 -R /tmp/vGdHfQK99f/view.001.fogn (SAM input).. ok + 61: Filter -r grp2 -R /tmp/s3TWm1fqcD/view.001.fogn (SAM input).. ok - 62: Count -r grp2 -R /tmp/vGdHfQK99f/view.001.fogn (SAM input).. ok + 62: Count -r grp2 -R /tmp/s3TWm1fqcD/view.001.fogn (SAM input).. ok - 63: Filter -r grp2 -R /tmp/vGdHfQK99f/view.001.fogn (BAM input).. ok + 63: Filter -r grp2 -R /tmp/s3TWm1fqcD/view.001.fogn (BAM input).. ok - 64: Count -r grp2 -R /tmp/vGdHfQK99f/view.001.fogn (BAM input).. ok + 64: Count -r grp2 -R /tmp/s3TWm1fqcD/view.001.fogn (BAM input).. ok - 65: Filter -r grp2 -R /tmp/vGdHfQK99f/view.001.fogn (CRAM input).. ok + 65: Filter -r grp2 -R /tmp/s3TWm1fqcD/view.001.fogn (CRAM input).. ok - 66: Count -r grp2 -R /tmp/vGdHfQK99f/view.001.fogn (CRAM input).. ok + 66: Count -r grp2 -R /tmp/s3TWm1fqcD/view.001.fogn (CRAM input).. ok - 67: Filter -N /tmp/vGdHfQK99f/view.001.forn (SAM input) .. ok + 67: Filter -N /tmp/s3TWm1fqcD/view.001.forn (SAM input) .. ok - 68: Count -N /tmp/vGdHfQK99f/view.001.forn (SAM input) .. ok + 68: Count -N /tmp/s3TWm1fqcD/view.001.forn (SAM input) .. ok - 69: Filter -N /tmp/vGdHfQK99f/view.001.forn (BAM input) .. ok + 69: Filter -N /tmp/s3TWm1fqcD/view.001.forn (BAM input) .. ok - 70: Count -N /tmp/vGdHfQK99f/view.001.forn (BAM input) .. ok + 70: Count -N /tmp/s3TWm1fqcD/view.001.forn (BAM input) .. ok - 71: Filter -N /tmp/vGdHfQK99f/view.001.forn (CRAM input) .. ok + 71: Filter -N /tmp/s3TWm1fqcD/view.001.forn (CRAM input) .. ok - 72: Count -N /tmp/vGdHfQK99f/view.001.forn (CRAM input) .. ok + 72: Count -N /tmp/s3TWm1fqcD/view.001.forn (CRAM input) .. ok 73: Filter -d BC (SAM input) .. ok @@ -1350,53 +1386,53 @@ 84: Count -d BC:TGCA (CRAM input) .. ok - 85: Filter -D BC:/tmp/vGdHfQK99f/view.001.fobc (SAM input) .. ok + 85: Filter -D BC:/tmp/s3TWm1fqcD/view.001.fobc (SAM input) .. ok - 86: Count -D BC:/tmp/vGdHfQK99f/view.001.fobc (SAM input) .. ok + 86: Count -D BC:/tmp/s3TWm1fqcD/view.001.fobc (SAM input) .. ok - 87: Filter -D BC:/tmp/vGdHfQK99f/view.001.fobc (BAM input) .. ok + 87: Filter -D BC:/tmp/s3TWm1fqcD/view.001.fobc (BAM input) .. ok - 88: Count -D BC:/tmp/vGdHfQK99f/view.001.fobc (BAM input) .. ok + 88: Count -D BC:/tmp/s3TWm1fqcD/view.001.fobc (BAM input) .. ok - 89: Filter -D BC:/tmp/vGdHfQK99f/view.001.fobc (CRAM input) .. ok + 89: Filter -D BC:/tmp/s3TWm1fqcD/view.001.fobc (CRAM input) .. ok - 90: Count -D BC:/tmp/vGdHfQK99f/view.001.fobc (CRAM input) .. ok + 90: Count -D BC:/tmp/s3TWm1fqcD/view.001.fobc (CRAM input) .. ok - 91: Filter -D BC:/tmp/vGdHfQK99f/view.001.fobc -d BC:TGCA (SAM input).. ok + 91: Filter -D BC:/tmp/s3TWm1fqcD/view.001.fobc -d BC:TGCA (SAM input).. ok - 92: Count -D BC:/tmp/vGdHfQK99f/view.001.fobc -d BC:TGCA (SAM input).. ok + 92: Count -D BC:/tmp/s3TWm1fqcD/view.001.fobc -d BC:TGCA (SAM input).. ok - 93: Filter -D BC:/tmp/vGdHfQK99f/view.001.fobc -d BC:TGCA (BAM input).. ok + 93: Filter -D BC:/tmp/s3TWm1fqcD/view.001.fobc -d BC:TGCA (BAM input).. ok - 94: Count -D BC:/tmp/vGdHfQK99f/view.001.fobc -d BC:TGCA (BAM input).. ok + 94: Count -D BC:/tmp/s3TWm1fqcD/view.001.fobc -d BC:TGCA (BAM input).. ok - 95: Filter -D BC:/tmp/vGdHfQK99f/view.001.fobc -d BC:TGCA (CRAM input).. ok + 95: Filter -D BC:/tmp/s3TWm1fqcD/view.001.fobc -d BC:TGCA (CRAM input).. ok - 96: Count -D BC:/tmp/vGdHfQK99f/view.001.fobc -d BC:TGCA (CRAM input).. ok + 96: Count -D BC:/tmp/s3TWm1fqcD/view.001.fobc -d BC:TGCA (CRAM input).. ok - 97: Filter -d BC:TGCA -D BC:/tmp/vGdHfQK99f/view.001.fobc (SAM input).. ok + 97: Filter -d BC:TGCA -D BC:/tmp/s3TWm1fqcD/view.001.fobc (SAM input).. ok - 98: Count -d BC:TGCA -D BC:/tmp/vGdHfQK99f/view.001.fobc (SAM input).. ok + 98: Count -d BC:TGCA -D BC:/tmp/s3TWm1fqcD/view.001.fobc (SAM input).. ok - 99: Filter -d BC:TGCA -D BC:/tmp/vGdHfQK99f/view.001.fobc (BAM input).. ok + 99: Filter -d BC:TGCA -D BC:/tmp/s3TWm1fqcD/view.001.fobc (BAM input).. ok - 100: Count -d BC:TGCA -D BC:/tmp/vGdHfQK99f/view.001.fobc (BAM input).. ok + 100: Count -d BC:TGCA -D BC:/tmp/s3TWm1fqcD/view.001.fobc (BAM input).. ok - 101: Filter -d BC:TGCA -D BC:/tmp/vGdHfQK99f/view.001.fobc (CRAM input).. ok + 101: Filter -d BC:TGCA -D BC:/tmp/s3TWm1fqcD/view.001.fobc (CRAM input).. ok - 102: Count -d BC:TGCA -D BC:/tmp/vGdHfQK99f/view.001.fobc (CRAM input).. ok + 102: Count -d BC:TGCA -D BC:/tmp/s3TWm1fqcD/view.001.fobc (CRAM input).. ok - 103: Filter -D RG:/tmp/vGdHfQK99f/view.001.fogn (SAM input) .. ok + 103: Filter -D RG:/tmp/s3TWm1fqcD/view.001.fogn (SAM input) .. ok - 104: Count -D RG:/tmp/vGdHfQK99f/view.001.fogn (SAM input) .. ok + 104: Count -D RG:/tmp/s3TWm1fqcD/view.001.fogn (SAM input) .. ok - 105: Filter -D RG:/tmp/vGdHfQK99f/view.001.fogn (BAM input) .. ok + 105: Filter -D RG:/tmp/s3TWm1fqcD/view.001.fogn (BAM input) .. ok - 106: Count -D RG:/tmp/vGdHfQK99f/view.001.fogn (BAM input) .. ok + 106: Count -D RG:/tmp/s3TWm1fqcD/view.001.fogn (BAM input) .. ok - 107: Filter -D RG:/tmp/vGdHfQK99f/view.001.fogn (CRAM input).. ok + 107: Filter -D RG:/tmp/s3TWm1fqcD/view.001.fogn (CRAM input).. ok - 108: Count -D RG:/tmp/vGdHfQK99f/view.001.fogn (CRAM input) .. ok + 108: Count -D RG:/tmp/s3TWm1fqcD/view.001.fogn (CRAM input) .. ok 109: Filter -d NE:TGCA (SAM input) .. ok @@ -1412,126 +1448,126 @@ 115: Filter -d TGCA (SAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: - /build/reproducible-path/samtools-1.19.2/samtools view -o /tmp/vGdHfQK99f/view.test115.sam -h -d TGCA /tmp/vGdHfQK99f/view.001.sam --no-PG + /build/reproducible-path/samtools-1.19.2/samtools view -o /tmp/s3TWm1fqcD/view.test115.sam -h -d TGCA /tmp/s3TWm1fqcD/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-1.19.2/samtools view -c -d TGCA /tmp/vGdHfQK99f/view.001.sam --no-PG + /build/reproducible-path/samtools-1.19.2/samtools view -c -d TGCA /tmp/s3TWm1fqcD/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-1.19.2/samtools view -o /tmp/vGdHfQK99f/view.test117.sam -h -d TGCA /tmp/vGdHfQK99f/view.test001.bam --no-PG + /build/reproducible-path/samtools-1.19.2/samtools view -o /tmp/s3TWm1fqcD/view.test117.sam -h -d TGCA /tmp/s3TWm1fqcD/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-1.19.2/samtools view -c -d TGCA /tmp/vGdHfQK99f/view.test001.bam --no-PG + /build/reproducible-path/samtools-1.19.2/samtools view -c -d TGCA /tmp/s3TWm1fqcD/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-1.19.2/samtools view -o /tmp/vGdHfQK99f/view.test119.sam -h -d TGCA /tmp/vGdHfQK99f/view.test006.cram --no-PG + /build/reproducible-path/samtools-1.19.2/samtools view -o /tmp/s3TWm1fqcD/view.test119.sam -h -d TGCA /tmp/s3TWm1fqcD/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-1.19.2/samtools view -c -d TGCA /tmp/vGdHfQK99f/view.test006.cram --no-PG + /build/reproducible-path/samtools-1.19.2/samtools view -c -d TGCA /tmp/s3TWm1fqcD/view.test006.cram --no-PG .. expected failure - 121: Filter -D BClong:/tmp/vGdHfQK99f/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/vGdHfQK99f/view.001.fobc" + 121: Filter -D BClong:/tmp/s3TWm1fqcD/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/s3TWm1fqcD/view.001.fobc" Failed command: - /build/reproducible-path/samtools-1.19.2/samtools view -o /tmp/vGdHfQK99f/view.test121.sam -h -D BClong:/tmp/vGdHfQK99f/view.001.fobc /tmp/vGdHfQK99f/view.001.sam --no-PG + /build/reproducible-path/samtools-1.19.2/samtools view -o /tmp/s3TWm1fqcD/view.test121.sam -h -D BClong:/tmp/s3TWm1fqcD/view.001.fobc /tmp/s3TWm1fqcD/view.001.sam --no-PG .. expected failure - 122: Count -D BClong:/tmp/vGdHfQK99f/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/vGdHfQK99f/view.001.fobc" + 122: Count -D BClong:/tmp/s3TWm1fqcD/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/s3TWm1fqcD/view.001.fobc" Failed command: - /build/reproducible-path/samtools-1.19.2/samtools view -c -D BClong:/tmp/vGdHfQK99f/view.001.fobc /tmp/vGdHfQK99f/view.001.sam --no-PG + /build/reproducible-path/samtools-1.19.2/samtools view -c -D BClong:/tmp/s3TWm1fqcD/view.001.fobc /tmp/s3TWm1fqcD/view.001.sam --no-PG .. expected failure - 123: Filter -D BClong:/tmp/vGdHfQK99f/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/vGdHfQK99f/view.001.fobc" + 123: Filter -D BClong:/tmp/s3TWm1fqcD/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/s3TWm1fqcD/view.001.fobc" Failed command: - /build/reproducible-path/samtools-1.19.2/samtools view -o /tmp/vGdHfQK99f/view.test123.sam -h -D BClong:/tmp/vGdHfQK99f/view.001.fobc /tmp/vGdHfQK99f/view.test001.bam --no-PG + /build/reproducible-path/samtools-1.19.2/samtools view -o /tmp/s3TWm1fqcD/view.test123.sam -h -D BClong:/tmp/s3TWm1fqcD/view.001.fobc /tmp/s3TWm1fqcD/view.test001.bam --no-PG .. expected failure - 124: Count -D BClong:/tmp/vGdHfQK99f/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/vGdHfQK99f/view.001.fobc" + 124: Count -D BClong:/tmp/s3TWm1fqcD/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/s3TWm1fqcD/view.001.fobc" Failed command: - /build/reproducible-path/samtools-1.19.2/samtools view -c -D BClong:/tmp/vGdHfQK99f/view.001.fobc /tmp/vGdHfQK99f/view.test001.bam --no-PG + /build/reproducible-path/samtools-1.19.2/samtools view -c -D BClong:/tmp/s3TWm1fqcD/view.001.fobc /tmp/s3TWm1fqcD/view.test001.bam --no-PG .. expected failure - 125: Filter -D BClong:/tmp/vGdHfQK99f/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/vGdHfQK99f/view.001.fobc" + 125: Filter -D BClong:/tmp/s3TWm1fqcD/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/s3TWm1fqcD/view.001.fobc" Failed command: - /build/reproducible-path/samtools-1.19.2/samtools view -o /tmp/vGdHfQK99f/view.test125.sam -h -D BClong:/tmp/vGdHfQK99f/view.001.fobc /tmp/vGdHfQK99f/view.test006.cram --no-PG + /build/reproducible-path/samtools-1.19.2/samtools view -o /tmp/s3TWm1fqcD/view.test125.sam -h -D BClong:/tmp/s3TWm1fqcD/view.001.fobc /tmp/s3TWm1fqcD/view.test006.cram --no-PG .. expected failure - 126: Count -D BClong:/tmp/vGdHfQK99f/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/vGdHfQK99f/view.001.fobc" + 126: Count -D BClong:/tmp/s3TWm1fqcD/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/s3TWm1fqcD/view.001.fobc" Failed command: - /build/reproducible-path/samtools-1.19.2/samtools view -c -D BClong:/tmp/vGdHfQK99f/view.001.fobc /tmp/vGdHfQK99f/view.test006.cram --no-PG + /build/reproducible-path/samtools-1.19.2/samtools view -c -D BClong:/tmp/s3TWm1fqcD/view.001.fobc /tmp/s3TWm1fqcD/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-1.19.2/samtools view -o /tmp/vGdHfQK99f/view.test127.sam -h -d BC:ACGT -d RG:grp2 /tmp/vGdHfQK99f/view.001.sam --no-PG + /build/reproducible-path/samtools-1.19.2/samtools view -o /tmp/s3TWm1fqcD/view.test127.sam -h -d BC:ACGT -d RG:grp2 /tmp/s3TWm1fqcD/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-1.19.2/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/vGdHfQK99f/view.001.sam --no-PG + /build/reproducible-path/samtools-1.19.2/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/s3TWm1fqcD/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-1.19.2/samtools view -o /tmp/vGdHfQK99f/view.test129.sam -h -d BC:ACGT -d RG:grp2 /tmp/vGdHfQK99f/view.test001.bam --no-PG + /build/reproducible-path/samtools-1.19.2/samtools view -o /tmp/s3TWm1fqcD/view.test129.sam -h -d BC:ACGT -d RG:grp2 /tmp/s3TWm1fqcD/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-1.19.2/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/vGdHfQK99f/view.test001.bam --no-PG + /build/reproducible-path/samtools-1.19.2/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/s3TWm1fqcD/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-1.19.2/samtools view -o /tmp/vGdHfQK99f/view.test131.sam -h -d BC:ACGT -d RG:grp2 /tmp/vGdHfQK99f/view.test006.cram --no-PG + /build/reproducible-path/samtools-1.19.2/samtools view -o /tmp/s3TWm1fqcD/view.test131.sam -h -d BC:ACGT -d RG:grp2 /tmp/s3TWm1fqcD/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-1.19.2/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/vGdHfQK99f/view.test006.cram --no-PG + /build/reproducible-path/samtools-1.19.2/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/s3TWm1fqcD/view.test006.cram --no-PG .. expected failure @@ -2413,7 +2449,7 @@ .. ok test_bam2fq: - /build/reproducible-path/samtools-1.19.2/samtools fastq -N -s /tmp/vGdHfQK99f/bam2fq.discard.s.fq -0 /tmp/vGdHfQK99f/bam2fq.discard.0.fq /build/reproducible-path/samtools-1.19.2/test/dat/bam2fq.001.sam + /build/reproducible-path/samtools-1.19.2/samtools fastq -N -s /tmp/s3TWm1fqcD/bam2fq.discard.s.fq -0 /tmp/s3TWm1fqcD/bam2fq.discard.0.fq /build/reproducible-path/samtools-1.19.2/test/dat/bam2fq.001.sam .. ok test_bam2fq: @@ -2542,7 +2578,7 @@ .. ok test_bam2fq: - /build/reproducible-path/samtools-1.19.2/samtools fastq -@ 2 -N -s /tmp/vGdHfQK99f/bam2fq.discard.s.fq -0 /tmp/vGdHfQK99f/bam2fq.discard.0.fq /build/reproducible-path/samtools-1.19.2/test/dat/bam2fq.001.sam + /build/reproducible-path/samtools-1.19.2/samtools fastq -@ 2 -N -s /tmp/s3TWm1fqcD/bam2fq.discard.s.fq -0 /tmp/s3TWm1fqcD/bam2fq.discard.0.fq /build/reproducible-path/samtools-1.19.2/test/dat/bam2fq.001.sam .. ok test_bam2fq: @@ -2747,7 +2783,7 @@ .. ok test_merge: - /build/reproducible-path/samtools-1.19.2/samtools merge -s 1 -O sam -b /tmp/ItrIxTgSHC - /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.bam + /build/reproducible-path/samtools-1.19.2/samtools merge -s 1 -O sam -b /tmp/Bw4xs_36ei - /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.bam .. ok test_merge: @@ -2771,11 +2807,11 @@ .. ok test_merge: - /build/reproducible-path/samtools-1.19.2/samtools merge -s 1 -p -c -t PG -O SAM - /tmp/vGdHfQK99f/merge.tag.1.bam /tmp/vGdHfQK99f/merge.tag.2.bam + /build/reproducible-path/samtools-1.19.2/samtools merge -s 1 -p -c -t PG -O SAM - /tmp/s3TWm1fqcD/merge.tag.1.bam /tmp/s3TWm1fqcD/merge.tag.2.bam .. ok test_merge: - /build/reproducible-path/samtools-1.19.2/samtools merge -s 1 -p -c -n -t PG -O SAM - /tmp/vGdHfQK99f/merge.tag.3.bam /tmp/vGdHfQK99f/merge.tag.4.bam + /build/reproducible-path/samtools-1.19.2/samtools merge -s 1 -p -c -n -t PG -O SAM - /tmp/s3TWm1fqcD/merge.tag.3.bam /tmp/s3TWm1fqcD/merge.tag.4.bam .. ok test_merge: @@ -2783,7 +2819,7 @@ .. ok test_merge: - /build/reproducible-path/samtools-1.19.2/samtools merge --no-PG -O SAM -L /build/reproducible-path/samtools-1.19.2/test/merge/merge.bed - /tmp/vGdHfQK99f/merge.bed.1.bam /tmp/vGdHfQK99f/merge.bed.2.bam + /build/reproducible-path/samtools-1.19.2/samtools merge --no-PG -O SAM -L /build/reproducible-path/samtools-1.19.2/test/merge/merge.bed - /tmp/s3TWm1fqcD/merge.bed.1.bam /tmp/s3TWm1fqcD/merge.bed.2.bam .. ok test_merge: @@ -2799,7 +2835,7 @@ .. ok test_merge: - /build/reproducible-path/samtools-1.19.2/samtools merge -@ 2 -s 1 -O sam -b /tmp/42w3BFRTNX - /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.bam + /build/reproducible-path/samtools-1.19.2/samtools merge -@ 2 -s 1 -O sam -b /tmp/9_y819QgvW - /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.bam .. ok test_merge: @@ -2823,11 +2859,11 @@ .. ok test_merge: - /build/reproducible-path/samtools-1.19.2/samtools merge -@ 2 -s 1 -p -c -t PG -O SAM - /tmp/vGdHfQK99f/merge.tag.1.bam /tmp/vGdHfQK99f/merge.tag.2.bam + /build/reproducible-path/samtools-1.19.2/samtools merge -@ 2 -s 1 -p -c -t PG -O SAM - /tmp/s3TWm1fqcD/merge.tag.1.bam /tmp/s3TWm1fqcD/merge.tag.2.bam .. ok test_merge: - /build/reproducible-path/samtools-1.19.2/samtools merge -@ 2 -s 1 -p -c -n -t PG -O SAM - /tmp/vGdHfQK99f/merge.tag.3.bam /tmp/vGdHfQK99f/merge.tag.4.bam + /build/reproducible-path/samtools-1.19.2/samtools merge -@ 2 -s 1 -p -c -n -t PG -O SAM - /tmp/s3TWm1fqcD/merge.tag.3.bam /tmp/s3TWm1fqcD/merge.tag.4.bam .. ok test_merge: @@ -2835,7 +2871,7 @@ .. ok test_merge: - /build/reproducible-path/samtools-1.19.2/samtools merge -@ 2 --no-PG -O SAM -L /build/reproducible-path/samtools-1.19.2/test/merge/merge.bed - /tmp/vGdHfQK99f/merge.bed.1.bam /tmp/vGdHfQK99f/merge.bed.2.bam + /build/reproducible-path/samtools-1.19.2/samtools merge -@ 2 --no-PG -O SAM -L /build/reproducible-path/samtools-1.19.2/test/merge/merge.bed - /tmp/s3TWm1fqcD/merge.bed.1.bam /tmp/s3TWm1fqcD/merge.bed.2.bam .. ok test_merge: @@ -2843,15 +2879,15 @@ .. ok test_sort: - /build/reproducible-path/samtools-1.19.2/samtools sort /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.bam /tmp/vGdHfQK99f/sortout + /build/reproducible-path/samtools-1.19.2/samtools sort /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.bam /tmp/s3TWm1fqcD/sortout .. ok test_sort: - /build/reproducible-path/samtools-1.19.2/samtools sort -f /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.bam /tmp/vGdHfQK99f/sortout.bam + /build/reproducible-path/samtools-1.19.2/samtools sort -f /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.bam /tmp/s3TWm1fqcD/sortout.bam .. ok test_sort: - /build/reproducible-path/samtools-1.19.2/samtools sort -o /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.bam /tmp/vGdHfQK99f/sorttmp + /build/reproducible-path/samtools-1.19.2/samtools sort -o /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.bam /tmp/s3TWm1fqcD/sorttmp .. ok test_sort: @@ -2899,15 +2935,15 @@ .. ok test_sort: - /build/reproducible-path/samtools-1.19.2/samtools sort -@ 2 /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.bam /tmp/vGdHfQK99f/sortout + /build/reproducible-path/samtools-1.19.2/samtools sort -@ 2 /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.bam /tmp/s3TWm1fqcD/sortout .. ok test_sort: - /build/reproducible-path/samtools-1.19.2/samtools sort -@ 2 -f /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.bam /tmp/vGdHfQK99f/sortout.bam + /build/reproducible-path/samtools-1.19.2/samtools sort -@ 2 -f /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.bam /tmp/s3TWm1fqcD/sortout.bam .. ok test_sort: - /build/reproducible-path/samtools-1.19.2/samtools sort -@ 2 -o /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.bam /tmp/vGdHfQK99f/sorttmp + /build/reproducible-path/samtools-1.19.2/samtools sort -@ 2 -o /build/reproducible-path/samtools-1.19.2/test/dat/test_input_1_a.bam /tmp/s3TWm1fqcD/sorttmp .. ok test_sort: @@ -3479,15 +3515,15 @@ .. ok test_large_positions: - /build/reproducible-path/samtools-1.19.2/samtools view -h --no-PG /tmp/vGdHfQK99f/longref.sam.gz + /build/reproducible-path/samtools-1.19.2/samtools view -h --no-PG /tmp/s3TWm1fqcD/longref.sam.gz .. ok test_large_positions: - /build/reproducible-path/samtools-1.19.2/samtools view -h --no-PG /tmp/vGdHfQK99f/longref.sam.gz CHROMOSOME_I:10000000114-10000000168 + /build/reproducible-path/samtools-1.19.2/samtools view -h --no-PG /tmp/s3TWm1fqcD/longref.sam.gz CHROMOSOME_I:10000000114-10000000168 .. ok test_large_positions: - /build/reproducible-path/samtools-1.19.2/samtools view -h --no-PG -L /build/reproducible-path/samtools-1.19.2/test/large_pos/test.bed /tmp/vGdHfQK99f/longref.sam.gz + /build/reproducible-path/samtools-1.19.2/samtools view -h --no-PG -L /build/reproducible-path/samtools-1.19.2/test/large_pos/test.bed /tmp/s3TWm1fqcD/longref.sam.gz .. ok test_large_positions: @@ -3507,7 +3543,7 @@ .. ok test_large_positions: - /build/reproducible-path/samtools-1.19.2/samtools tview -d T -p CHROMOSOME_I:10000000000 /tmp/vGdHfQK99f/longref.sam.gz + /build/reproducible-path/samtools-1.19.2/samtools tview -d T -p CHROMOSOME_I:10000000000 /tmp/s3TWm1fqcD/longref.sam.gz .. ok test_large_positions: @@ -3726,7 +3762,7 @@ Unexpected failures: 0 => PASS make[2]: Leaving directory '/build/reproducible-path/samtools-1.19.2' - rm -fr -- /tmp/dh-xdg-rundir-BoDOWfux + rm -fr -- /tmp/dh-xdg-rundir-m2l2aJrt make[1]: Leaving directory '/build/reproducible-path/samtools-1.19.2' create-stamp debian/debhelper-build-stamp dh_prep @@ -3738,7 +3774,7 @@ dh_auto_install -- \ prefix=/usr install -m0755 -d /build/reproducible-path/samtools-1.19.2/debian/tmp - make -j20 install DESTDIR=/build/reproducible-path/samtools-1.19.2/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr + make -j42 install DESTDIR=/build/reproducible-path/samtools-1.19.2/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr make[2]: Entering directory '/build/reproducible-path/samtools-1.19.2' mkdir -p -m 755 /build/reproducible-path/samtools-1.19.2/debian/tmp/usr/bin /build/reproducible-path/samtools-1.19.2/debian/tmp/usr/bin /build/reproducible-path/samtools-1.19.2/debian/tmp/usr/share/man/man1 install -p samtools /build/reproducible-path/samtools-1.19.2/debian/tmp/usr/bin @@ -3823,79 +3859,93 @@ 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/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-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/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-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-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-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-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-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-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-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/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 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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/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 + 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/wgsim.1.dh-new debian/samtools/usr/share/man/man1/wgsim.1 chmod 0644 -- debian/samtools/usr/share/man/man1/wgsim.1 - mv 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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-cram-size.1 debian/samtools/usr/share/man/man1/samtools-depad.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-import.1 debian/samtools/usr/share/man/man1/samtools-index.1 mv debian/samtools/usr/share/man/man1/samtools-depth.1.dh-new debian/samtools/usr/share/man/man1/samtools-depth.1 mv debian/samtools/usr/share/man/man1/samtools-dict.1.dh-new debian/samtools/usr/share/man/man1/samtools-dict.1 + 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-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-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-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-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 + 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-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-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-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-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-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-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 + 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-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-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-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 - 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-flagstat.1 debian/samtools/usr/share/man/man1/samtools-fqidx.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 - mv debian/samtools/usr/share/man/man1/samtools-stats.1.dh-new debian/samtools/usr/share/man/man1/samtools-stats.1 - mv debian/samtools/usr/share/man/man1/samtools-targetcut.1.dh-new debian/samtools/usr/share/man/man1/samtools-targetcut.1 - mv debian/samtools/usr/share/man/man1/samtools-tview.1.dh-new debian/samtools/usr/share/man/man1/samtools-tview.1 - 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-idxstats.1.dh-new debian/samtools/usr/share/man/man1/samtools-idxstats.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 - 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/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-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 + chmod 0644 -- debian/samtools/usr/share/man/man1/samtools.1 debian/samtools/usr/share/man/man1/samtools.pl.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-tview.1.dh-new debian/samtools/usr/share/man/man1/samtools-tview.1 + mv debian/samtools/usr/share/man/man1/samtools-view.1.dh-new debian/samtools/usr/share/man/man1/samtools-view.1 + chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-tview.1 debian/samtools/usr/share/man/man1/samtools-view.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 - mv debian/samtools/usr/share/man/man1/samtools-coverage.1.dh-new debian/samtools/usr/share/man/man1/samtools-coverage.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 + chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-sort.1 debian/samtools/usr/share/man/man1/samtools-split.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 @@ -3913,10 +3963,10 @@ dh_compress cd debian/samtools cd debian/samtools-test - chmod a-x usr/share/doc/samtools/README usr/share/doc/samtools/changelog usr/share/doc/samtools/changelog.Debian usr/share/man/man1/ace2sam.1 usr/share/man/man1/samtools-addreplacerg.1 usr/share/man/man1/samtools-ampliconclip.1 usr/share/man/man1/samtools-ampliconstats.1 usr/share/man/man1/samtools-bedcov.1 usr/share/man/man1/samtools-calmd.1 usr/share/man/man1/samtools-cat.1 usr/share/man/man1/samtools-collate.1 usr/share/man/man1/samtools-consensus.1 usr/share/man/man1/samtools-coverage.1 usr/share/man/man1/samtools-cram-size.1 usr/share/man/man1/samtools-depad.1 usr/share/man/man1/samtools-depth.1 usr/share/man/man1/samtools-dict.1 usr/share/man/man1/samtools-faidx.1 usr/share/man/man1/samtools-fasta.1 usr/share/man/man1/samtools-fixmate.1 usr/share/man/man1/samtools-flags.1 usr/share/man/man1/samtools-flagstat.1 usr/share/man/man1/samtools-fqidx.1 usr/share/man/man1/samtools-head.1 usr/share/man/man1/samtools-idxstats.1 usr/share/man/man1/samtools-import.1 usr/share/man/man1/samtools-index.1 usr/share/man/man1/samtools-markdup.1 usr/share/man/man1/samtools-merge.1 usr/share/man/man1/samtools-mpileup.1 usr/share/man/man1/samtools-phase.1 usr/share/man/man1/samtools-quickcheck.1 usr/share/man/man1/samtools-reference.1 usr/share/man/man1/samtools-reheader.1 usr/share/man/man1/samtools-reset.1 usr/share/man/man1/samtools-rmdup.1 usr/share/man/man1/samtools-samples.1 usr/share/man/man1/samtools-sort.1 usr/share/man/man1/samtools-split.1 usr/share/man/man1/samtools-stats.1 usr/share/man/man1/samtools-targetcut.1 usr/share/man/man1/samtools-tview.1 usr/share/man/man1/samtools-view.1 usr/share/man/man1/samtools.1 usr/share/man/man1/samtools.pl.1 usr/share/man/man1/wgsim.1 chmod a-x usr/share/doc/samtools-test/changelog usr/share/doc/samtools-test/changelog.Debian - gzip -9nf usr/share/doc/samtools/README usr/share/doc/samtools/changelog usr/share/doc/samtools/changelog.Debian usr/share/man/man1/ace2sam.1 usr/share/man/man1/samtools-addreplacerg.1 usr/share/man/man1/samtools-ampliconclip.1 usr/share/man/man1/samtools-ampliconstats.1 usr/share/man/man1/samtools-bedcov.1 usr/share/man/man1/samtools-calmd.1 usr/share/man/man1/samtools-cat.1 usr/share/man/man1/samtools-collate.1 usr/share/man/man1/samtools-consensus.1 usr/share/man/man1/samtools-coverage.1 usr/share/man/man1/samtools-cram-size.1 usr/share/man/man1/samtools-depad.1 usr/share/man/man1/samtools-depth.1 usr/share/man/man1/samtools-dict.1 usr/share/man/man1/samtools-faidx.1 usr/share/man/man1/samtools-fasta.1 usr/share/man/man1/samtools-fixmate.1 usr/share/man/man1/samtools-flags.1 usr/share/man/man1/samtools-flagstat.1 usr/share/man/man1/samtools-fqidx.1 usr/share/man/man1/samtools-head.1 usr/share/man/man1/samtools-idxstats.1 usr/share/man/man1/samtools-import.1 usr/share/man/man1/samtools-index.1 usr/share/man/man1/samtools-markdup.1 usr/share/man/man1/samtools-merge.1 usr/share/man/man1/samtools-mpileup.1 usr/share/man/man1/samtools-phase.1 usr/share/man/man1/samtools-quickcheck.1 usr/share/man/man1/samtools-reference.1 usr/share/man/man1/samtools-reheader.1 usr/share/man/man1/samtools-reset.1 usr/share/man/man1/samtools-rmdup.1 usr/share/man/man1/samtools-samples.1 usr/share/man/man1/samtools-sort.1 usr/share/man/man1/samtools-split.1 usr/share/man/man1/samtools-stats.1 usr/share/man/man1/samtools-targetcut.1 usr/share/man/man1/samtools-tview.1 usr/share/man/man1/samtools-view.1 usr/share/man/man1/samtools.1 usr/share/man/man1/samtools.pl.1 usr/share/man/man1/wgsim.1 gzip -9nf usr/share/doc/samtools-test/changelog usr/share/doc/samtools-test/changelog.Debian + chmod a-x usr/share/doc/samtools/README usr/share/doc/samtools/changelog usr/share/doc/samtools/changelog.Debian usr/share/man/man1/ace2sam.1 usr/share/man/man1/samtools-addreplacerg.1 usr/share/man/man1/samtools-ampliconclip.1 usr/share/man/man1/samtools-ampliconstats.1 usr/share/man/man1/samtools-bedcov.1 usr/share/man/man1/samtools-calmd.1 usr/share/man/man1/samtools-cat.1 usr/share/man/man1/samtools-collate.1 usr/share/man/man1/samtools-consensus.1 usr/share/man/man1/samtools-coverage.1 usr/share/man/man1/samtools-cram-size.1 usr/share/man/man1/samtools-depad.1 usr/share/man/man1/samtools-depth.1 usr/share/man/man1/samtools-dict.1 usr/share/man/man1/samtools-faidx.1 usr/share/man/man1/samtools-fasta.1 usr/share/man/man1/samtools-fixmate.1 usr/share/man/man1/samtools-flags.1 usr/share/man/man1/samtools-flagstat.1 usr/share/man/man1/samtools-fqidx.1 usr/share/man/man1/samtools-head.1 usr/share/man/man1/samtools-idxstats.1 usr/share/man/man1/samtools-import.1 usr/share/man/man1/samtools-index.1 usr/share/man/man1/samtools-markdup.1 usr/share/man/man1/samtools-merge.1 usr/share/man/man1/samtools-mpileup.1 usr/share/man/man1/samtools-phase.1 usr/share/man/man1/samtools-quickcheck.1 usr/share/man/man1/samtools-reference.1 usr/share/man/man1/samtools-reheader.1 usr/share/man/man1/samtools-reset.1 usr/share/man/man1/samtools-rmdup.1 usr/share/man/man1/samtools-samples.1 usr/share/man/man1/samtools-sort.1 usr/share/man/man1/samtools-split.1 usr/share/man/man1/samtools-stats.1 usr/share/man/man1/samtools-targetcut.1 usr/share/man/man1/samtools-tview.1 usr/share/man/man1/samtools-view.1 usr/share/man/man1/samtools.1 usr/share/man/man1/samtools.pl.1 usr/share/man/man1/wgsim.1 + gzip -9nf usr/share/doc/samtools/README usr/share/doc/samtools/changelog usr/share/doc/samtools/changelog.Debian usr/share/man/man1/ace2sam.1 usr/share/man/man1/samtools-addreplacerg.1 usr/share/man/man1/samtools-ampliconclip.1 usr/share/man/man1/samtools-ampliconstats.1 usr/share/man/man1/samtools-bedcov.1 usr/share/man/man1/samtools-calmd.1 usr/share/man/man1/samtools-cat.1 usr/share/man/man1/samtools-collate.1 usr/share/man/man1/samtools-consensus.1 usr/share/man/man1/samtools-coverage.1 usr/share/man/man1/samtools-cram-size.1 usr/share/man/man1/samtools-depad.1 usr/share/man/man1/samtools-depth.1 usr/share/man/man1/samtools-dict.1 usr/share/man/man1/samtools-faidx.1 usr/share/man/man1/samtools-fasta.1 usr/share/man/man1/samtools-fixmate.1 usr/share/man/man1/samtools-flags.1 usr/share/man/man1/samtools-flagstat.1 usr/share/man/man1/samtools-fqidx.1 usr/share/man/man1/samtools-head.1 usr/share/man/man1/samtools-idxstats.1 usr/share/man/man1/samtools-import.1 usr/share/man/man1/samtools-index.1 usr/share/man/man1/samtools-markdup.1 usr/share/man/man1/samtools-merge.1 usr/share/man/man1/samtools-mpileup.1 usr/share/man/man1/samtools-phase.1 usr/share/man/man1/samtools-quickcheck.1 usr/share/man/man1/samtools-reference.1 usr/share/man/man1/samtools-reheader.1 usr/share/man/man1/samtools-reset.1 usr/share/man/man1/samtools-rmdup.1 usr/share/man/man1/samtools-samples.1 usr/share/man/man1/samtools-sort.1 usr/share/man/man1/samtools-split.1 usr/share/man/man1/samtools-stats.1 usr/share/man/man1/samtools-targetcut.1 usr/share/man/man1/samtools-tview.1 usr/share/man/man1/samtools-view.1 usr/share/man/man1/samtools.1 usr/share/man/man1/samtools.pl.1 usr/share/man/man1/wgsim.1 cd '/build/reproducible-path/samtools-1.19.2' cd '/build/reproducible-path/samtools-1.19.2' rm -f debian/samtools/usr/share/man/man1/samtools-fastq.1 debian/samtools/usr/share/man/man1/samtools-fastq.1.gz @@ -3925,8 +3975,8 @@ 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 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/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 @@ -3940,41 +3990,41 @@ 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/8a - objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/ace2sam debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/8a/ee45924ca3b4aa63bffcc21fd52a88e95e5ca0.debug - chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/8a/ee45924ca3b4aa63bffcc21fd52a88e95e5ca0.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/8a/ee45924ca3b4aa63bffcc21fd52a88e95e5ca0.debug debian/samtools/usr/bin/ace2sam - install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/06 - objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/samtools debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/06/08a75d667249deaeb0d9a2a31c52034afc9495.debug - chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/06/08a75d667249deaeb0d9a2a31c52034afc9495.debug - strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/samtools - objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/06/08a75d667249deaeb0d9a2a31c52034afc9495.debug debian/samtools/usr/bin/samtools - install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/43 - objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5sum-lite debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/43/51ddf591ff0fdcf0d9614d7413c3261aeec537.debug - chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/43/51ddf591ff0fdcf0d9614d7413c3261aeec537.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/43/51ddf591ff0fdcf0d9614d7413c3261aeec537.debug debian/samtools/usr/bin/md5sum-lite - install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/00 - objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-short debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/00/71990dab202227aca433f71981363033f6f3d0.debug - chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/00/71990dab202227aca433f71981363033f6f3d0.debug - strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/maq2sam-short - objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/00/71990dab202227aca433f71981363033f6f3d0.debug debian/samtools/usr/bin/maq2sam-short install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/1a objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5fa debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/1a/fbedf936abe41e068fab9162ad13e435ed6113.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/1a/fbedf936abe41e068fab9162ad13e435ed6113.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/1a/fbedf936abe41e068fab9162ad13e435ed6113.debug debian/samtools/usr/bin/md5fa + install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/43 + objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5sum-lite debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/43/51ddf591ff0fdcf0d9614d7413c3261aeec537.debug + chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/43/51ddf591ff0fdcf0d9614d7413c3261aeec537.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/43/51ddf591ff0fdcf0d9614d7413c3261aeec537.debug debian/samtools/usr/bin/md5sum-lite install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/2a objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-long debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/2a/aef13fbea7b632d9f39f247fbe330b03a002af.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/2a/aef13fbea7b632d9f39f247fbe330b03a002af.debug strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/maq2sam-long objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/2a/aef13fbea7b632d9f39f247fbe330b03a002af.debug debian/samtools/usr/bin/maq2sam-long + install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/8a + objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/ace2sam debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/8a/ee45924ca3b4aa63bffcc21fd52a88e95e5ca0.debug + chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/8a/ee45924ca3b4aa63bffcc21fd52a88e95e5ca0.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/8a/ee45924ca3b4aa63bffcc21fd52a88e95e5ca0.debug debian/samtools/usr/bin/ace2sam install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/48 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/wgsim debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/48/c87f1bd0e53758f9ada9acd0e81dedfb95a314.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/48/c87f1bd0e53758f9ada9acd0e81dedfb95a314.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/48/c87f1bd0e53758f9ada9acd0e81dedfb95a314.debug debian/samtools/usr/bin/wgsim + install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/06 + objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/samtools debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/06/08a75d667249deaeb0d9a2a31c52034afc9495.debug + chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/06/08a75d667249deaeb0d9a2a31c52034afc9495.debug + strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/samtools + objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/06/08a75d667249deaeb0d9a2a31c52034afc9495.debug debian/samtools/usr/bin/samtools + install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/00 + objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-short debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/00/71990dab202227aca433f71981363033f6f3d0.debug + chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/00/71990dab202227aca433f71981363033f6f3d0.debug + strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/maq2sam-short + objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/00/71990dab202227aca433f71981363033f6f3d0.debug debian/samtools/usr/bin/maq2sam-short install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.dwz cp --reflink=auto -a debian/samtools/usr/lib/debug/.dwz/x86_64-linux-gnu debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.dwz rm -fr debian/samtools/usr/lib/debug/.dwz @@ -3986,20 +4036,20 @@ rm -f debian/samtools/DEBIAN/shlibs dh_shlibdeps -a install -m0755 -d debian/samtools/DEBIAN - dpkg-shlibdeps -Tdebian/samtools.substvars debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/samtools debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/wgsim + 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=0071990dab202227aca433f71981363033f6f3d0 0608a75d667249deaeb0d9a2a31c52034afc9495 1afbedf936abe41e068fab9162ad13e435ed6113 2aaef13fbea7b632d9f39f247fbe330b03a002af 4351ddf591ff0fdcf0d9614d7413c3261aeec537 48c87f1bd0e53758f9ada9acd0e81dedfb95a314 8aee45924ca3b4aa63bffcc21fd52a88e95e5ca0" -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: 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 @@ -4008,15 +4058,15 @@ 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-test/DEBIAN install -m0755 -d debian/samtools/DEBIAN + 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 cd debian/.debhelper/samtools/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums - chmod 0644 -- debian/samtools-test/DEBIAN/md5sums chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/DEBIAN/md5sums + chmod 0644 -- debian/samtools-test/DEBIAN/md5sums dh_builddeb dpkg-deb --root-owner-group --build debian/samtools .. dpkg-deb --root-owner-group --build debian/.debhelper/samtools/dbgsym-root .. @@ -4032,12 +4082,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/323021/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/323021/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/2682622 and its subdirectories -I: Current time: Fri May 10 22:57:48 -12 2024 -I: pbuilder-time-stamp: 1715425068 +I: removing directory /srv/workspace/pbuilder/323021 and its subdirectories +I: Current time: Sat Jun 14 07:23:13 +14 2025 +I: pbuilder-time-stamp: 1749835393