Diff of the two buildlogs: -- --- b1/build.log 2023-04-25 02:19:08.786825663 +0000 +++ b2/build.log 2023-04-25 02:21:39.940127177 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun May 26 20:36:22 -12 2024 -I: pbuilder-time-stamp: 1716798982 +I: Current time: Tue Apr 25 16:19:12 +14 2023 +I: pbuilder-time-stamp: 1682389152 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -16,7 +16,7 @@ I: copying [./samtools_1.16.1.orig.tar.gz] I: copying [./samtools_1.16.1-1.debian.tar.xz] I: Extracting source -gpgv: Signature made Thu Sep 29 21:55:42 2022 -12 +gpgv: Signature made Fri Sep 30 23:55:42 2022 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -29,52 +29,84 @@ dpkg-source: info: applying samtools-fasta-q-whatis.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/32369/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/11145/tmp/hooks/D01_modify_environment starting +debug: Running on codethink16-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Apr 25 16:19 /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/11145/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/11145/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.15(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8' - DISTRIBUTION='bookworm' - HOME='/var/lib/jenkins' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/var/lib/jenkins + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - 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='32369' - PS1='# ' - PS2='> ' + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=11145 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.ULTEwsVN/pbuilderrc_R9vt --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ULTEwsVN/b1 --logfile b1/build.log samtools_1.16.1-1.dsc' - SUDO_GID='117' - SUDO_UID='110' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - USERNAME='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.16:3128' + 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.ULTEwsVN/pbuilderrc_JYR4 --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ULTEwsVN/b2 --logfile b2/build.log --extrapackages usrmerge samtools_1.16.1-1.dsc' + SUDO_GID=117 + SUDO_UID=110 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + USERNAME=root + _='I: set' + http_proxy=http://192.168.101.16:3128 I: uname -a - Linux codethink15-arm64 4.15.0-209-generic #220-Ubuntu SMP Tue Mar 21 19:52:44 UTC 2023 aarch64 GNU/Linux + Linux i-capture-the-hostname 4.15.0-209-generic #220-Ubuntu SMP Tue Mar 21 19:52:44 UTC 2023 aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 24 04:47 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/32369/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Apr 24 00:25 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/11145/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -191,7 +223,7 @@ Get: 57 http://deb.debian.org/debian bookworm/main arm64 pkgconf arm64 1.8.1-1 [25.9 kB] Get: 58 http://deb.debian.org/debian bookworm/main arm64 pkg-config arm64 1.8.1-1 [13.7 kB] Get: 59 http://deb.debian.org/debian bookworm/main arm64 tabix arm64 1.16+ds-3 [427 kB] -Fetched 25.3 MB in 1s (27.5 MB/s) +Fetched 25.3 MB in 1s (45.3 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 ... 19616 files and directories currently installed.) @@ -441,8 +473,17 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +usrmerge is already the newest version (35). +0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/samtools-1.16.1/ && 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_1.16.1-1_source.changes +I: user script /srv/workspace/pbuilder/11145/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +I: user script /srv/workspace/pbuilder/11145/tmp/hooks/A99_set_merged_usr finished +hostname: Temporary failure in name resolution +I: Running cd /build/samtools-1.16.1/ && 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_1.16.1-1_source.changes dpkg-buildpackage: info: source package samtools dpkg-buildpackage: info: source version 1.16.1-1 dpkg-buildpackage: info: source distribution unstable @@ -550,8 +591,6 @@ gcc -g -O2 -ffile-prefix-map=/build/samtools-1.16.1=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_aux.o bam_aux.c gcc -g -O2 -ffile-prefix-map=/build/samtools-1.16.1=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_index.o bam_index.c gcc -g -O2 -ffile-prefix-map=/build/samtools-1.16.1=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_plcmd.o bam_plcmd.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 -ffile-prefix-map=/build/samtools-1.16.1=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_view.o sam_view.c gcc -g -O2 -ffile-prefix-map=/build/samtools-1.16.1=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_fastq.o bam_fastq.c gcc -g -O2 -ffile-prefix-map=/build/samtools-1.16.1=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_cat.o bam_cat.c @@ -563,6 +602,8 @@ cc1: warning: command-line option '-frelease' is valid for D but not for C cc1: warning: command-line option '-frelease' is valid for D but not for C cc1: warning: command-line option '-frelease' is valid for D but not for C +cc1: warning: command-line option '-frelease' is valid for D but not for C +cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -ffile-prefix-map=/build/samtools-1.16.1=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_reheader.o bam_reheader.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -ffile-prefix-map=/build/samtools-1.16.1=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_sort.o bam_sort.c @@ -572,9 +613,9 @@ gcc -g -O2 -ffile-prefix-map=/build/samtools-1.16.1=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/samtools-1.16.1=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/samtools-1.16.1=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/samtools-1.16.1=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_color.o bam_color.c cc1: warning: command-line option '-frelease' is valid for D but not for C echo '#define SAMTOOLS_VERSION "1.16.1"' > version.h @@ -639,9 +680,9 @@ gcc -g -O2 -ffile-prefix-map=/build/samtools-1.16.1=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_import.o bam_import.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -ffile-prefix-map=/build/samtools-1.16.1=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_samples.o bam_samples.c -cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -ffile-prefix-map=/build/samtools-1.16.1=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_consensus.o bam_consensus.c cc1: warning: command-line option '-frelease' is valid for D but not for C +cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -ffile-prefix-map=/build/samtools-1.16.1=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/samtools-1.16.1=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o reference.o reference.c @@ -659,25 +700,19 @@ gcc -g -O2 -ffile-prefix-map=/build/samtools-1.16.1=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/ace2sam.o misc/ace2sam.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -ffile-prefix-map=/build/samtools-1.16.1=. -fstack-protector-strong -Wformat -Werror=format-security -DMAQ_LONGREADS -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/maq2sam-long.o misc/maq2sam.c -cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -ffile-prefix-map=/build/samtools-1.16.1=. -fstack-protector-strong -Wformat -Werror=format-security -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 +cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -ffile-prefix-map=/build/samtools-1.16.1=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/samtools-1.16.1=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/md5sum-lite.o misc/md5sum-lite.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -ffile-prefix-map=/build/samtools-1.16.1=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/samtools-1.16.1=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_bam_translate.o test/merge/test_bam_translate.c -cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -ffile-prefix-map=/build/samtools-1.16.1=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test.o test/test.c -cc1: warning: command-line option '-frelease' is valid for D but not for C -gcc -g -O2 -ffile-prefix-map=/build/samtools-1.16.1=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_rtrans_build.o test/merge/test_rtrans_build.c -cc1: warning: command-line option '-frelease' is valid for D but not for C -gcc -g -O2 -ffile-prefix-map=/build/samtools-1.16.1=. -fstack-protector-strong -Wformat -Werror=format-security -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 gcc -g -O2 -ffile-prefix-map=/build/samtools-1.16.1=. -fstack-protector-strong -Wformat -Werror=format-security -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 +cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -ffile-prefix-map=/build/samtools-1.16.1=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_expand_format_string.o test/split/test_expand_format_string.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -ffile-prefix-map=/build/samtools-1.16.1=. -fstack-protector-strong -Wformat -Werror=format-security -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 @@ -694,16 +729,22 @@ gcc -Wl,-z,relro -Wl,-z,now -o misc/maq2sam-short misc/maq2sam-short.o -lz gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/md5fa misc/md5fa.o -lhts -lz gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/md5sum-lite misc/md5sum-lite.o -lhts -lz +gcc -g -O2 -ffile-prefix-map=/build/samtools-1.16.1=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_bam_translate.o test/merge/test_bam_translate.c +cc1: warning: command-line option '-frelease' is valid for D but not for C +gcc -g -O2 -ffile-prefix-map=/build/samtools-1.16.1=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_rtrans_build.o test/merge/test_rtrans_build.c +cc1: warning: command-line option '-frelease' is valid for D but not for C +gcc -g -O2 -ffile-prefix-map=/build/samtools-1.16.1=. -fstack-protector-strong -Wformat -Werror=format-security -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 +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 test/split/test_count_rg test/split/test_count_rg.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/split/test_expand_format_string test/split/test_expand_format_string.o test/test.o libst.a -lhts -lz -lpthread -gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/split/test_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 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 ./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_trans_tbl_init test/merge/test_trans_tbl_init.o test/test.o libst.a -lhts -lz -lpthread make[2]: Leaving directory '/build/samtools-1.16.1' make[1]: Leaving directory '/build/samtools-1.16.1' rm -f debian/samtools-test.debhelper.log debian/samtools.debhelper.log @@ -749,75 +790,75 @@ /build/samtools-1.16.1/samtools reference -@ 2 -r 17:1000-1500 -e test/reference/mpileup.1.tmp.cram .. ok -/usr/bin/bgzip -c -b 65272 -s 5 /tmp/34w9Wt0Ykb/bgzip.dat.gz +/usr/bin/bgzip -c -b 65272 -s 5 /tmp/erVyqJXN6Q/bgzip.dat.gz .. ok -/usr/bin/bgzip -c -b 979200 -s 6 /tmp/34w9Wt0Ykb/bgzip.dat.gz +/usr/bin/bgzip -c -b 979200 -s 6 /tmp/erVyqJXN6Q/bgzip.dat.gz .. ok -/usr/bin/bgzip -c -b 652804 -s 6 /tmp/34w9Wt0Ykb/bgzip.dat.gz +/usr/bin/bgzip -c -b 652804 -s 6 /tmp/erVyqJXN6Q/bgzip.dat.gz .. ok -/build/samtools-1.16.1/samtools faidx /tmp/34w9Wt0Ykb/faidx.fa 3:11-13 | grep -v '^>' +/build/samtools-1.16.1/samtools faidx /tmp/erVyqJXN6Q/faidx.fa 3:11-13 | grep -v '^>' .. ok -/build/samtools-1.16.1/samtools faidx /tmp/34w9Wt0Ykb/faidx.fa.gz 3:11-13 | grep -v '^>' +/build/samtools-1.16.1/samtools faidx /tmp/erVyqJXN6Q/faidx.fa.gz 3:11-13 | grep -v '^>' .. ok -/build/samtools-1.16.1/samtools faidx /tmp/34w9Wt0Ykb/faidx.fa 2:998-1003 | grep -v '^>' +/build/samtools-1.16.1/samtools faidx /tmp/erVyqJXN6Q/faidx.fa 2:998-1003 | grep -v '^>' .. ok -/build/samtools-1.16.1/samtools faidx /tmp/34w9Wt0Ykb/faidx.fa.gz 2:998-1003 | grep -v '^>' +/build/samtools-1.16.1/samtools faidx /tmp/erVyqJXN6Q/faidx.fa.gz 2:998-1003 | grep -v '^>' .. ok -/build/samtools-1.16.1/samtools faidx /tmp/34w9Wt0Ykb/faidx.fa 1:100-104 | grep -v '^>' +/build/samtools-1.16.1/samtools faidx /tmp/erVyqJXN6Q/faidx.fa 1:100-104 | grep -v '^>' .. ok -/build/samtools-1.16.1/samtools faidx /tmp/34w9Wt0Ykb/faidx.fa.gz 1:100-104 | grep -v '^>' +/build/samtools-1.16.1/samtools faidx /tmp/erVyqJXN6Q/faidx.fa.gz 1:100-104 | grep -v '^>' .. ok -/build/samtools-1.16.1/samtools faidx /tmp/34w9Wt0Ykb/faidx.fa 1:99998-100007 | grep -v '^>' +/build/samtools-1.16.1/samtools faidx /tmp/erVyqJXN6Q/faidx.fa 1:99998-100007 | grep -v '^>' .. ok -/build/samtools-1.16.1/samtools faidx /tmp/34w9Wt0Ykb/faidx.fa.gz 1:99998-100007 | grep -v '^>' +/build/samtools-1.16.1/samtools faidx /tmp/erVyqJXN6Q/faidx.fa.gz 1:99998-100007 | grep -v '^>' .. ok -/build/samtools-1.16.1/samtools fqidx /tmp/34w9Wt0Ykb/fqidx.fq 3:11-13 +/build/samtools-1.16.1/samtools fqidx /tmp/erVyqJXN6Q/fqidx.fq 3:11-13 .. ok .. ok -/build/samtools-1.16.1/samtools fqidx /tmp/34w9Wt0Ykb/fqidx.fq.gz 3:11-13 +/build/samtools-1.16.1/samtools fqidx /tmp/erVyqJXN6Q/fqidx.fq.gz 3:11-13 .. ok .. ok -/build/samtools-1.16.1/samtools fqidx /tmp/34w9Wt0Ykb/fqidx.fq 2:998-1003 +/build/samtools-1.16.1/samtools fqidx /tmp/erVyqJXN6Q/fqidx.fq 2:998-1003 .. ok .. ok -/build/samtools-1.16.1/samtools fqidx /tmp/34w9Wt0Ykb/fqidx.fq.gz 2:998-1003 +/build/samtools-1.16.1/samtools fqidx /tmp/erVyqJXN6Q/fqidx.fq.gz 2:998-1003 .. ok .. ok -/build/samtools-1.16.1/samtools fqidx /tmp/34w9Wt0Ykb/fqidx.fq 1:100-104 +/build/samtools-1.16.1/samtools fqidx /tmp/erVyqJXN6Q/fqidx.fq 1:100-104 .. ok .. ok -/build/samtools-1.16.1/samtools fqidx /tmp/34w9Wt0Ykb/fqidx.fq.gz 1:100-104 +/build/samtools-1.16.1/samtools fqidx /tmp/erVyqJXN6Q/fqidx.fq.gz 1:100-104 .. ok .. ok -/build/samtools-1.16.1/samtools fqidx /tmp/34w9Wt0Ykb/fqidx.fq 1:99998-100007 +/build/samtools-1.16.1/samtools fqidx /tmp/erVyqJXN6Q/fqidx.fq 1:99998-100007 .. ok .. ok -/build/samtools-1.16.1/samtools fqidx /tmp/34w9Wt0Ykb/fqidx.fq.gz 1:99998-100007 +/build/samtools-1.16.1/samtools fqidx /tmp/erVyqJXN6Q/fqidx.fq.gz 1:99998-100007 .. ok .. ok @@ -827,7 +868,7 @@ .. ok test_dict: - /build/samtools-1.16.1/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /tmp/34w9Wt0Ykb/dict.fa.gz + /build/samtools-1.16.1/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /tmp/erVyqJXN6Q/dict.fa.gz .. ok test_dict: @@ -843,11 +884,11 @@ .. ok test_index: - /build/samtools-1.16.1/samtools view /tmp/34w9Wt0Ykb/large_chrom.bam ref2 + /build/samtools-1.16.1/samtools view /tmp/erVyqJXN6Q/large_chrom.bam ref2 .. ok test_index: - /build/samtools-1.16.1/samtools view /tmp/34w9Wt0Ykb/large_chrom.bam ref2:1-541556283 + /build/samtools-1.16.1/samtools view /tmp/erVyqJXN6Q/large_chrom.bam ref2:1-541556283 .. ok test_index: @@ -855,15 +896,15 @@ .. ok test_index: - /build/samtools-1.16.1/samtools view -X /build/samtools-1.16.1/test/dat/test_input_1_b.bam /tmp/34w9Wt0Ykb/test_input_1_b.bam.bai ref2 + /build/samtools-1.16.1/samtools view -X /build/samtools-1.16.1/test/dat/test_input_1_b.bam /tmp/erVyqJXN6Q/test_input_1_b.bam.bai ref2 .. ok test_index: - /build/samtools-1.16.1/samtools merge -O sam - -X -cp -R ref2 /build/samtools-1.16.1/test/dat/test_input_1_a.bam /build/samtools-1.16.1/test/dat/test_input_1_b.bam /build/samtools-1.16.1/test/dat/test_input_1_a.bam.bai /tmp/34w9Wt0Ykb/test_input_1_b.bam.bai + /build/samtools-1.16.1/samtools merge -O sam - -X -cp -R ref2 /build/samtools-1.16.1/test/dat/test_input_1_a.bam /build/samtools-1.16.1/test/dat/test_input_1_b.bam /build/samtools-1.16.1/test/dat/test_input_1_a.bam.bai /tmp/erVyqJXN6Q/test_input_1_b.bam.bai .. ok test_index: - /build/samtools-1.16.1/samtools view -X /build/samtools-1.16.1/test/dat/test_input_1_b.bam /tmp/34w9Wt0Ykb/test_input_1_b_opt.bam.bai ref2 + /build/samtools-1.16.1/samtools view -X /build/samtools-1.16.1/test/dat/test_input_1_b.bam /tmp/erVyqJXN6Q/test_input_1_b_opt.bam.bai ref2 .. ok test_index: @@ -879,23 +920,23 @@ .. ok test_index: - /build/samtools-1.16.1/samtools index -c /build/samtools-1.16.1/test/dat/auto_indexed.tmp.bam /tmp/34w9Wt0Ykb/auto_indexed.csi && cat /tmp/34w9Wt0Ykb/auto_indexed.csi + /build/samtools-1.16.1/samtools index -c /build/samtools-1.16.1/test/dat/auto_indexed.tmp.bam /tmp/erVyqJXN6Q/auto_indexed.csi && cat /tmp/erVyqJXN6Q/auto_indexed.csi .. ok test_index: - /build/samtools-1.16.1/samtools index /build/samtools-1.16.1/test/dat/auto_indexed.tmp.cram /tmp/34w9Wt0Ykb/auto_indexed.crai && cat /tmp/34w9Wt0Ykb/auto_indexed.crai + /build/samtools-1.16.1/samtools index /build/samtools-1.16.1/test/dat/auto_indexed.tmp.cram /tmp/erVyqJXN6Q/auto_indexed.crai && cat /tmp/erVyqJXN6Q/auto_indexed.crai .. ok test_index: - /build/samtools-1.16.1/samtools index -c /build/samtools-1.16.1/test/dat/auto_indexed.tmp.sam /tmp/34w9Wt0Ykb/auto_indexed.csi && cat /tmp/34w9Wt0Ykb/auto_indexed.csi + /build/samtools-1.16.1/samtools index -c /build/samtools-1.16.1/test/dat/auto_indexed.tmp.sam /tmp/erVyqJXN6Q/auto_indexed.csi && cat /tmp/erVyqJXN6Q/auto_indexed.csi .. ok test_index: - /build/samtools-1.16.1/samtools view -@ 2 /tmp/34w9Wt0Ykb/large_chrom.bam ref2 + /build/samtools-1.16.1/samtools view -@ 2 /tmp/erVyqJXN6Q/large_chrom.bam ref2 .. ok test_index: - /build/samtools-1.16.1/samtools view -@ 2 /tmp/34w9Wt0Ykb/large_chrom.bam ref2:1-541556283 + /build/samtools-1.16.1/samtools view -@ 2 /tmp/erVyqJXN6Q/large_chrom.bam ref2:1-541556283 .. ok test_index: @@ -903,15 +944,15 @@ .. ok test_index: - /build/samtools-1.16.1/samtools view -@ 2 -X /build/samtools-1.16.1/test/dat/test_input_1_b.bam /tmp/34w9Wt0Ykb/test_input_1_b.bam.bai ref2 + /build/samtools-1.16.1/samtools view -@ 2 -X /build/samtools-1.16.1/test/dat/test_input_1_b.bam /tmp/erVyqJXN6Q/test_input_1_b.bam.bai ref2 .. ok test_index: - /build/samtools-1.16.1/samtools merge -@ 2 -O sam - -X -cp -R ref2 /build/samtools-1.16.1/test/dat/test_input_1_a.bam /build/samtools-1.16.1/test/dat/test_input_1_b.bam /build/samtools-1.16.1/test/dat/test_input_1_a.bam.bai /tmp/34w9Wt0Ykb/test_input_1_b.bam.bai + /build/samtools-1.16.1/samtools merge -@ 2 -O sam - -X -cp -R ref2 /build/samtools-1.16.1/test/dat/test_input_1_a.bam /build/samtools-1.16.1/test/dat/test_input_1_b.bam /build/samtools-1.16.1/test/dat/test_input_1_a.bam.bai /tmp/erVyqJXN6Q/test_input_1_b.bam.bai .. ok test_index: - /build/samtools-1.16.1/samtools view -@ 2 -X /build/samtools-1.16.1/test/dat/test_input_1_b.bam /tmp/34w9Wt0Ykb/test_input_1_b_opt.bam.bai ref2 + /build/samtools-1.16.1/samtools view -@ 2 -X /build/samtools-1.16.1/test/dat/test_input_1_b.bam /tmp/erVyqJXN6Q/test_input_1_b_opt.bam.bai ref2 .. ok test_index: @@ -927,39 +968,39 @@ .. ok test_index: - /build/samtools-1.16.1/samtools index -@ 2 -c /build/samtools-1.16.1/test/dat/auto_indexed.tmp.bam /tmp/34w9Wt0Ykb/auto_indexed.csi && cat /tmp/34w9Wt0Ykb/auto_indexed.csi + /build/samtools-1.16.1/samtools index -@ 2 -c /build/samtools-1.16.1/test/dat/auto_indexed.tmp.bam /tmp/erVyqJXN6Q/auto_indexed.csi && cat /tmp/erVyqJXN6Q/auto_indexed.csi .. ok test_index: - /build/samtools-1.16.1/samtools index -@ 2 /build/samtools-1.16.1/test/dat/auto_indexed.tmp.cram /tmp/34w9Wt0Ykb/auto_indexed.crai && cat /tmp/34w9Wt0Ykb/auto_indexed.crai + /build/samtools-1.16.1/samtools index -@ 2 /build/samtools-1.16.1/test/dat/auto_indexed.tmp.cram /tmp/erVyqJXN6Q/auto_indexed.crai && cat /tmp/erVyqJXN6Q/auto_indexed.crai .. ok test_index: - /build/samtools-1.16.1/samtools index -@ 2 -c /build/samtools-1.16.1/test/dat/auto_indexed.tmp.sam /tmp/34w9Wt0Ykb/auto_indexed.csi && cat /tmp/34w9Wt0Ykb/auto_indexed.csi + /build/samtools-1.16.1/samtools index -@ 2 -c /build/samtools-1.16.1/test/dat/auto_indexed.tmp.sam /tmp/erVyqJXN6Q/auto_indexed.csi && cat /tmp/erVyqJXN6Q/auto_indexed.csi .. ok test_mpileup: - /build/samtools-1.16.1/samtools mpileup -b /tmp/34w9Wt0Ykb/mpileup.bam.list -f /tmp/34w9Wt0Ykb/mpileup.ref.fa.gz -r17:100-150 + /build/samtools-1.16.1/samtools mpileup -b /tmp/erVyqJXN6Q/mpileup.bam.list -f /tmp/erVyqJXN6Q/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: - /build/samtools-1.16.1/samtools mpileup -b /tmp/34w9Wt0Ykb/mpileup.cram.list -f /tmp/34w9Wt0Ykb/mpileup.ref.fa.gz -r17:100-150 + /build/samtools-1.16.1/samtools mpileup -b /tmp/erVyqJXN6Q/mpileup.cram.list -f /tmp/erVyqJXN6Q/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: - /build/samtools-1.16.1/samtools mpileup -b /tmp/34w9Wt0Ykb/mpileup.bam.urllist -f /tmp/34w9Wt0Ykb/mpileup.ref.fa.gz -r17:100-150 + /build/samtools-1.16.1/samtools mpileup -b /tmp/erVyqJXN6Q/mpileup.bam.urllist -f /tmp/erVyqJXN6Q/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: - /build/samtools-1.16.1/samtools mpileup -b /tmp/34w9Wt0Ykb/mpileup.cram.urllist -f /tmp/34w9Wt0Ykb/mpileup.ref.fa.gz -r17:100-150 + /build/samtools-1.16.1/samtools mpileup -b /tmp/erVyqJXN6Q/mpileup.cram.urllist -f /tmp/erVyqJXN6Q/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: - /build/samtools-1.16.1/samtools mpileup -B --ff 0x14 -f /tmp/34w9Wt0Ykb/mpileup.ref.fa.gz -r17:1050-1060 /tmp/34w9Wt0Ykb/mpileup.1.bam | grep -v mpileup + /build/samtools-1.16.1/samtools mpileup -B --ff 0x14 -f /tmp/erVyqJXN6Q/mpileup.ref.fa.gz -r17:1050-1060 /tmp/erVyqJXN6Q/mpileup.1.bam | grep -v mpileup .. ok test_mpileup: - /build/samtools-1.16.1/samtools mpileup -B --ff 0x14 -f /tmp/34w9Wt0Ykb/mpileup.ref.fa.gz -r17:1050-1060 /tmp/34w9Wt0Ykb/mpileup.1.cram | grep -v mpileup + /build/samtools-1.16.1/samtools mpileup -B --ff 0x14 -f /tmp/erVyqJXN6Q/mpileup.ref.fa.gz -r17:1050-1060 /tmp/erVyqJXN6Q/mpileup.1.cram | grep -v mpileup .. ok test_mpileup: @@ -1245,53 +1286,53 @@ 48: Count -r grp2 (CRAM input) .. ok - 49: Filter -R /tmp/34w9Wt0Ykb/view.001.fogn (SAM input) .. ok + 49: Filter -R /tmp/erVyqJXN6Q/view.001.fogn (SAM input) .. ok - 50: Count -R /tmp/34w9Wt0Ykb/view.001.fogn (SAM input) .. ok + 50: Count -R /tmp/erVyqJXN6Q/view.001.fogn (SAM input) .. ok - 51: Filter -R /tmp/34w9Wt0Ykb/view.001.fogn (BAM input) .. ok + 51: Filter -R /tmp/erVyqJXN6Q/view.001.fogn (BAM input) .. ok - 52: Count -R /tmp/34w9Wt0Ykb/view.001.fogn (BAM input) .. ok + 52: Count -R /tmp/erVyqJXN6Q/view.001.fogn (BAM input) .. ok - 53: Filter -R /tmp/34w9Wt0Ykb/view.001.fogn (CRAM input) .. ok + 53: Filter -R /tmp/erVyqJXN6Q/view.001.fogn (CRAM input) .. ok - 54: Count -R /tmp/34w9Wt0Ykb/view.001.fogn (CRAM input) .. ok + 54: Count -R /tmp/erVyqJXN6Q/view.001.fogn (CRAM input) .. ok - 55: Filter -R /tmp/34w9Wt0Ykb/view.001.fogn -r grp2 (SAM input).. ok + 55: Filter -R /tmp/erVyqJXN6Q/view.001.fogn -r grp2 (SAM input).. ok - 56: Count -R /tmp/34w9Wt0Ykb/view.001.fogn -r grp2 (SAM input).. ok + 56: Count -R /tmp/erVyqJXN6Q/view.001.fogn -r grp2 (SAM input).. ok - 57: Filter -R /tmp/34w9Wt0Ykb/view.001.fogn -r grp2 (BAM input).. ok + 57: Filter -R /tmp/erVyqJXN6Q/view.001.fogn -r grp2 (BAM input).. ok - 58: Count -R /tmp/34w9Wt0Ykb/view.001.fogn -r grp2 (BAM input).. ok + 58: Count -R /tmp/erVyqJXN6Q/view.001.fogn -r grp2 (BAM input).. ok - 59: Filter -R /tmp/34w9Wt0Ykb/view.001.fogn -r grp2 (CRAM input).. ok + 59: Filter -R /tmp/erVyqJXN6Q/view.001.fogn -r grp2 (CRAM input).. ok - 60: Count -R /tmp/34w9Wt0Ykb/view.001.fogn -r grp2 (CRAM input).. ok + 60: Count -R /tmp/erVyqJXN6Q/view.001.fogn -r grp2 (CRAM input).. ok - 61: Filter -r grp2 -R /tmp/34w9Wt0Ykb/view.001.fogn (SAM input).. ok + 61: Filter -r grp2 -R /tmp/erVyqJXN6Q/view.001.fogn (SAM input).. ok - 62: Count -r grp2 -R /tmp/34w9Wt0Ykb/view.001.fogn (SAM input).. ok + 62: Count -r grp2 -R /tmp/erVyqJXN6Q/view.001.fogn (SAM input).. ok - 63: Filter -r grp2 -R /tmp/34w9Wt0Ykb/view.001.fogn (BAM input).. ok + 63: Filter -r grp2 -R /tmp/erVyqJXN6Q/view.001.fogn (BAM input).. ok - 64: Count -r grp2 -R /tmp/34w9Wt0Ykb/view.001.fogn (BAM input).. ok + 64: Count -r grp2 -R /tmp/erVyqJXN6Q/view.001.fogn (BAM input).. ok - 65: Filter -r grp2 -R /tmp/34w9Wt0Ykb/view.001.fogn (CRAM input).. ok + 65: Filter -r grp2 -R /tmp/erVyqJXN6Q/view.001.fogn (CRAM input).. ok - 66: Count -r grp2 -R /tmp/34w9Wt0Ykb/view.001.fogn (CRAM input).. ok + 66: Count -r grp2 -R /tmp/erVyqJXN6Q/view.001.fogn (CRAM input).. ok - 67: Filter -N /tmp/34w9Wt0Ykb/view.001.forn (SAM input) .. ok + 67: Filter -N /tmp/erVyqJXN6Q/view.001.forn (SAM input) .. ok - 68: Count -N /tmp/34w9Wt0Ykb/view.001.forn (SAM input) .. ok + 68: Count -N /tmp/erVyqJXN6Q/view.001.forn (SAM input) .. ok - 69: Filter -N /tmp/34w9Wt0Ykb/view.001.forn (BAM input) .. ok + 69: Filter -N /tmp/erVyqJXN6Q/view.001.forn (BAM input) .. ok - 70: Count -N /tmp/34w9Wt0Ykb/view.001.forn (BAM input) .. ok + 70: Count -N /tmp/erVyqJXN6Q/view.001.forn (BAM input) .. ok - 71: Filter -N /tmp/34w9Wt0Ykb/view.001.forn (CRAM input) .. ok + 71: Filter -N /tmp/erVyqJXN6Q/view.001.forn (CRAM input) .. ok - 72: Count -N /tmp/34w9Wt0Ykb/view.001.forn (CRAM input) .. ok + 72: Count -N /tmp/erVyqJXN6Q/view.001.forn (CRAM input) .. ok 73: Filter -d BC (SAM input) .. ok @@ -1317,53 +1358,53 @@ 84: Count -d BC:TGCA (CRAM input) .. ok - 85: Filter -D BC:/tmp/34w9Wt0Ykb/view.001.fobc (SAM input) .. ok + 85: Filter -D BC:/tmp/erVyqJXN6Q/view.001.fobc (SAM input) .. ok - 86: Count -D BC:/tmp/34w9Wt0Ykb/view.001.fobc (SAM input) .. ok + 86: Count -D BC:/tmp/erVyqJXN6Q/view.001.fobc (SAM input) .. ok - 87: Filter -D BC:/tmp/34w9Wt0Ykb/view.001.fobc (BAM input) .. ok + 87: Filter -D BC:/tmp/erVyqJXN6Q/view.001.fobc (BAM input) .. ok - 88: Count -D BC:/tmp/34w9Wt0Ykb/view.001.fobc (BAM input) .. ok + 88: Count -D BC:/tmp/erVyqJXN6Q/view.001.fobc (BAM input) .. ok - 89: Filter -D BC:/tmp/34w9Wt0Ykb/view.001.fobc (CRAM input) .. ok + 89: Filter -D BC:/tmp/erVyqJXN6Q/view.001.fobc (CRAM input) .. ok - 90: Count -D BC:/tmp/34w9Wt0Ykb/view.001.fobc (CRAM input) .. ok + 90: Count -D BC:/tmp/erVyqJXN6Q/view.001.fobc (CRAM input) .. ok - 91: Filter -D BC:/tmp/34w9Wt0Ykb/view.001.fobc -d BC:TGCA (SAM input).. ok + 91: Filter -D BC:/tmp/erVyqJXN6Q/view.001.fobc -d BC:TGCA (SAM input).. ok - 92: Count -D BC:/tmp/34w9Wt0Ykb/view.001.fobc -d BC:TGCA (SAM input).. ok + 92: Count -D BC:/tmp/erVyqJXN6Q/view.001.fobc -d BC:TGCA (SAM input).. ok - 93: Filter -D BC:/tmp/34w9Wt0Ykb/view.001.fobc -d BC:TGCA (BAM input).. ok + 93: Filter -D BC:/tmp/erVyqJXN6Q/view.001.fobc -d BC:TGCA (BAM input).. ok - 94: Count -D BC:/tmp/34w9Wt0Ykb/view.001.fobc -d BC:TGCA (BAM input).. ok + 94: Count -D BC:/tmp/erVyqJXN6Q/view.001.fobc -d BC:TGCA (BAM input).. ok - 95: Filter -D BC:/tmp/34w9Wt0Ykb/view.001.fobc -d BC:TGCA (CRAM input).. ok + 95: Filter -D BC:/tmp/erVyqJXN6Q/view.001.fobc -d BC:TGCA (CRAM input).. ok - 96: Count -D BC:/tmp/34w9Wt0Ykb/view.001.fobc -d BC:TGCA (CRAM input).. ok + 96: Count -D BC:/tmp/erVyqJXN6Q/view.001.fobc -d BC:TGCA (CRAM input).. ok - 97: Filter -d BC:TGCA -D BC:/tmp/34w9Wt0Ykb/view.001.fobc (SAM input).. ok + 97: Filter -d BC:TGCA -D BC:/tmp/erVyqJXN6Q/view.001.fobc (SAM input).. ok - 98: Count -d BC:TGCA -D BC:/tmp/34w9Wt0Ykb/view.001.fobc (SAM input).. ok + 98: Count -d BC:TGCA -D BC:/tmp/erVyqJXN6Q/view.001.fobc (SAM input).. ok - 99: Filter -d BC:TGCA -D BC:/tmp/34w9Wt0Ykb/view.001.fobc (BAM input).. ok + 99: Filter -d BC:TGCA -D BC:/tmp/erVyqJXN6Q/view.001.fobc (BAM input).. ok - 100: Count -d BC:TGCA -D BC:/tmp/34w9Wt0Ykb/view.001.fobc (BAM input).. ok + 100: Count -d BC:TGCA -D BC:/tmp/erVyqJXN6Q/view.001.fobc (BAM input).. ok - 101: Filter -d BC:TGCA -D BC:/tmp/34w9Wt0Ykb/view.001.fobc (CRAM input).. ok + 101: Filter -d BC:TGCA -D BC:/tmp/erVyqJXN6Q/view.001.fobc (CRAM input).. ok - 102: Count -d BC:TGCA -D BC:/tmp/34w9Wt0Ykb/view.001.fobc (CRAM input).. ok + 102: Count -d BC:TGCA -D BC:/tmp/erVyqJXN6Q/view.001.fobc (CRAM input).. ok - 103: Filter -D RG:/tmp/34w9Wt0Ykb/view.001.fogn (SAM input) .. ok + 103: Filter -D RG:/tmp/erVyqJXN6Q/view.001.fogn (SAM input) .. ok - 104: Count -D RG:/tmp/34w9Wt0Ykb/view.001.fogn (SAM input) .. ok + 104: Count -D RG:/tmp/erVyqJXN6Q/view.001.fogn (SAM input) .. ok - 105: Filter -D RG:/tmp/34w9Wt0Ykb/view.001.fogn (BAM input) .. ok + 105: Filter -D RG:/tmp/erVyqJXN6Q/view.001.fogn (BAM input) .. ok - 106: Count -D RG:/tmp/34w9Wt0Ykb/view.001.fogn (BAM input) .. ok + 106: Count -D RG:/tmp/erVyqJXN6Q/view.001.fogn (BAM input) .. ok - 107: Filter -D RG:/tmp/34w9Wt0Ykb/view.001.fogn (CRAM input).. ok + 107: Filter -D RG:/tmp/erVyqJXN6Q/view.001.fogn (CRAM input).. ok - 108: Count -D RG:/tmp/34w9Wt0Ykb/view.001.fogn (CRAM input) .. ok + 108: Count -D RG:/tmp/erVyqJXN6Q/view.001.fogn (CRAM input) .. ok 109: Filter -d NE:TGCA (SAM input) .. ok @@ -1379,126 +1420,126 @@ 115: Filter -d TGCA (SAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: - /build/samtools-1.16.1/samtools view -o /tmp/34w9Wt0Ykb/view.test115.sam -h -d TGCA /tmp/34w9Wt0Ykb/view.001.sam --no-PG + /build/samtools-1.16.1/samtools view -o /tmp/erVyqJXN6Q/view.test115.sam -h -d TGCA /tmp/erVyqJXN6Q/view.001.sam --no-PG .. expected failure 116: Count -d TGCA (SAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: - /build/samtools-1.16.1/samtools view -c -d TGCA /tmp/34w9Wt0Ykb/view.001.sam --no-PG + /build/samtools-1.16.1/samtools view -c -d TGCA /tmp/erVyqJXN6Q/view.001.sam --no-PG .. expected failure 117: Filter -d TGCA (BAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: - /build/samtools-1.16.1/samtools view -o /tmp/34w9Wt0Ykb/view.test117.sam -h -d TGCA /tmp/34w9Wt0Ykb/view.test001.bam --no-PG + /build/samtools-1.16.1/samtools view -o /tmp/erVyqJXN6Q/view.test117.sam -h -d TGCA /tmp/erVyqJXN6Q/view.test001.bam --no-PG .. expected failure 118: Count -d TGCA (BAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: - /build/samtools-1.16.1/samtools view -c -d TGCA /tmp/34w9Wt0Ykb/view.test001.bam --no-PG + /build/samtools-1.16.1/samtools view -c -d TGCA /tmp/erVyqJXN6Q/view.test001.bam --no-PG .. expected failure 119: Filter -d TGCA (CRAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: - /build/samtools-1.16.1/samtools view -o /tmp/34w9Wt0Ykb/view.test119.sam -h -d TGCA /tmp/34w9Wt0Ykb/view.test006.cram --no-PG + /build/samtools-1.16.1/samtools view -o /tmp/erVyqJXN6Q/view.test119.sam -h -d TGCA /tmp/erVyqJXN6Q/view.test006.cram --no-PG .. expected failure 120: Count -d TGCA (CRAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: - /build/samtools-1.16.1/samtools view -c -d TGCA /tmp/34w9Wt0Ykb/view.test006.cram --no-PG + /build/samtools-1.16.1/samtools view -c -d TGCA /tmp/erVyqJXN6Q/view.test006.cram --no-PG .. expected failure - 121: Filter -D BClong:/tmp/34w9Wt0Ykb/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/34w9Wt0Ykb/view.001.fobc" + 121: Filter -D BClong:/tmp/erVyqJXN6Q/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/erVyqJXN6Q/view.001.fobc" Failed command: - /build/samtools-1.16.1/samtools view -o /tmp/34w9Wt0Ykb/view.test121.sam -h -D BClong:/tmp/34w9Wt0Ykb/view.001.fobc /tmp/34w9Wt0Ykb/view.001.sam --no-PG + /build/samtools-1.16.1/samtools view -o /tmp/erVyqJXN6Q/view.test121.sam -h -D BClong:/tmp/erVyqJXN6Q/view.001.fobc /tmp/erVyqJXN6Q/view.001.sam --no-PG .. expected failure - 122: Count -D BClong:/tmp/34w9Wt0Ykb/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/34w9Wt0Ykb/view.001.fobc" + 122: Count -D BClong:/tmp/erVyqJXN6Q/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/erVyqJXN6Q/view.001.fobc" Failed command: - /build/samtools-1.16.1/samtools view -c -D BClong:/tmp/34w9Wt0Ykb/view.001.fobc /tmp/34w9Wt0Ykb/view.001.sam --no-PG + /build/samtools-1.16.1/samtools view -c -D BClong:/tmp/erVyqJXN6Q/view.001.fobc /tmp/erVyqJXN6Q/view.001.sam --no-PG .. expected failure - 123: Filter -D BClong:/tmp/34w9Wt0Ykb/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/34w9Wt0Ykb/view.001.fobc" + 123: Filter -D BClong:/tmp/erVyqJXN6Q/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/erVyqJXN6Q/view.001.fobc" Failed command: - /build/samtools-1.16.1/samtools view -o /tmp/34w9Wt0Ykb/view.test123.sam -h -D BClong:/tmp/34w9Wt0Ykb/view.001.fobc /tmp/34w9Wt0Ykb/view.test001.bam --no-PG + /build/samtools-1.16.1/samtools view -o /tmp/erVyqJXN6Q/view.test123.sam -h -D BClong:/tmp/erVyqJXN6Q/view.001.fobc /tmp/erVyqJXN6Q/view.test001.bam --no-PG .. expected failure - 124: Count -D BClong:/tmp/34w9Wt0Ykb/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/34w9Wt0Ykb/view.001.fobc" + 124: Count -D BClong:/tmp/erVyqJXN6Q/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/erVyqJXN6Q/view.001.fobc" Failed command: - /build/samtools-1.16.1/samtools view -c -D BClong:/tmp/34w9Wt0Ykb/view.001.fobc /tmp/34w9Wt0Ykb/view.test001.bam --no-PG + /build/samtools-1.16.1/samtools view -c -D BClong:/tmp/erVyqJXN6Q/view.001.fobc /tmp/erVyqJXN6Q/view.test001.bam --no-PG .. expected failure - 125: Filter -D BClong:/tmp/34w9Wt0Ykb/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/34w9Wt0Ykb/view.001.fobc" + 125: Filter -D BClong:/tmp/erVyqJXN6Q/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/erVyqJXN6Q/view.001.fobc" Failed command: - /build/samtools-1.16.1/samtools view -o /tmp/34w9Wt0Ykb/view.test125.sam -h -D BClong:/tmp/34w9Wt0Ykb/view.001.fobc /tmp/34w9Wt0Ykb/view.test006.cram --no-PG + /build/samtools-1.16.1/samtools view -o /tmp/erVyqJXN6Q/view.test125.sam -h -D BClong:/tmp/erVyqJXN6Q/view.001.fobc /tmp/erVyqJXN6Q/view.test006.cram --no-PG .. expected failure - 126: Count -D BClong:/tmp/34w9Wt0Ykb/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/34w9Wt0Ykb/view.001.fobc" + 126: Count -D BClong:/tmp/erVyqJXN6Q/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/erVyqJXN6Q/view.001.fobc" Failed command: - /build/samtools-1.16.1/samtools view -c -D BClong:/tmp/34w9Wt0Ykb/view.001.fobc /tmp/34w9Wt0Ykb/view.test006.cram --no-PG + /build/samtools-1.16.1/samtools view -c -D BClong:/tmp/erVyqJXN6Q/view.001.fobc /tmp/erVyqJXN6Q/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/samtools-1.16.1/samtools view -o /tmp/34w9Wt0Ykb/view.test127.sam -h -d BC:ACGT -d RG:grp2 /tmp/34w9Wt0Ykb/view.001.sam --no-PG + /build/samtools-1.16.1/samtools view -o /tmp/erVyqJXN6Q/view.test127.sam -h -d BC:ACGT -d RG:grp2 /tmp/erVyqJXN6Q/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/samtools-1.16.1/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/34w9Wt0Ykb/view.001.sam --no-PG + /build/samtools-1.16.1/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/erVyqJXN6Q/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/samtools-1.16.1/samtools view -o /tmp/34w9Wt0Ykb/view.test129.sam -h -d BC:ACGT -d RG:grp2 /tmp/34w9Wt0Ykb/view.test001.bam --no-PG + /build/samtools-1.16.1/samtools view -o /tmp/erVyqJXN6Q/view.test129.sam -h -d BC:ACGT -d RG:grp2 /tmp/erVyqJXN6Q/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/samtools-1.16.1/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/34w9Wt0Ykb/view.test001.bam --no-PG + /build/samtools-1.16.1/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/erVyqJXN6Q/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/samtools-1.16.1/samtools view -o /tmp/34w9Wt0Ykb/view.test131.sam -h -d BC:ACGT -d RG:grp2 /tmp/34w9Wt0Ykb/view.test006.cram --no-PG + /build/samtools-1.16.1/samtools view -o /tmp/erVyqJXN6Q/view.test131.sam -h -d BC:ACGT -d RG:grp2 /tmp/erVyqJXN6Q/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/samtools-1.16.1/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/34w9Wt0Ykb/view.test006.cram --no-PG + /build/samtools-1.16.1/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/erVyqJXN6Q/view.test006.cram --no-PG .. expected failure @@ -2372,7 +2413,7 @@ .. ok test_bam2fq: - /build/samtools-1.16.1/samtools fastq -N -s /tmp/34w9Wt0Ykb/bam2fq.discard.s.fq -0 /tmp/34w9Wt0Ykb/bam2fq.discard.0.fq /build/samtools-1.16.1/test/dat/bam2fq.001.sam + /build/samtools-1.16.1/samtools fastq -N -s /tmp/erVyqJXN6Q/bam2fq.discard.s.fq -0 /tmp/erVyqJXN6Q/bam2fq.discard.0.fq /build/samtools-1.16.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: @@ -2493,7 +2534,7 @@ .. ok test_bam2fq: - /build/samtools-1.16.1/samtools fastq -@ 2 -N -s /tmp/34w9Wt0Ykb/bam2fq.discard.s.fq -0 /tmp/34w9Wt0Ykb/bam2fq.discard.0.fq /build/samtools-1.16.1/test/dat/bam2fq.001.sam + /build/samtools-1.16.1/samtools fastq -@ 2 -N -s /tmp/erVyqJXN6Q/bam2fq.discard.s.fq -0 /tmp/erVyqJXN6Q/bam2fq.discard.0.fq /build/samtools-1.16.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: @@ -2686,7 +2727,7 @@ .. ok test_merge: - /build/samtools-1.16.1/samtools merge -s 1 -O sam -b /tmp/ac9DrLWd3j - /build/samtools-1.16.1/test/dat/test_input_1_a.bam + /build/samtools-1.16.1/samtools merge -s 1 -O sam -b /tmp/LVYfBJadLd - /build/samtools-1.16.1/test/dat/test_input_1_a.bam .. ok test_merge: @@ -2710,11 +2751,11 @@ .. ok test_merge: - /build/samtools-1.16.1/samtools merge -s 1 -p -c -t PG -O SAM - /tmp/34w9Wt0Ykb/merge.tag.1.bam /tmp/34w9Wt0Ykb/merge.tag.2.bam + /build/samtools-1.16.1/samtools merge -s 1 -p -c -t PG -O SAM - /tmp/erVyqJXN6Q/merge.tag.1.bam /tmp/erVyqJXN6Q/merge.tag.2.bam .. ok test_merge: - /build/samtools-1.16.1/samtools merge -s 1 -p -c -n -t PG -O SAM - /tmp/34w9Wt0Ykb/merge.tag.3.bam /tmp/34w9Wt0Ykb/merge.tag.4.bam + /build/samtools-1.16.1/samtools merge -s 1 -p -c -n -t PG -O SAM - /tmp/erVyqJXN6Q/merge.tag.3.bam /tmp/erVyqJXN6Q/merge.tag.4.bam .. ok test_merge: @@ -2722,7 +2763,7 @@ .. ok test_merge: - /build/samtools-1.16.1/samtools merge --no-PG -O SAM -L /build/samtools-1.16.1/test/merge/merge.bed - /tmp/34w9Wt0Ykb/merge.bed.1.bam /tmp/34w9Wt0Ykb/merge.bed.2.bam + /build/samtools-1.16.1/samtools merge --no-PG -O SAM -L /build/samtools-1.16.1/test/merge/merge.bed - /tmp/erVyqJXN6Q/merge.bed.1.bam /tmp/erVyqJXN6Q/merge.bed.2.bam .. ok test_merge: @@ -2738,7 +2779,7 @@ .. ok test_merge: - /build/samtools-1.16.1/samtools merge -@ 2 -s 1 -O sam -b /tmp/nBqIiGpfqm - /build/samtools-1.16.1/test/dat/test_input_1_a.bam + /build/samtools-1.16.1/samtools merge -@ 2 -s 1 -O sam -b /tmp/87QuiqQXQT - /build/samtools-1.16.1/test/dat/test_input_1_a.bam .. ok test_merge: @@ -2762,11 +2803,11 @@ .. ok test_merge: - /build/samtools-1.16.1/samtools merge -@ 2 -s 1 -p -c -t PG -O SAM - /tmp/34w9Wt0Ykb/merge.tag.1.bam /tmp/34w9Wt0Ykb/merge.tag.2.bam + /build/samtools-1.16.1/samtools merge -@ 2 -s 1 -p -c -t PG -O SAM - /tmp/erVyqJXN6Q/merge.tag.1.bam /tmp/erVyqJXN6Q/merge.tag.2.bam .. ok test_merge: - /build/samtools-1.16.1/samtools merge -@ 2 -s 1 -p -c -n -t PG -O SAM - /tmp/34w9Wt0Ykb/merge.tag.3.bam /tmp/34w9Wt0Ykb/merge.tag.4.bam + /build/samtools-1.16.1/samtools merge -@ 2 -s 1 -p -c -n -t PG -O SAM - /tmp/erVyqJXN6Q/merge.tag.3.bam /tmp/erVyqJXN6Q/merge.tag.4.bam .. ok test_merge: @@ -2774,7 +2815,7 @@ .. ok test_merge: - /build/samtools-1.16.1/samtools merge -@ 2 --no-PG -O SAM -L /build/samtools-1.16.1/test/merge/merge.bed - /tmp/34w9Wt0Ykb/merge.bed.1.bam /tmp/34w9Wt0Ykb/merge.bed.2.bam + /build/samtools-1.16.1/samtools merge -@ 2 --no-PG -O SAM -L /build/samtools-1.16.1/test/merge/merge.bed - /tmp/erVyqJXN6Q/merge.bed.1.bam /tmp/erVyqJXN6Q/merge.bed.2.bam .. ok test_merge: @@ -2782,15 +2823,15 @@ .. ok test_sort: - /build/samtools-1.16.1/samtools sort /build/samtools-1.16.1/test/dat/test_input_1_a.bam /tmp/34w9Wt0Ykb/sortout + /build/samtools-1.16.1/samtools sort /build/samtools-1.16.1/test/dat/test_input_1_a.bam /tmp/erVyqJXN6Q/sortout .. ok test_sort: - /build/samtools-1.16.1/samtools sort -f /build/samtools-1.16.1/test/dat/test_input_1_a.bam /tmp/34w9Wt0Ykb/sortout.bam + /build/samtools-1.16.1/samtools sort -f /build/samtools-1.16.1/test/dat/test_input_1_a.bam /tmp/erVyqJXN6Q/sortout.bam .. ok test_sort: - /build/samtools-1.16.1/samtools sort -o /build/samtools-1.16.1/test/dat/test_input_1_a.bam /tmp/34w9Wt0Ykb/sorttmp + /build/samtools-1.16.1/samtools sort -o /build/samtools-1.16.1/test/dat/test_input_1_a.bam /tmp/erVyqJXN6Q/sorttmp .. ok test_sort: @@ -2822,15 +2863,15 @@ .. ok test_sort: - /build/samtools-1.16.1/samtools sort -@ 2 /build/samtools-1.16.1/test/dat/test_input_1_a.bam /tmp/34w9Wt0Ykb/sortout + /build/samtools-1.16.1/samtools sort -@ 2 /build/samtools-1.16.1/test/dat/test_input_1_a.bam /tmp/erVyqJXN6Q/sortout .. ok test_sort: - /build/samtools-1.16.1/samtools sort -@ 2 -f /build/samtools-1.16.1/test/dat/test_input_1_a.bam /tmp/34w9Wt0Ykb/sortout.bam + /build/samtools-1.16.1/samtools sort -@ 2 -f /build/samtools-1.16.1/test/dat/test_input_1_a.bam /tmp/erVyqJXN6Q/sortout.bam .. ok test_sort: - /build/samtools-1.16.1/samtools sort -@ 2 -o /build/samtools-1.16.1/test/dat/test_input_1_a.bam /tmp/34w9Wt0Ykb/sorttmp + /build/samtools-1.16.1/samtools sort -@ 2 -o /build/samtools-1.16.1/test/dat/test_input_1_a.bam /tmp/erVyqJXN6Q/sorttmp .. ok test_sort: @@ -3326,15 +3367,15 @@ .. ok test_large_positions: - /build/samtools-1.16.1/samtools view -h --no-PG /tmp/34w9Wt0Ykb/longref.sam.gz + /build/samtools-1.16.1/samtools view -h --no-PG /tmp/erVyqJXN6Q/longref.sam.gz .. ok test_large_positions: - /build/samtools-1.16.1/samtools view -h --no-PG /tmp/34w9Wt0Ykb/longref.sam.gz CHROMOSOME_I:10000000114-10000000168 + /build/samtools-1.16.1/samtools view -h --no-PG /tmp/erVyqJXN6Q/longref.sam.gz CHROMOSOME_I:10000000114-10000000168 .. ok test_large_positions: - /build/samtools-1.16.1/samtools view -h --no-PG -L /build/samtools-1.16.1/test/large_pos/test.bed /tmp/34w9Wt0Ykb/longref.sam.gz + /build/samtools-1.16.1/samtools view -h --no-PG -L /build/samtools-1.16.1/test/large_pos/test.bed /tmp/erVyqJXN6Q/longref.sam.gz .. ok test_large_positions: @@ -3354,7 +3395,7 @@ .. ok test_large_positions: - /build/samtools-1.16.1/samtools tview -d T -p CHROMOSOME_I:10000000000 /tmp/34w9Wt0Ykb/longref.sam.gz + /build/samtools-1.16.1/samtools tview -d T -p CHROMOSOME_I:10000000000 /tmp/erVyqJXN6Q/longref.sam.gz .. ok test_large_positions: @@ -3484,7 +3525,7 @@ Unexpected failures: 0 => PASS make[2]: Leaving directory '/build/samtools-1.16.1' - rm -fr -- /tmp/dh-xdg-rundir-ogl3JzKr + rm -fr -- /tmp/dh-xdg-rundir-jm1wX1u8 make[1]: Leaving directory '/build/samtools-1.16.1' create-stamp debian/debhelper-build-stamp dh_prep @@ -3551,14 +3592,14 @@ debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/samtools-1.16.1' dh_installchangelogs NEWS - install -m0755 -d debian/samtools/usr/share/doc/samtools - install -p -m0644 debian/.debhelper/generated/samtools/dh_installchangelogs.dch.trimmed debian/samtools/usr/share/doc/samtools/changelog.Debian - install -p -m0644 debian/NEWS debian/samtools/usr/share/doc/samtools/NEWS.Debian - install -p -m0644 NEWS debian/samtools/usr/share/doc/samtools/changelog install -m0755 -d debian/samtools-test/usr/share/doc/samtools-test install -p -m0644 debian/.debhelper/generated/samtools-test/dh_installchangelogs.dch.trimmed debian/samtools-test/usr/share/doc/samtools-test/changelog.Debian install -p -m0644 debian/NEWS debian/samtools-test/usr/share/doc/samtools-test/NEWS.Debian install -p -m0644 NEWS debian/samtools-test/usr/share/doc/samtools-test/changelog + install -m0755 -d debian/samtools/usr/share/doc/samtools + install -p -m0644 debian/.debhelper/generated/samtools/dh_installchangelogs.dch.trimmed debian/samtools/usr/share/doc/samtools/changelog.Debian + install -p -m0644 debian/NEWS debian/samtools/usr/share/doc/samtools/NEWS.Debian + install -p -m0644 NEWS debian/samtools/usr/share/doc/samtools/changelog make[1]: Leaving directory '/build/samtools-1.16.1' dh_installexamples install -m0755 -d debian/samtools/usr/share/doc/samtools/examples @@ -3581,25 +3622,25 @@ rm -f debian/samtools/usr/share/man/man1/samtools-fastq.1 ln -s samtools-fasta.1 debian/samtools/usr/share/man/man1/samtools-fastq.1 man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/ace2sam.1 debian/samtools/usr/share/man/man1/samtools-addreplacerg.1 debian/samtools/usr/share/man/man1/samtools-ampliconclip.1 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-merge.1 debian/samtools/usr/share/man/man1/samtools-mpileup.1 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 debian/samtools/usr/share/man/man1/samtools-reheader.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-fqidx.1 debian/samtools/usr/share/man/man1/samtools-head.1 debian/samtools/usr/share/man/man1/samtools-idxstats.1 debian/samtools/usr/share/man/man1/samtools-import.1 debian/samtools/usr/share/man/man1/samtools-index.1 debian/samtools/usr/share/man/man1/samtools-markdup.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 debian/samtools/usr/share/man/man1/samtools-coverage.1 debian/samtools/usr/share/man/man1/samtools-depad.1 debian/samtools/usr/share/man/man1/samtools-depth.1 man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-dict.1 debian/samtools/usr/share/man/man1/samtools-faidx.1 debian/samtools/usr/share/man/man1/samtools-fasta.1 debian/samtools/usr/share/man/man1/samtools-fixmate.1 debian/samtools/usr/share/man/man1/samtools-flags.1 debian/samtools/usr/share/man/man1/samtools-flagstat.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-fqidx.1 debian/samtools/usr/share/man/man1/samtools-head.1 debian/samtools/usr/share/man/man1/samtools-idxstats.1 debian/samtools/usr/share/man/man1/samtools-import.1 debian/samtools/usr/share/man/man1/samtools-index.1 debian/samtools/usr/share/man/man1/samtools-markdup.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-merge.1 debian/samtools/usr/share/man/man1/samtools-mpileup.1 debian/samtools/usr/share/man/man1/samtools-phase.1 debian/samtools/usr/share/man/man1/samtools-quickcheck.1 debian/samtools/usr/share/man/man1/samtools-reference.1 debian/samtools/usr/share/man/man1/samtools-reheader.1 man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-rmdup.1 debian/samtools/usr/share/man/man1/samtools-samples.1 debian/samtools/usr/share/man/man1/samtools-sort.1 debian/samtools/usr/share/man/man1/samtools-split.1 debian/samtools/usr/share/man/man1/samtools-stats.1 debian/samtools/usr/share/man/man1/samtools-targetcut.1 man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-tview.1 debian/samtools/usr/share/man/man1/samtools-view.1 debian/samtools/usr/share/man/man1/samtools.1 debian/samtools/usr/share/man/man1/samtools.pl.1 debian/samtools/usr/share/man/man1/wgsim.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-cat.1 debian/samtools/usr/share/man/man1/samtools-collate.1 debian/samtools/usr/share/man/man1/samtools-consensus.1 debian/samtools/usr/share/man/man1/samtools-coverage.1 debian/samtools/usr/share/man/man1/samtools-depad.1 debian/samtools/usr/share/man/man1/samtools-depth.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 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 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/samtools-tview.1 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 debian/samtools/usr/share/man/man1/wgsim.1 - mv debian/samtools/usr/share/man/man1/samtools-dict.1.dh-new debian/samtools/usr/share/man/man1/samtools-dict.1 - mv debian/samtools/usr/share/man/man1/samtools-faidx.1.dh-new debian/samtools/usr/share/man/man1/samtools-faidx.1 - mv debian/samtools/usr/share/man/man1/samtools-fasta.1.dh-new debian/samtools/usr/share/man/man1/samtools-fasta.1 - mv debian/samtools/usr/share/man/man1/samtools-fixmate.1.dh-new debian/samtools/usr/share/man/man1/samtools-fixmate.1 - mv debian/samtools/usr/share/man/man1/samtools-flags.1.dh-new debian/samtools/usr/share/man/man1/samtools-flags.1 - mv debian/samtools/usr/share/man/man1/samtools-flagstat.1.dh-new debian/samtools/usr/share/man/man1/samtools-flagstat.1 - chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-dict.1 debian/samtools/usr/share/man/man1/samtools-faidx.1 debian/samtools/usr/share/man/man1/samtools-fasta.1 debian/samtools/usr/share/man/man1/samtools-fixmate.1 debian/samtools/usr/share/man/man1/samtools-flags.1 debian/samtools/usr/share/man/man1/samtools-flagstat.1 + mv debian/samtools/usr/share/man/man1/samtools-rmdup.1.dh-new debian/samtools/usr/share/man/man1/samtools-rmdup.1 + mv debian/samtools/usr/share/man/man1/samtools-samples.1.dh-new debian/samtools/usr/share/man/man1/samtools-samples.1 + mv debian/samtools/usr/share/man/man1/samtools-sort.1.dh-new debian/samtools/usr/share/man/man1/samtools-sort.1 + mv debian/samtools/usr/share/man/man1/samtools-split.1.dh-new debian/samtools/usr/share/man/man1/samtools-split.1 + 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-rmdup.1 debian/samtools/usr/share/man/man1/samtools-samples.1 debian/samtools/usr/share/man/man1/samtools-sort.1 debian/samtools/usr/share/man/man1/samtools-split.1 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/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 @@ -3614,20 +3655,13 @@ mv debian/samtools/usr/share/man/man1/samtools-depad.1.dh-new debian/samtools/usr/share/man/man1/samtools-depad.1 mv debian/samtools/usr/share/man/man1/samtools-depth.1.dh-new debian/samtools/usr/share/man/man1/samtools-depth.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 debian/samtools/usr/share/man/man1/samtools-coverage.1 debian/samtools/usr/share/man/man1/samtools-depad.1 debian/samtools/usr/share/man/man1/samtools-depth.1 - mv debian/samtools/usr/share/man/man1/samtools-rmdup.1.dh-new debian/samtools/usr/share/man/man1/samtools-rmdup.1 - mv debian/samtools/usr/share/man/man1/samtools-samples.1.dh-new debian/samtools/usr/share/man/man1/samtools-samples.1 - mv debian/samtools/usr/share/man/man1/samtools-sort.1.dh-new debian/samtools/usr/share/man/man1/samtools-sort.1 - mv debian/samtools/usr/share/man/man1/samtools-split.1.dh-new debian/samtools/usr/share/man/man1/samtools-split.1 - 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-rmdup.1 debian/samtools/usr/share/man/man1/samtools-samples.1 debian/samtools/usr/share/man/man1/samtools-sort.1 debian/samtools/usr/share/man/man1/samtools-split.1 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-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 - 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 - mv debian/samtools/usr/share/man/man1/samtools-reheader.1.dh-new debian/samtools/usr/share/man/man1/samtools-reheader.1 - chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-merge.1 debian/samtools/usr/share/man/man1/samtools-mpileup.1 debian/samtools/usr/share/man/man1/samtools-phase.1 debian/samtools/usr/share/man/man1/samtools-quickcheck.1 debian/samtools/usr/share/man/man1/samtools-reference.1 debian/samtools/usr/share/man/man1/samtools-reheader.1 + mv debian/samtools/usr/share/man/man1/samtools-dict.1.dh-new debian/samtools/usr/share/man/man1/samtools-dict.1 + mv debian/samtools/usr/share/man/man1/samtools-faidx.1.dh-new debian/samtools/usr/share/man/man1/samtools-faidx.1 + mv debian/samtools/usr/share/man/man1/samtools-fasta.1.dh-new debian/samtools/usr/share/man/man1/samtools-fasta.1 + mv debian/samtools/usr/share/man/man1/samtools-fixmate.1.dh-new debian/samtools/usr/share/man/man1/samtools-fixmate.1 + mv debian/samtools/usr/share/man/man1/samtools-flags.1.dh-new debian/samtools/usr/share/man/man1/samtools-flags.1 + mv debian/samtools/usr/share/man/man1/samtools-flagstat.1.dh-new debian/samtools/usr/share/man/man1/samtools-flagstat.1 + chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-dict.1 debian/samtools/usr/share/man/man1/samtools-faidx.1 debian/samtools/usr/share/man/man1/samtools-fasta.1 debian/samtools/usr/share/man/man1/samtools-fixmate.1 debian/samtools/usr/share/man/man1/samtools-flags.1 debian/samtools/usr/share/man/man1/samtools-flagstat.1 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 mv debian/samtools/usr/share/man/man1/samtools-idxstats.1.dh-new debian/samtools/usr/share/man/man1/samtools-idxstats.1 @@ -3635,6 +3669,13 @@ mv debian/samtools/usr/share/man/man1/samtools-index.1.dh-new debian/samtools/usr/share/man/man1/samtools-index.1 mv debian/samtools/usr/share/man/man1/samtools-markdup.1.dh-new debian/samtools/usr/share/man/man1/samtools-markdup.1 chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-fqidx.1 debian/samtools/usr/share/man/man1/samtools-head.1 debian/samtools/usr/share/man/man1/samtools-idxstats.1 debian/samtools/usr/share/man/man1/samtools-import.1 debian/samtools/usr/share/man/man1/samtools-index.1 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 + 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 + mv debian/samtools/usr/share/man/man1/samtools-reheader.1.dh-new debian/samtools/usr/share/man/man1/samtools-reheader.1 + chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-merge.1 debian/samtools/usr/share/man/man1/samtools-mpileup.1 debian/samtools/usr/share/man/man1/samtools-phase.1 debian/samtools/usr/share/man/man1/samtools-quickcheck.1 debian/samtools/usr/share/man/man1/samtools-reference.1 debian/samtools/usr/share/man/man1/samtools-reheader.1 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 @@ -3653,8 +3694,8 @@ cd debian/samtools cd debian/samtools-test chmod a-x usr/share/doc/samtools-test/NEWS.Debian usr/share/doc/samtools-test/changelog usr/share/doc/samtools-test/changelog.Debian - chmod a-x usr/share/doc/samtools/NEWS.Debian 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-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-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/NEWS.Debian usr/share/doc/samtools-test/changelog usr/share/doc/samtools-test/changelog.Debian + chmod a-x usr/share/doc/samtools/NEWS.Debian 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-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-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/NEWS.Debian 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-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-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/samtools-1.16.1' cd '/build/samtools-1.16.1' @@ -3664,8 +3705,8 @@ 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 @@ -3730,15 +3771,15 @@ 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 -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 -Pdebian/.debhelper/samtools/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -UBuilt-Using -DAuto-Built-Package=debug-symbols -UProtected -DPackage=samtools-dbgsym "-DDepends=samtools (= \${binary:Version})" "-DDescription=debug symbols for samtools" "-DBuild-Ids=5278fc07a6632f21227d5b56df1a2f657cdaeab5 79d396e316290a81c196903f906d4f5df08636c1 aa2ee60e1566139f7ef5f11423130b91f748f1e3 ad5d2924c695dab417b6292e6902d4c9882187f3 cbaf4ebac91819dcbbfb156cef83e34cf67022ca d908986e9ec6a941abce3b7bd98aa459b92b4cf6 da2c277449605fba402447178c1428b30ebc413d" -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 -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 -Pdebian/samtools @@ -3747,8 +3788,8 @@ dpkg-gencontrol: warning: package samtools: substitution variable ${perl:Depends} unused, but is defined chmod 0644 -- debian/samtools/DEBIAN/control dh_md5sums - install -m0755 -d debian/samtools/DEBIAN install -m0755 -d debian/samtools-test/DEBIAN + install -m0755 -d debian/samtools/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 @@ -3771,12 +3812,14 @@ 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/11145/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/11145/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/32369 and its subdirectories -I: Current time: Sun May 26 20:42:07 -12 2024 -I: pbuilder-time-stamp: 1716799327 +I: removing directory /srv/workspace/pbuilder/11145 and its subdirectories +I: Current time: Tue Apr 25 16:21:39 +14 2023 +I: pbuilder-time-stamp: 1682389299