Diff of the two buildlogs: -- --- b1/build.log 2023-04-14 19:45:03.704283790 +0000 +++ b2/build.log 2023-04-14 19:52:12.705229908 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu May 16 14:02:22 -12 2024 -I: pbuilder-time-stamp: 1715911342 +I: Current time: Sat Apr 15 09:45:06 +14 2023 +I: pbuilder-time-stamp: 1681501506 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 @@ -29,135 +29,144 @@ 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/1554661/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1487910/tmp/hooks/D01_modify_environment starting +debug: Running on ionos1-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 +lrwxrwxrwx 1 root root 4 Jan 6 03:20 /bin/sh -> dash +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/1487910/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1487910/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' + 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=16' + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15' DISTRIBUTION='bookworm' HOME='/root' HOST_ARCH='amd64' IFS=' ' - INVOCATION_ID='9e51ff200bbe43a7a4d3284fec8ab725' + INVOCATION_ID='3c3e3550b2c247a0b559b6937faca910' LANG='C' - LANGUAGE='en_US:en' + LANGUAGE='et_EE:et' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' + 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' - PPID='1554661' + PPID='1487910' PS1='# ' PS2='> ' 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.0TWNWg1O/pbuilderrc_qQnV --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.0TWNWg1O/b1 --logfile b1/build.log samtools_1.16.1-1.dsc' - SUDO_GID='111' - SUDO_UID='106' + 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.0TWNWg1O/pbuilderrc_7MM4 --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.0TWNWg1O/b2 --logfile b2/build.log --extrapackages usrmerge samtools_1.16.1-1.dsc' + SUDO_GID='110' + SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' + TZ='/usr/share/zoneinfo/Etc/GMT-14' USER='root' _='/usr/bin/systemd-run' - http_proxy='http://85.184.249.68:3128' + http_proxy='http://78.137.99.97:3128' I: uname -a - Linux ionos15-amd64 6.1.0-0.deb11.5-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.12-1~bpo11+1 (2023-03-05) x86_64 GNU/Linux + Linux i-capture-the-hostname 5.10.0-21-amd64 #1 SMP Debian 5.10.162-1 (2023-01-21) x86_64 GNU/Linux I: ls -l /bin total 5632 - -rwxr-xr-x 1 root root 1265648 Feb 12 2023 bash - -rwxr-xr-x 3 root root 39224 Sep 18 2022 bunzip2 - -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzcat - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep - -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzip2 - -rwxr-xr-x 1 root root 14568 Sep 18 2022 bzip2recover - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore - -rwxr-xr-x 1 root root 44016 Sep 20 2022 cat - -rwxr-xr-x 1 root root 68656 Sep 20 2022 chgrp - -rwxr-xr-x 1 root root 64496 Sep 20 2022 chmod - -rwxr-xr-x 1 root root 72752 Sep 20 2022 chown - -rwxr-xr-x 1 root root 151152 Sep 20 2022 cp - -rwxr-xr-x 1 root root 125640 Jan 5 2023 dash - -rwxr-xr-x 1 root root 121904 Sep 20 2022 date - -rwxr-xr-x 1 root root 89240 Sep 20 2022 dd - -rwxr-xr-x 1 root root 102200 Sep 20 2022 df - -rwxr-xr-x 1 root root 151344 Sep 20 2022 dir - -rwxr-xr-x 1 root root 88656 Mar 22 2023 dmesg - lrwxrwxrwx 1 root root 8 Dec 19 2022 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Dec 19 2022 domainname -> hostname - -rwxr-xr-x 1 root root 43856 Sep 20 2022 echo - -rwxr-xr-x 1 root root 41 Jan 24 2023 egrep - -rwxr-xr-x 1 root root 35664 Sep 20 2022 false - -rwxr-xr-x 1 root root 41 Jan 24 2023 fgrep - -rwxr-xr-x 1 root root 85600 Mar 22 2023 findmnt - -rwsr-xr-x 1 root root 35128 Mar 22 2023 fusermount - -rwxr-xr-x 1 root root 203152 Jan 24 2023 grep - -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip - -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe - -rwxr-xr-x 1 root root 98136 Apr 9 2022 gzip - -rwxr-xr-x 1 root root 22680 Dec 19 2022 hostname - -rwxr-xr-x 1 root root 72824 Sep 20 2022 ln - -rwxr-xr-x 1 root root 53024 Mar 23 2023 login - -rwxr-xr-x 1 root root 151344 Sep 20 2022 ls - -rwxr-xr-x 1 root root 207168 Mar 22 2023 lsblk - -rwxr-xr-x 1 root root 97552 Sep 20 2022 mkdir - -rwxr-xr-x 1 root root 72912 Sep 20 2022 mknod - -rwxr-xr-x 1 root root 43952 Sep 20 2022 mktemp - -rwxr-xr-x 1 root root 59712 Mar 22 2023 more - -rwsr-xr-x 1 root root 59704 Mar 22 2023 mount - -rwxr-xr-x 1 root root 18744 Mar 22 2023 mountpoint - -rwxr-xr-x 1 root root 142968 Sep 20 2022 mv - lrwxrwxrwx 1 root root 8 Dec 19 2022 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 2 2023 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 43952 Sep 20 2022 pwd - lrwxrwxrwx 1 root root 4 Feb 12 2023 rbash -> bash - -rwxr-xr-x 1 root root 52112 Sep 20 2022 readlink - -rwxr-xr-x 1 root root 72752 Sep 20 2022 rm - -rwxr-xr-x 1 root root 56240 Sep 20 2022 rmdir - -rwxr-xr-x 1 root root 27560 Nov 2 2022 run-parts - -rwxr-xr-x 1 root root 126424 Jan 5 2023 sed - lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash - -rwxr-xr-x 1 root root 43888 Sep 20 2022 sleep - -rwxr-xr-x 1 root root 85008 Sep 20 2022 stty - -rwsr-xr-x 1 root root 72000 Mar 22 2023 su - -rwxr-xr-x 1 root root 39824 Sep 20 2022 sync - -rwxr-xr-x 1 root root 531984 Apr 6 2023 tar - -rwxr-xr-x 1 root root 14520 Nov 2 2022 tempfile - -rwxr-xr-x 1 root root 109616 Sep 20 2022 touch - -rwxr-xr-x 1 root root 35664 Sep 20 2022 true - -rwxr-xr-x 1 root root 14568 Mar 22 2023 ulockmgr_server - -rwsr-xr-x 1 root root 35128 Mar 22 2023 umount - -rwxr-xr-x 1 root root 43888 Sep 20 2022 uname - -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress - -rwxr-xr-x 1 root root 151344 Sep 20 2022 vdir - -rwxr-xr-x 1 root root 72024 Mar 22 2023 wdctl - lrwxrwxrwx 1 root root 8 Dec 19 2022 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat - -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp - -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff - -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep - -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep - -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce - -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep - -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless - -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore - -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew -I: user script /srv/workspace/pbuilder/1554661/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1265648 Feb 13 10:05 bash + -rwxr-xr-x 3 root root 39224 Sep 19 2022 bunzip2 + -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzcat + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4893 Nov 28 2021 bzexe + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep + -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzip2 + -rwxr-xr-x 1 root root 14568 Sep 19 2022 bzip2recover + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore + -rwxr-xr-x 1 root root 44016 Sep 21 2022 cat + -rwxr-xr-x 1 root root 68656 Sep 21 2022 chgrp + -rwxr-xr-x 1 root root 64496 Sep 21 2022 chmod + -rwxr-xr-x 1 root root 72752 Sep 21 2022 chown + -rwxr-xr-x 1 root root 151152 Sep 21 2022 cp + -rwxr-xr-x 1 root root 125640 Jan 6 03:20 dash + -rwxr-xr-x 1 root root 121904 Sep 21 2022 date + -rwxr-xr-x 1 root root 89240 Sep 21 2022 dd + -rwxr-xr-x 1 root root 102200 Sep 21 2022 df + -rwxr-xr-x 1 root root 151344 Sep 21 2022 dir + -rwxr-xr-x 1 root root 88656 Mar 24 00:02 dmesg + lrwxrwxrwx 1 root root 8 Dec 20 03:33 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Dec 20 03:33 domainname -> hostname + -rwxr-xr-x 1 root root 43856 Sep 21 2022 echo + -rwxr-xr-x 1 root root 41 Jan 25 04:43 egrep + -rwxr-xr-x 1 root root 35664 Sep 21 2022 false + -rwxr-xr-x 1 root root 41 Jan 25 04:43 fgrep + -rwxr-xr-x 1 root root 85600 Mar 24 00:02 findmnt + -rwsr-xr-x 1 root root 35128 Mar 23 22:35 fusermount + -rwxr-xr-x 1 root root 203152 Jan 25 04:43 grep + -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip + -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe + -rwxr-xr-x 1 root root 98136 Apr 10 2022 gzip + -rwxr-xr-x 1 root root 22680 Dec 20 03:33 hostname + -rwxr-xr-x 1 root root 72824 Sep 21 2022 ln + -rwxr-xr-x 1 root root 53024 Mar 24 02:40 login + -rwxr-xr-x 1 root root 151344 Sep 21 2022 ls + -rwxr-xr-x 1 root root 207168 Mar 24 00:02 lsblk + -rwxr-xr-x 1 root root 97552 Sep 21 2022 mkdir + -rwxr-xr-x 1 root root 72912 Sep 21 2022 mknod + -rwxr-xr-x 1 root root 43952 Sep 21 2022 mktemp + -rwxr-xr-x 1 root root 59712 Mar 24 00:02 more + -rwsr-xr-x 1 root root 59704 Mar 24 00:02 mount + -rwxr-xr-x 1 root root 18744 Mar 24 00:02 mountpoint + -rwxr-xr-x 1 root root 142968 Sep 21 2022 mv + lrwxrwxrwx 1 root root 8 Dec 20 03:33 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 3 20:25 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 43952 Sep 21 2022 pwd + lrwxrwxrwx 1 root root 4 Feb 13 10:05 rbash -> bash + -rwxr-xr-x 1 root root 52112 Sep 21 2022 readlink + -rwxr-xr-x 1 root root 72752 Sep 21 2022 rm + -rwxr-xr-x 1 root root 56240 Sep 21 2022 rmdir + -rwxr-xr-x 1 root root 27560 Nov 3 06:31 run-parts + -rwxr-xr-x 1 root root 126424 Jan 6 09:55 sed + lrwxrwxrwx 1 root root 4 Jan 6 03:20 sh -> dash + -rwxr-xr-x 1 root root 43888 Sep 21 2022 sleep + -rwxr-xr-x 1 root root 85008 Sep 21 2022 stty + -rwsr-xr-x 1 root root 72000 Mar 24 00:02 su + -rwxr-xr-x 1 root root 39824 Sep 21 2022 sync + -rwxr-xr-x 1 root root 531984 Apr 7 04:25 tar + -rwxr-xr-x 1 root root 14520 Nov 3 06:31 tempfile + -rwxr-xr-x 1 root root 109616 Sep 21 2022 touch + -rwxr-xr-x 1 root root 35664 Sep 21 2022 true + -rwxr-xr-x 1 root root 14568 Mar 23 22:35 ulockmgr_server + -rwsr-xr-x 1 root root 35128 Mar 24 00:02 umount + -rwxr-xr-x 1 root root 43888 Sep 21 2022 uname + -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress + -rwxr-xr-x 1 root root 151344 Sep 21 2022 vdir + -rwxr-xr-x 1 root root 72024 Mar 24 00:02 wdctl + lrwxrwxrwx 1 root root 8 Dec 20 03:33 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat + -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp + -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff + -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep + -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep + -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce + -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep + -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless + -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore + -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew +I: user script /srv/workspace/pbuilder/1487910/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -274,7 +283,7 @@ Get: 57 http://deb.debian.org/debian bookworm/main amd64 pkgconf amd64 1.8.1-1 [25.9 kB] Get: 58 http://deb.debian.org/debian bookworm/main amd64 pkg-config amd64 1.8.1-1 [13.7 kB] Get: 59 http://deb.debian.org/debian bookworm/main amd64 tabix amd64 1.16+ds-3 [457 kB] -Fetched 26.0 MB in 1s (34.7 MB/s) +Fetched 26.0 MB in 1s (30.5 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 ... 19596 files and directories currently installed.) @@ -524,8 +533,19 @@ 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/1487910/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +removed '/etc/unsupported-skip-usrmerge-conversion' +The system has been successfully converted. +I: user script /srv/workspace/pbuilder/1487910/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +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 @@ -540,7 +560,7 @@ rm -f config.mk touch config.mk dh_auto_clean -- - make -j16 distclean + make -j15 distclean make[2]: Entering directory '/build/samtools-1.16.1' rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp test/*/*.tmp.* cd test/dat && rm -f test_input_*.bam.bai view.*.bam.bai @@ -602,7 +622,7 @@ checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed -checking for grep that handles long lines and -e... /bin/grep +checking for grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no @@ -628,30 +648,30 @@ CFLAGS="$(dpkg-buildflags --get CFLAGS)" \ CPPFLAGS="\$(DFLAGS) \$(INCLUDES) $(dpkg-buildflags --get CPPFLAGS)" \ LDFLAGS="$(dpkg-buildflags --get LDFLAGS)" - make -j16 "CFLAGS=-g -O2 -ffile-prefix-map=/build/samtools-1.16.1=. -fstack-protector-strong -Wformat -Werror=format-security" "CPPFLAGS=\$(DFLAGS) \$(INCLUDES) -Wdate-time -D_FORTIFY_SOURCE=2" "LDFLAGS=-Wl,-z,relro -Wl,-z,now" + make -j15 "CFLAGS=-g -O2 -ffile-prefix-map=/build/samtools-1.16.1=. -fstack-protector-strong -Wformat -Werror=format-security" "CPPFLAGS=\$(DFLAGS) \$(INCLUDES) -Wdate-time -D_FORTIFY_SOURCE=2" "LDFLAGS=-Wl,-z,relro -Wl,-z,now" make[2]: Entering directory '/build/samtools-1.16.1' 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 +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 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 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_cat.o bam_cat.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_md.o bam_md.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_plbuf.o bam_plbuf.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 -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 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_rmdup.o bam_rmdup.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_rmdupse.o bam_rmdupse.c cc1: warning: command-line option '-frelease' is valid for D but not for C cc1: warning: command-line option '-frelease' is valid for D but not for C +gcc -g -O2 -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 @@ -659,20 +679,20 @@ 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 cc1: warning: command-line option '-frelease' is valid for D but not for C -echo '#define SAMTOOLS_VERSION "1.16.1"' > version.h cc1: warning: command-line option '-frelease' is valid for D but not for C +echo '#define SAMTOOLS_VERSION "1.16.1"' > version.h echo '#define SAMTOOLS_CC "gcc"' >> version.h echo '#define SAMTOOLS_CPPFLAGS "-frelease -Wdate-time -D_FORTIFY_SOURCE=2"' >> version.h echo '#define SAMTOOLS_CFLAGS "-g -O2 -ffile-prefix-map=/build/samtools-1.16.1=. -fstack-protector-strong -Wformat -Werror=format-security"' >> version.h echo '#define SAMTOOLS_LDFLAGS "-Wl,-z,relro -Wl,-z,now"' >> version.h echo '#define SAMTOOLS_HTSDIR ""' >> version.h echo '#define SAMTOOLS_LIBS ""' >> version.h +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 bam2bcf.o bam2bcf.c echo '#define SAMTOOLS_CURSES_LIB "-lcurses"' >> version.h +cc1: warning: command-line option '-frelease' is valid for D but not for C sed -i -e 's@/build/samtools-1.16.1@«BUILDPATH»@g' version.h -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 bam2bcf.o bam2bcf.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 sample.o sample.c cc1: warning: command-line option '-frelease' is valid for D but not for C -cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -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 cut_target.o cut_target.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 phase.o phase.c @@ -692,8 +712,8 @@ 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 dict.o dict.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 stats.o stats.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 stats_isize.o stats_isize.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 stats_isize.o stats_isize.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_flags.o bam_flags.c cc1: warning: command-line option '-frelease' is valid for D but not for C @@ -702,9 +722,9 @@ 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_tview.o bam_tview.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_tview_curses.o bam_tview_curses.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_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 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_lpileup.o bam_lpileup.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_quickcheck.o bam_quickcheck.c @@ -714,20 +734,20 @@ 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_markdup.o bam_markdup.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 tmp_file.o tmp_file.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_ampliconclip.o bam_ampliconclip.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 amplicon_stats.o amplicon_stats.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_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 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 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 -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 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 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 lz4/lz4.o lz4/lz4.c cc1: warning: command-line option '-frelease' is valid for D but not for C @@ -736,22 +756,22 @@ 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_utils.o sam_utils.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 bedidx.o bedidx.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.o bam.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/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 -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 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 +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 -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/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/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 @@ -770,30 +790,30 @@ gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/md5fa misc/md5fa.o -lhts -lz gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/md5sum-lite misc/md5sum-lite.o -lhts -lz gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/vcf-miniview test/vcf-miniview.o -lhts -lz -lpthread -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_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 misc/ace2sam misc/ace2sam.o -lhts -lz gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/split/test_filter_header_rg test/split/test_filter_header_rg.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/split/test_parse_args test/split/test_parse_args.o test/test.o libst.a -lhts -lz -lpthread -gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/ace2sam misc/ace2sam.o -lhts -lz +gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/split/test_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_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 misc/wgsim misc/wgsim.o -lm -lhts -lz +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 -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 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 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 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 ./lz4/lz4.o libst.a -lhts -lcurses -lm -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 +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 debian/rules override_dh_auto_test make[1]: Entering directory '/build/samtools-1.16.1' dh_auto_test -- BGZIP=/usr/bin/bgzip - make -j16 test "TESTSUITEFLAGS=-j16 --verbose" VERBOSE=1 BGZIP=/usr/bin/bgzip + make -j15 test "TESTSUITEFLAGS=-j15 --verbose" VERBOSE=1 BGZIP=/usr/bin/bgzip make[2]: Entering directory '/build/samtools-1.16.1' test/split/test_count_rg test/split/test_expand_format_string @@ -832,75 +852,75 @@ /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/c4A9qCDWOK/bgzip.dat.gz +/usr/bin/bgzip -c -b 65272 -s 5 /tmp/RFXhHuoSEX/bgzip.dat.gz .. ok -/usr/bin/bgzip -c -b 979200 -s 6 /tmp/c4A9qCDWOK/bgzip.dat.gz +/usr/bin/bgzip -c -b 979200 -s 6 /tmp/RFXhHuoSEX/bgzip.dat.gz .. ok -/usr/bin/bgzip -c -b 652804 -s 6 /tmp/c4A9qCDWOK/bgzip.dat.gz +/usr/bin/bgzip -c -b 652804 -s 6 /tmp/RFXhHuoSEX/bgzip.dat.gz .. ok -/build/samtools-1.16.1/samtools faidx /tmp/c4A9qCDWOK/faidx.fa 3:11-13 | grep -v '^>' +/build/samtools-1.16.1/samtools faidx /tmp/RFXhHuoSEX/faidx.fa 3:11-13 | grep -v '^>' .. ok -/build/samtools-1.16.1/samtools faidx /tmp/c4A9qCDWOK/faidx.fa.gz 3:11-13 | grep -v '^>' +/build/samtools-1.16.1/samtools faidx /tmp/RFXhHuoSEX/faidx.fa.gz 3:11-13 | grep -v '^>' .. ok -/build/samtools-1.16.1/samtools faidx /tmp/c4A9qCDWOK/faidx.fa 2:998-1003 | grep -v '^>' +/build/samtools-1.16.1/samtools faidx /tmp/RFXhHuoSEX/faidx.fa 2:998-1003 | grep -v '^>' .. ok -/build/samtools-1.16.1/samtools faidx /tmp/c4A9qCDWOK/faidx.fa.gz 2:998-1003 | grep -v '^>' +/build/samtools-1.16.1/samtools faidx /tmp/RFXhHuoSEX/faidx.fa.gz 2:998-1003 | grep -v '^>' .. ok -/build/samtools-1.16.1/samtools faidx /tmp/c4A9qCDWOK/faidx.fa 1:100-104 | grep -v '^>' +/build/samtools-1.16.1/samtools faidx /tmp/RFXhHuoSEX/faidx.fa 1:100-104 | grep -v '^>' .. ok -/build/samtools-1.16.1/samtools faidx /tmp/c4A9qCDWOK/faidx.fa.gz 1:100-104 | grep -v '^>' +/build/samtools-1.16.1/samtools faidx /tmp/RFXhHuoSEX/faidx.fa.gz 1:100-104 | grep -v '^>' .. ok -/build/samtools-1.16.1/samtools faidx /tmp/c4A9qCDWOK/faidx.fa 1:99998-100007 | grep -v '^>' +/build/samtools-1.16.1/samtools faidx /tmp/RFXhHuoSEX/faidx.fa 1:99998-100007 | grep -v '^>' .. ok -/build/samtools-1.16.1/samtools faidx /tmp/c4A9qCDWOK/faidx.fa.gz 1:99998-100007 | grep -v '^>' +/build/samtools-1.16.1/samtools faidx /tmp/RFXhHuoSEX/faidx.fa.gz 1:99998-100007 | grep -v '^>' .. ok -/build/samtools-1.16.1/samtools fqidx /tmp/c4A9qCDWOK/fqidx.fq 3:11-13 +/build/samtools-1.16.1/samtools fqidx /tmp/RFXhHuoSEX/fqidx.fq 3:11-13 .. ok .. ok -/build/samtools-1.16.1/samtools fqidx /tmp/c4A9qCDWOK/fqidx.fq.gz 3:11-13 +/build/samtools-1.16.1/samtools fqidx /tmp/RFXhHuoSEX/fqidx.fq.gz 3:11-13 .. ok .. ok -/build/samtools-1.16.1/samtools fqidx /tmp/c4A9qCDWOK/fqidx.fq 2:998-1003 +/build/samtools-1.16.1/samtools fqidx /tmp/RFXhHuoSEX/fqidx.fq 2:998-1003 .. ok .. ok -/build/samtools-1.16.1/samtools fqidx /tmp/c4A9qCDWOK/fqidx.fq.gz 2:998-1003 +/build/samtools-1.16.1/samtools fqidx /tmp/RFXhHuoSEX/fqidx.fq.gz 2:998-1003 .. ok .. ok -/build/samtools-1.16.1/samtools fqidx /tmp/c4A9qCDWOK/fqidx.fq 1:100-104 +/build/samtools-1.16.1/samtools fqidx /tmp/RFXhHuoSEX/fqidx.fq 1:100-104 .. ok .. ok -/build/samtools-1.16.1/samtools fqidx /tmp/c4A9qCDWOK/fqidx.fq.gz 1:100-104 +/build/samtools-1.16.1/samtools fqidx /tmp/RFXhHuoSEX/fqidx.fq.gz 1:100-104 .. ok .. ok -/build/samtools-1.16.1/samtools fqidx /tmp/c4A9qCDWOK/fqidx.fq 1:99998-100007 +/build/samtools-1.16.1/samtools fqidx /tmp/RFXhHuoSEX/fqidx.fq 1:99998-100007 .. ok .. ok -/build/samtools-1.16.1/samtools fqidx /tmp/c4A9qCDWOK/fqidx.fq.gz 1:99998-100007 +/build/samtools-1.16.1/samtools fqidx /tmp/RFXhHuoSEX/fqidx.fq.gz 1:99998-100007 .. ok .. ok @@ -910,7 +930,7 @@ .. ok test_dict: - /build/samtools-1.16.1/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /tmp/c4A9qCDWOK/dict.fa.gz + /build/samtools-1.16.1/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /tmp/RFXhHuoSEX/dict.fa.gz .. ok test_dict: @@ -926,11 +946,11 @@ .. ok test_index: - /build/samtools-1.16.1/samtools view /tmp/c4A9qCDWOK/large_chrom.bam ref2 + /build/samtools-1.16.1/samtools view /tmp/RFXhHuoSEX/large_chrom.bam ref2 .. ok test_index: - /build/samtools-1.16.1/samtools view /tmp/c4A9qCDWOK/large_chrom.bam ref2:1-541556283 + /build/samtools-1.16.1/samtools view /tmp/RFXhHuoSEX/large_chrom.bam ref2:1-541556283 .. ok test_index: @@ -938,15 +958,15 @@ .. ok test_index: - /build/samtools-1.16.1/samtools view -X /build/samtools-1.16.1/test/dat/test_input_1_b.bam /tmp/c4A9qCDWOK/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/RFXhHuoSEX/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/c4A9qCDWOK/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/RFXhHuoSEX/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/c4A9qCDWOK/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/RFXhHuoSEX/test_input_1_b_opt.bam.bai ref2 .. ok test_index: @@ -962,23 +982,23 @@ .. ok test_index: - /build/samtools-1.16.1/samtools index -c /build/samtools-1.16.1/test/dat/auto_indexed.tmp.bam /tmp/c4A9qCDWOK/auto_indexed.csi && cat /tmp/c4A9qCDWOK/auto_indexed.csi + /build/samtools-1.16.1/samtools index -c /build/samtools-1.16.1/test/dat/auto_indexed.tmp.bam /tmp/RFXhHuoSEX/auto_indexed.csi && cat /tmp/RFXhHuoSEX/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/c4A9qCDWOK/auto_indexed.crai && cat /tmp/c4A9qCDWOK/auto_indexed.crai + /build/samtools-1.16.1/samtools index /build/samtools-1.16.1/test/dat/auto_indexed.tmp.cram /tmp/RFXhHuoSEX/auto_indexed.crai && cat /tmp/RFXhHuoSEX/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/c4A9qCDWOK/auto_indexed.csi && cat /tmp/c4A9qCDWOK/auto_indexed.csi + /build/samtools-1.16.1/samtools index -c /build/samtools-1.16.1/test/dat/auto_indexed.tmp.sam /tmp/RFXhHuoSEX/auto_indexed.csi && cat /tmp/RFXhHuoSEX/auto_indexed.csi .. ok test_index: - /build/samtools-1.16.1/samtools view -@ 2 /tmp/c4A9qCDWOK/large_chrom.bam ref2 + /build/samtools-1.16.1/samtools view -@ 2 /tmp/RFXhHuoSEX/large_chrom.bam ref2 .. ok test_index: - /build/samtools-1.16.1/samtools view -@ 2 /tmp/c4A9qCDWOK/large_chrom.bam ref2:1-541556283 + /build/samtools-1.16.1/samtools view -@ 2 /tmp/RFXhHuoSEX/large_chrom.bam ref2:1-541556283 .. ok test_index: @@ -986,15 +1006,15 @@ .. 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/c4A9qCDWOK/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/RFXhHuoSEX/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/c4A9qCDWOK/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/RFXhHuoSEX/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/c4A9qCDWOK/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/RFXhHuoSEX/test_input_1_b_opt.bam.bai ref2 .. ok test_index: @@ -1010,39 +1030,39 @@ .. ok test_index: - /build/samtools-1.16.1/samtools index -@ 2 -c /build/samtools-1.16.1/test/dat/auto_indexed.tmp.bam /tmp/c4A9qCDWOK/auto_indexed.csi && cat /tmp/c4A9qCDWOK/auto_indexed.csi + /build/samtools-1.16.1/samtools index -@ 2 -c /build/samtools-1.16.1/test/dat/auto_indexed.tmp.bam /tmp/RFXhHuoSEX/auto_indexed.csi && cat /tmp/RFXhHuoSEX/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/c4A9qCDWOK/auto_indexed.crai && cat /tmp/c4A9qCDWOK/auto_indexed.crai + /build/samtools-1.16.1/samtools index -@ 2 /build/samtools-1.16.1/test/dat/auto_indexed.tmp.cram /tmp/RFXhHuoSEX/auto_indexed.crai && cat /tmp/RFXhHuoSEX/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/c4A9qCDWOK/auto_indexed.csi && cat /tmp/c4A9qCDWOK/auto_indexed.csi + /build/samtools-1.16.1/samtools index -@ 2 -c /build/samtools-1.16.1/test/dat/auto_indexed.tmp.sam /tmp/RFXhHuoSEX/auto_indexed.csi && cat /tmp/RFXhHuoSEX/auto_indexed.csi .. ok test_mpileup: - /build/samtools-1.16.1/samtools mpileup -b /tmp/c4A9qCDWOK/mpileup.bam.list -f /tmp/c4A9qCDWOK/mpileup.ref.fa.gz -r17:100-150 + /build/samtools-1.16.1/samtools mpileup -b /tmp/RFXhHuoSEX/mpileup.bam.list -f /tmp/RFXhHuoSEX/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: - /build/samtools-1.16.1/samtools mpileup -b /tmp/c4A9qCDWOK/mpileup.cram.list -f /tmp/c4A9qCDWOK/mpileup.ref.fa.gz -r17:100-150 + /build/samtools-1.16.1/samtools mpileup -b /tmp/RFXhHuoSEX/mpileup.cram.list -f /tmp/RFXhHuoSEX/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: - /build/samtools-1.16.1/samtools mpileup -b /tmp/c4A9qCDWOK/mpileup.bam.urllist -f /tmp/c4A9qCDWOK/mpileup.ref.fa.gz -r17:100-150 + /build/samtools-1.16.1/samtools mpileup -b /tmp/RFXhHuoSEX/mpileup.bam.urllist -f /tmp/RFXhHuoSEX/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: - /build/samtools-1.16.1/samtools mpileup -b /tmp/c4A9qCDWOK/mpileup.cram.urllist -f /tmp/c4A9qCDWOK/mpileup.ref.fa.gz -r17:100-150 + /build/samtools-1.16.1/samtools mpileup -b /tmp/RFXhHuoSEX/mpileup.cram.urllist -f /tmp/RFXhHuoSEX/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: - /build/samtools-1.16.1/samtools mpileup -B --ff 0x14 -f /tmp/c4A9qCDWOK/mpileup.ref.fa.gz -r17:1050-1060 /tmp/c4A9qCDWOK/mpileup.1.bam | grep -v mpileup + /build/samtools-1.16.1/samtools mpileup -B --ff 0x14 -f /tmp/RFXhHuoSEX/mpileup.ref.fa.gz -r17:1050-1060 /tmp/RFXhHuoSEX/mpileup.1.bam | grep -v mpileup .. ok test_mpileup: - /build/samtools-1.16.1/samtools mpileup -B --ff 0x14 -f /tmp/c4A9qCDWOK/mpileup.ref.fa.gz -r17:1050-1060 /tmp/c4A9qCDWOK/mpileup.1.cram | grep -v mpileup + /build/samtools-1.16.1/samtools mpileup -B --ff 0x14 -f /tmp/RFXhHuoSEX/mpileup.ref.fa.gz -r17:1050-1060 /tmp/RFXhHuoSEX/mpileup.1.cram | grep -v mpileup .. ok test_mpileup: @@ -1328,53 +1348,53 @@ 48: Count -r grp2 (CRAM input) .. ok - 49: Filter -R /tmp/c4A9qCDWOK/view.001.fogn (SAM input) .. ok + 49: Filter -R /tmp/RFXhHuoSEX/view.001.fogn (SAM input) .. ok - 50: Count -R /tmp/c4A9qCDWOK/view.001.fogn (SAM input) .. ok + 50: Count -R /tmp/RFXhHuoSEX/view.001.fogn (SAM input) .. ok - 51: Filter -R /tmp/c4A9qCDWOK/view.001.fogn (BAM input) .. ok + 51: Filter -R /tmp/RFXhHuoSEX/view.001.fogn (BAM input) .. ok - 52: Count -R /tmp/c4A9qCDWOK/view.001.fogn (BAM input) .. ok + 52: Count -R /tmp/RFXhHuoSEX/view.001.fogn (BAM input) .. ok - 53: Filter -R /tmp/c4A9qCDWOK/view.001.fogn (CRAM input) .. ok + 53: Filter -R /tmp/RFXhHuoSEX/view.001.fogn (CRAM input) .. ok - 54: Count -R /tmp/c4A9qCDWOK/view.001.fogn (CRAM input) .. ok + 54: Count -R /tmp/RFXhHuoSEX/view.001.fogn (CRAM input) .. ok - 55: Filter -R /tmp/c4A9qCDWOK/view.001.fogn -r grp2 (SAM input).. ok + 55: Filter -R /tmp/RFXhHuoSEX/view.001.fogn -r grp2 (SAM input).. ok - 56: Count -R /tmp/c4A9qCDWOK/view.001.fogn -r grp2 (SAM input).. ok + 56: Count -R /tmp/RFXhHuoSEX/view.001.fogn -r grp2 (SAM input).. ok - 57: Filter -R /tmp/c4A9qCDWOK/view.001.fogn -r grp2 (BAM input).. ok + 57: Filter -R /tmp/RFXhHuoSEX/view.001.fogn -r grp2 (BAM input).. ok - 58: Count -R /tmp/c4A9qCDWOK/view.001.fogn -r grp2 (BAM input).. ok + 58: Count -R /tmp/RFXhHuoSEX/view.001.fogn -r grp2 (BAM input).. ok - 59: Filter -R /tmp/c4A9qCDWOK/view.001.fogn -r grp2 (CRAM input).. ok + 59: Filter -R /tmp/RFXhHuoSEX/view.001.fogn -r grp2 (CRAM input).. ok - 60: Count -R /tmp/c4A9qCDWOK/view.001.fogn -r grp2 (CRAM input).. ok + 60: Count -R /tmp/RFXhHuoSEX/view.001.fogn -r grp2 (CRAM input).. ok - 61: Filter -r grp2 -R /tmp/c4A9qCDWOK/view.001.fogn (SAM input).. ok + 61: Filter -r grp2 -R /tmp/RFXhHuoSEX/view.001.fogn (SAM input).. ok - 62: Count -r grp2 -R /tmp/c4A9qCDWOK/view.001.fogn (SAM input).. ok + 62: Count -r grp2 -R /tmp/RFXhHuoSEX/view.001.fogn (SAM input).. ok - 63: Filter -r grp2 -R /tmp/c4A9qCDWOK/view.001.fogn (BAM input).. ok + 63: Filter -r grp2 -R /tmp/RFXhHuoSEX/view.001.fogn (BAM input).. ok - 64: Count -r grp2 -R /tmp/c4A9qCDWOK/view.001.fogn (BAM input).. ok + 64: Count -r grp2 -R /tmp/RFXhHuoSEX/view.001.fogn (BAM input).. ok - 65: Filter -r grp2 -R /tmp/c4A9qCDWOK/view.001.fogn (CRAM input).. ok + 65: Filter -r grp2 -R /tmp/RFXhHuoSEX/view.001.fogn (CRAM input).. ok - 66: Count -r grp2 -R /tmp/c4A9qCDWOK/view.001.fogn (CRAM input).. ok + 66: Count -r grp2 -R /tmp/RFXhHuoSEX/view.001.fogn (CRAM input).. ok - 67: Filter -N /tmp/c4A9qCDWOK/view.001.forn (SAM input) .. ok + 67: Filter -N /tmp/RFXhHuoSEX/view.001.forn (SAM input) .. ok - 68: Count -N /tmp/c4A9qCDWOK/view.001.forn (SAM input) .. ok + 68: Count -N /tmp/RFXhHuoSEX/view.001.forn (SAM input) .. ok - 69: Filter -N /tmp/c4A9qCDWOK/view.001.forn (BAM input) .. ok + 69: Filter -N /tmp/RFXhHuoSEX/view.001.forn (BAM input) .. ok - 70: Count -N /tmp/c4A9qCDWOK/view.001.forn (BAM input) .. ok + 70: Count -N /tmp/RFXhHuoSEX/view.001.forn (BAM input) .. ok - 71: Filter -N /tmp/c4A9qCDWOK/view.001.forn (CRAM input) .. ok + 71: Filter -N /tmp/RFXhHuoSEX/view.001.forn (CRAM input) .. ok - 72: Count -N /tmp/c4A9qCDWOK/view.001.forn (CRAM input) .. ok + 72: Count -N /tmp/RFXhHuoSEX/view.001.forn (CRAM input) .. ok 73: Filter -d BC (SAM input) .. ok @@ -1400,53 +1420,53 @@ 84: Count -d BC:TGCA (CRAM input) .. ok - 85: Filter -D BC:/tmp/c4A9qCDWOK/view.001.fobc (SAM input) .. ok + 85: Filter -D BC:/tmp/RFXhHuoSEX/view.001.fobc (SAM input) .. ok - 86: Count -D BC:/tmp/c4A9qCDWOK/view.001.fobc (SAM input) .. ok + 86: Count -D BC:/tmp/RFXhHuoSEX/view.001.fobc (SAM input) .. ok - 87: Filter -D BC:/tmp/c4A9qCDWOK/view.001.fobc (BAM input) .. ok + 87: Filter -D BC:/tmp/RFXhHuoSEX/view.001.fobc (BAM input) .. ok - 88: Count -D BC:/tmp/c4A9qCDWOK/view.001.fobc (BAM input) .. ok + 88: Count -D BC:/tmp/RFXhHuoSEX/view.001.fobc (BAM input) .. ok - 89: Filter -D BC:/tmp/c4A9qCDWOK/view.001.fobc (CRAM input) .. ok + 89: Filter -D BC:/tmp/RFXhHuoSEX/view.001.fobc (CRAM input) .. ok - 90: Count -D BC:/tmp/c4A9qCDWOK/view.001.fobc (CRAM input) .. ok + 90: Count -D BC:/tmp/RFXhHuoSEX/view.001.fobc (CRAM input) .. ok - 91: Filter -D BC:/tmp/c4A9qCDWOK/view.001.fobc -d BC:TGCA (SAM input).. ok + 91: Filter -D BC:/tmp/RFXhHuoSEX/view.001.fobc -d BC:TGCA (SAM input).. ok - 92: Count -D BC:/tmp/c4A9qCDWOK/view.001.fobc -d BC:TGCA (SAM input).. ok + 92: Count -D BC:/tmp/RFXhHuoSEX/view.001.fobc -d BC:TGCA (SAM input).. ok - 93: Filter -D BC:/tmp/c4A9qCDWOK/view.001.fobc -d BC:TGCA (BAM input).. ok + 93: Filter -D BC:/tmp/RFXhHuoSEX/view.001.fobc -d BC:TGCA (BAM input).. ok - 94: Count -D BC:/tmp/c4A9qCDWOK/view.001.fobc -d BC:TGCA (BAM input).. ok + 94: Count -D BC:/tmp/RFXhHuoSEX/view.001.fobc -d BC:TGCA (BAM input).. ok - 95: Filter -D BC:/tmp/c4A9qCDWOK/view.001.fobc -d BC:TGCA (CRAM input).. ok + 95: Filter -D BC:/tmp/RFXhHuoSEX/view.001.fobc -d BC:TGCA (CRAM input).. ok - 96: Count -D BC:/tmp/c4A9qCDWOK/view.001.fobc -d BC:TGCA (CRAM input).. ok + 96: Count -D BC:/tmp/RFXhHuoSEX/view.001.fobc -d BC:TGCA (CRAM input).. ok - 97: Filter -d BC:TGCA -D BC:/tmp/c4A9qCDWOK/view.001.fobc (SAM input).. ok + 97: Filter -d BC:TGCA -D BC:/tmp/RFXhHuoSEX/view.001.fobc (SAM input).. ok - 98: Count -d BC:TGCA -D BC:/tmp/c4A9qCDWOK/view.001.fobc (SAM input).. ok + 98: Count -d BC:TGCA -D BC:/tmp/RFXhHuoSEX/view.001.fobc (SAM input).. ok - 99: Filter -d BC:TGCA -D BC:/tmp/c4A9qCDWOK/view.001.fobc (BAM input).. ok + 99: Filter -d BC:TGCA -D BC:/tmp/RFXhHuoSEX/view.001.fobc (BAM input).. ok - 100: Count -d BC:TGCA -D BC:/tmp/c4A9qCDWOK/view.001.fobc (BAM input).. ok + 100: Count -d BC:TGCA -D BC:/tmp/RFXhHuoSEX/view.001.fobc (BAM input).. ok - 101: Filter -d BC:TGCA -D BC:/tmp/c4A9qCDWOK/view.001.fobc (CRAM input).. ok + 101: Filter -d BC:TGCA -D BC:/tmp/RFXhHuoSEX/view.001.fobc (CRAM input).. ok - 102: Count -d BC:TGCA -D BC:/tmp/c4A9qCDWOK/view.001.fobc (CRAM input).. ok + 102: Count -d BC:TGCA -D BC:/tmp/RFXhHuoSEX/view.001.fobc (CRAM input).. ok - 103: Filter -D RG:/tmp/c4A9qCDWOK/view.001.fogn (SAM input) .. ok + 103: Filter -D RG:/tmp/RFXhHuoSEX/view.001.fogn (SAM input) .. ok - 104: Count -D RG:/tmp/c4A9qCDWOK/view.001.fogn (SAM input) .. ok + 104: Count -D RG:/tmp/RFXhHuoSEX/view.001.fogn (SAM input) .. ok - 105: Filter -D RG:/tmp/c4A9qCDWOK/view.001.fogn (BAM input) .. ok + 105: Filter -D RG:/tmp/RFXhHuoSEX/view.001.fogn (BAM input) .. ok - 106: Count -D RG:/tmp/c4A9qCDWOK/view.001.fogn (BAM input) .. ok + 106: Count -D RG:/tmp/RFXhHuoSEX/view.001.fogn (BAM input) .. ok - 107: Filter -D RG:/tmp/c4A9qCDWOK/view.001.fogn (CRAM input).. ok + 107: Filter -D RG:/tmp/RFXhHuoSEX/view.001.fogn (CRAM input).. ok - 108: Count -D RG:/tmp/c4A9qCDWOK/view.001.fogn (CRAM input) .. ok + 108: Count -D RG:/tmp/RFXhHuoSEX/view.001.fogn (CRAM input) .. ok 109: Filter -d NE:TGCA (SAM input) .. ok @@ -1462,126 +1482,126 @@ 115: Filter -d TGCA (SAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: - /build/samtools-1.16.1/samtools view -o /tmp/c4A9qCDWOK/view.test115.sam -h -d TGCA /tmp/c4A9qCDWOK/view.001.sam --no-PG + /build/samtools-1.16.1/samtools view -o /tmp/RFXhHuoSEX/view.test115.sam -h -d TGCA /tmp/RFXhHuoSEX/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/c4A9qCDWOK/view.001.sam --no-PG + /build/samtools-1.16.1/samtools view -c -d TGCA /tmp/RFXhHuoSEX/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/c4A9qCDWOK/view.test117.sam -h -d TGCA /tmp/c4A9qCDWOK/view.test001.bam --no-PG + /build/samtools-1.16.1/samtools view -o /tmp/RFXhHuoSEX/view.test117.sam -h -d TGCA /tmp/RFXhHuoSEX/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/c4A9qCDWOK/view.test001.bam --no-PG + /build/samtools-1.16.1/samtools view -c -d TGCA /tmp/RFXhHuoSEX/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/c4A9qCDWOK/view.test119.sam -h -d TGCA /tmp/c4A9qCDWOK/view.test006.cram --no-PG + /build/samtools-1.16.1/samtools view -o /tmp/RFXhHuoSEX/view.test119.sam -h -d TGCA /tmp/RFXhHuoSEX/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/c4A9qCDWOK/view.test006.cram --no-PG + /build/samtools-1.16.1/samtools view -c -d TGCA /tmp/RFXhHuoSEX/view.test006.cram --no-PG .. expected failure - 121: Filter -D BClong:/tmp/c4A9qCDWOK/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/c4A9qCDWOK/view.001.fobc" + 121: Filter -D BClong:/tmp/RFXhHuoSEX/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/RFXhHuoSEX/view.001.fobc" Failed command: - /build/samtools-1.16.1/samtools view -o /tmp/c4A9qCDWOK/view.test121.sam -h -D BClong:/tmp/c4A9qCDWOK/view.001.fobc /tmp/c4A9qCDWOK/view.001.sam --no-PG + /build/samtools-1.16.1/samtools view -o /tmp/RFXhHuoSEX/view.test121.sam -h -D BClong:/tmp/RFXhHuoSEX/view.001.fobc /tmp/RFXhHuoSEX/view.001.sam --no-PG .. expected failure - 122: Count -D BClong:/tmp/c4A9qCDWOK/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/c4A9qCDWOK/view.001.fobc" + 122: Count -D BClong:/tmp/RFXhHuoSEX/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/RFXhHuoSEX/view.001.fobc" Failed command: - /build/samtools-1.16.1/samtools view -c -D BClong:/tmp/c4A9qCDWOK/view.001.fobc /tmp/c4A9qCDWOK/view.001.sam --no-PG + /build/samtools-1.16.1/samtools view -c -D BClong:/tmp/RFXhHuoSEX/view.001.fobc /tmp/RFXhHuoSEX/view.001.sam --no-PG .. expected failure - 123: Filter -D BClong:/tmp/c4A9qCDWOK/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/c4A9qCDWOK/view.001.fobc" + 123: Filter -D BClong:/tmp/RFXhHuoSEX/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/RFXhHuoSEX/view.001.fobc" Failed command: - /build/samtools-1.16.1/samtools view -o /tmp/c4A9qCDWOK/view.test123.sam -h -D BClong:/tmp/c4A9qCDWOK/view.001.fobc /tmp/c4A9qCDWOK/view.test001.bam --no-PG + /build/samtools-1.16.1/samtools view -o /tmp/RFXhHuoSEX/view.test123.sam -h -D BClong:/tmp/RFXhHuoSEX/view.001.fobc /tmp/RFXhHuoSEX/view.test001.bam --no-PG .. expected failure - 124: Count -D BClong:/tmp/c4A9qCDWOK/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/c4A9qCDWOK/view.001.fobc" + 124: Count -D BClong:/tmp/RFXhHuoSEX/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/RFXhHuoSEX/view.001.fobc" Failed command: - /build/samtools-1.16.1/samtools view -c -D BClong:/tmp/c4A9qCDWOK/view.001.fobc /tmp/c4A9qCDWOK/view.test001.bam --no-PG + /build/samtools-1.16.1/samtools view -c -D BClong:/tmp/RFXhHuoSEX/view.001.fobc /tmp/RFXhHuoSEX/view.test001.bam --no-PG .. expected failure - 125: Filter -D BClong:/tmp/c4A9qCDWOK/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/c4A9qCDWOK/view.001.fobc" + 125: Filter -D BClong:/tmp/RFXhHuoSEX/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/RFXhHuoSEX/view.001.fobc" Failed command: - /build/samtools-1.16.1/samtools view -o /tmp/c4A9qCDWOK/view.test125.sam -h -D BClong:/tmp/c4A9qCDWOK/view.001.fobc /tmp/c4A9qCDWOK/view.test006.cram --no-PG + /build/samtools-1.16.1/samtools view -o /tmp/RFXhHuoSEX/view.test125.sam -h -D BClong:/tmp/RFXhHuoSEX/view.001.fobc /tmp/RFXhHuoSEX/view.test006.cram --no-PG .. expected failure - 126: Count -D BClong:/tmp/c4A9qCDWOK/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/c4A9qCDWOK/view.001.fobc" + 126: Count -D BClong:/tmp/RFXhHuoSEX/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/RFXhHuoSEX/view.001.fobc" Failed command: - /build/samtools-1.16.1/samtools view -c -D BClong:/tmp/c4A9qCDWOK/view.001.fobc /tmp/c4A9qCDWOK/view.test006.cram --no-PG + /build/samtools-1.16.1/samtools view -c -D BClong:/tmp/RFXhHuoSEX/view.001.fobc /tmp/RFXhHuoSEX/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/c4A9qCDWOK/view.test127.sam -h -d BC:ACGT -d RG:grp2 /tmp/c4A9qCDWOK/view.001.sam --no-PG + /build/samtools-1.16.1/samtools view -o /tmp/RFXhHuoSEX/view.test127.sam -h -d BC:ACGT -d RG:grp2 /tmp/RFXhHuoSEX/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/c4A9qCDWOK/view.001.sam --no-PG + /build/samtools-1.16.1/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/RFXhHuoSEX/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/c4A9qCDWOK/view.test129.sam -h -d BC:ACGT -d RG:grp2 /tmp/c4A9qCDWOK/view.test001.bam --no-PG + /build/samtools-1.16.1/samtools view -o /tmp/RFXhHuoSEX/view.test129.sam -h -d BC:ACGT -d RG:grp2 /tmp/RFXhHuoSEX/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/c4A9qCDWOK/view.test001.bam --no-PG + /build/samtools-1.16.1/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/RFXhHuoSEX/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/c4A9qCDWOK/view.test131.sam -h -d BC:ACGT -d RG:grp2 /tmp/c4A9qCDWOK/view.test006.cram --no-PG + /build/samtools-1.16.1/samtools view -o /tmp/RFXhHuoSEX/view.test131.sam -h -d BC:ACGT -d RG:grp2 /tmp/RFXhHuoSEX/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/c4A9qCDWOK/view.test006.cram --no-PG + /build/samtools-1.16.1/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/RFXhHuoSEX/view.test006.cram --no-PG .. expected failure @@ -2455,7 +2475,7 @@ .. ok test_bam2fq: - /build/samtools-1.16.1/samtools fastq -N -s /tmp/c4A9qCDWOK/bam2fq.discard.s.fq -0 /tmp/c4A9qCDWOK/bam2fq.discard.0.fq /build/samtools-1.16.1/test/dat/bam2fq.001.sam + /build/samtools-1.16.1/samtools fastq -N -s /tmp/RFXhHuoSEX/bam2fq.discard.s.fq -0 /tmp/RFXhHuoSEX/bam2fq.discard.0.fq /build/samtools-1.16.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: @@ -2576,7 +2596,7 @@ .. ok test_bam2fq: - /build/samtools-1.16.1/samtools fastq -@ 2 -N -s /tmp/c4A9qCDWOK/bam2fq.discard.s.fq -0 /tmp/c4A9qCDWOK/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/RFXhHuoSEX/bam2fq.discard.s.fq -0 /tmp/RFXhHuoSEX/bam2fq.discard.0.fq /build/samtools-1.16.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: @@ -2769,7 +2789,7 @@ .. ok test_merge: - /build/samtools-1.16.1/samtools merge -s 1 -O sam -b /tmp/lJPUMzsTVb - /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/9a5ufoBbbS - /build/samtools-1.16.1/test/dat/test_input_1_a.bam .. ok test_merge: @@ -2793,11 +2813,11 @@ .. ok test_merge: - /build/samtools-1.16.1/samtools merge -s 1 -p -c -t PG -O SAM - /tmp/c4A9qCDWOK/merge.tag.1.bam /tmp/c4A9qCDWOK/merge.tag.2.bam + /build/samtools-1.16.1/samtools merge -s 1 -p -c -t PG -O SAM - /tmp/RFXhHuoSEX/merge.tag.1.bam /tmp/RFXhHuoSEX/merge.tag.2.bam .. ok test_merge: - /build/samtools-1.16.1/samtools merge -s 1 -p -c -n -t PG -O SAM - /tmp/c4A9qCDWOK/merge.tag.3.bam /tmp/c4A9qCDWOK/merge.tag.4.bam + /build/samtools-1.16.1/samtools merge -s 1 -p -c -n -t PG -O SAM - /tmp/RFXhHuoSEX/merge.tag.3.bam /tmp/RFXhHuoSEX/merge.tag.4.bam .. ok test_merge: @@ -2805,7 +2825,7 @@ .. 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/c4A9qCDWOK/merge.bed.1.bam /tmp/c4A9qCDWOK/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/RFXhHuoSEX/merge.bed.1.bam /tmp/RFXhHuoSEX/merge.bed.2.bam .. ok test_merge: @@ -2821,7 +2841,7 @@ .. ok test_merge: - /build/samtools-1.16.1/samtools merge -@ 2 -s 1 -O sam -b /tmp/MIiDUbk125 - /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/Ei5N75WKRo - /build/samtools-1.16.1/test/dat/test_input_1_a.bam .. ok test_merge: @@ -2845,11 +2865,11 @@ .. ok test_merge: - /build/samtools-1.16.1/samtools merge -@ 2 -s 1 -p -c -t PG -O SAM - /tmp/c4A9qCDWOK/merge.tag.1.bam /tmp/c4A9qCDWOK/merge.tag.2.bam + /build/samtools-1.16.1/samtools merge -@ 2 -s 1 -p -c -t PG -O SAM - /tmp/RFXhHuoSEX/merge.tag.1.bam /tmp/RFXhHuoSEX/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/c4A9qCDWOK/merge.tag.3.bam /tmp/c4A9qCDWOK/merge.tag.4.bam + /build/samtools-1.16.1/samtools merge -@ 2 -s 1 -p -c -n -t PG -O SAM - /tmp/RFXhHuoSEX/merge.tag.3.bam /tmp/RFXhHuoSEX/merge.tag.4.bam .. ok test_merge: @@ -2857,7 +2877,7 @@ .. 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/c4A9qCDWOK/merge.bed.1.bam /tmp/c4A9qCDWOK/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/RFXhHuoSEX/merge.bed.1.bam /tmp/RFXhHuoSEX/merge.bed.2.bam .. ok test_merge: @@ -2865,15 +2885,15 @@ .. ok test_sort: - /build/samtools-1.16.1/samtools sort /build/samtools-1.16.1/test/dat/test_input_1_a.bam /tmp/c4A9qCDWOK/sortout + /build/samtools-1.16.1/samtools sort /build/samtools-1.16.1/test/dat/test_input_1_a.bam /tmp/RFXhHuoSEX/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/c4A9qCDWOK/sortout.bam + /build/samtools-1.16.1/samtools sort -f /build/samtools-1.16.1/test/dat/test_input_1_a.bam /tmp/RFXhHuoSEX/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/c4A9qCDWOK/sorttmp + /build/samtools-1.16.1/samtools sort -o /build/samtools-1.16.1/test/dat/test_input_1_a.bam /tmp/RFXhHuoSEX/sorttmp .. ok test_sort: @@ -2905,15 +2925,15 @@ .. ok test_sort: - /build/samtools-1.16.1/samtools sort -@ 2 /build/samtools-1.16.1/test/dat/test_input_1_a.bam /tmp/c4A9qCDWOK/sortout + /build/samtools-1.16.1/samtools sort -@ 2 /build/samtools-1.16.1/test/dat/test_input_1_a.bam /tmp/RFXhHuoSEX/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/c4A9qCDWOK/sortout.bam + /build/samtools-1.16.1/samtools sort -@ 2 -f /build/samtools-1.16.1/test/dat/test_input_1_a.bam /tmp/RFXhHuoSEX/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/c4A9qCDWOK/sorttmp + /build/samtools-1.16.1/samtools sort -@ 2 -o /build/samtools-1.16.1/test/dat/test_input_1_a.bam /tmp/RFXhHuoSEX/sorttmp .. ok test_sort: @@ -3409,15 +3429,15 @@ .. ok test_large_positions: - /build/samtools-1.16.1/samtools view -h --no-PG /tmp/c4A9qCDWOK/longref.sam.gz + /build/samtools-1.16.1/samtools view -h --no-PG /tmp/RFXhHuoSEX/longref.sam.gz .. ok test_large_positions: - /build/samtools-1.16.1/samtools view -h --no-PG /tmp/c4A9qCDWOK/longref.sam.gz CHROMOSOME_I:10000000114-10000000168 + /build/samtools-1.16.1/samtools view -h --no-PG /tmp/RFXhHuoSEX/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/c4A9qCDWOK/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/RFXhHuoSEX/longref.sam.gz .. ok test_large_positions: @@ -3437,7 +3457,7 @@ .. ok test_large_positions: - /build/samtools-1.16.1/samtools tview -d T -p CHROMOSOME_I:10000000000 /tmp/c4A9qCDWOK/longref.sam.gz + /build/samtools-1.16.1/samtools tview -d T -p CHROMOSOME_I:10000000000 /tmp/RFXhHuoSEX/longref.sam.gz .. ok test_large_positions: @@ -3567,7 +3587,7 @@ Unexpected failures: 0 => PASS make[2]: Leaving directory '/build/samtools-1.16.1' - rm -fr -- /tmp/dh-xdg-rundir-pYU5Moji + rm -fr -- /tmp/dh-xdg-rundir-mUkcINQx make[1]: Leaving directory '/build/samtools-1.16.1' create-stamp debian/debhelper-build-stamp dh_prep @@ -3579,7 +3599,7 @@ dh_auto_install -- \ prefix=/usr install -m0755 -d /build/samtools-1.16.1/debian/tmp - make -j16 install DESTDIR=/build/samtools-1.16.1/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr + make -j15 install DESTDIR=/build/samtools-1.16.1/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr make[2]: Entering directory '/build/samtools-1.16.1' mkdir -p -m 755 /build/samtools-1.16.1/debian/tmp/usr/bin /build/samtools-1.16.1/debian/tmp/usr/bin /build/samtools-1.16.1/debian/tmp/usr/share/man/man1 install -p samtools /build/samtools-1.16.1/debian/tmp/usr/bin @@ -3634,14 +3654,14 @@ debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/samtools-1.16.1' dh_installchangelogs NEWS - 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 + 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 make[1]: Leaving directory '/build/samtools-1.16.1' dh_installexamples install -m0755 -d debian/samtools/usr/share/doc/samtools/examples @@ -3663,39 +3683,39 @@ 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-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-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/ace2sam.1 debian/samtools/usr/share/man/man1/samtools-addreplacerg.1 debian/samtools/usr/share/man/man1/samtools-ampliconclip.1 man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-ampliconstats.1 debian/samtools/usr/share/man/man1/samtools-bedcov.1 debian/samtools/usr/share/man/man1/samtools-calmd.1 man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-cat.1 debian/samtools/usr/share/man/man1/samtools-collate.1 debian/samtools/usr/share/man/man1/samtools-consensus.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-coverage.1 debian/samtools/usr/share/man/man1/samtools-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 - man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-fixmate.1 debian/samtools/usr/share/man/man1/samtools-flags.1 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 + 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 + man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-import.1 debian/samtools/usr/share/man/man1/samtools-index.1 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-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-merge.1 debian/samtools/usr/share/man/man1/samtools-mpileup.1 debian/samtools/usr/share/man/man1/samtools-phase.1 man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-rmdup.1 debian/samtools/usr/share/man/man1/samtools-samples.1 debian/samtools/usr/share/man/man1/samtools-sort.1 + man-recode --to-code UTF-8 --suffix .dh-new 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-tview.1 debian/samtools/usr/share/man/man1/samtools-view.1 debian/samtools/usr/share/man/man1/samtools.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-import.1 debian/samtools/usr/share/man/man1/samtools-index.1 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 man-recode --to-code UTF-8 --suffix .dh-new 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.pl.1 debian/samtools/usr/share/man/man1/wgsim.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-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-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-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-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-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 - 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 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.pl.1 debian/samtools/usr/share/man/man1/wgsim.1 + mv debian/samtools/usr/share/man/man1/ace2sam.1.dh-new debian/samtools/usr/share/man/man1/ace2sam.1 + mv debian/samtools/usr/share/man/man1/samtools-addreplacerg.1.dh-new debian/samtools/usr/share/man/man1/samtools-addreplacerg.1 + mv debian/samtools/usr/share/man/man1/samtools-ampliconclip.1.dh-new debian/samtools/usr/share/man/man1/samtools-ampliconclip.1 + chmod 0644 -- debian/samtools/usr/share/man/man1/ace2sam.1 debian/samtools/usr/share/man/man1/samtools-addreplacerg.1 debian/samtools/usr/share/man/man1/samtools-ampliconclip.1 mv debian/samtools/usr/share/man/man1/samtools-ampliconstats.1.dh-new debian/samtools/usr/share/man/man1/samtools-ampliconstats.1 mv debian/samtools/usr/share/man/man1/samtools-bedcov.1.dh-new debian/samtools/usr/share/man/man1/samtools-bedcov.1 mv debian/samtools/usr/share/man/man1/samtools-calmd.1.dh-new debian/samtools/usr/share/man/man1/samtools-calmd.1 chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-ampliconstats.1 debian/samtools/usr/share/man/man1/samtools-bedcov.1 debian/samtools/usr/share/man/man1/samtools-calmd.1 + mv debian/samtools/usr/share/man/man1/samtools-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 + 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 + 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-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 @@ -3704,34 +3724,34 @@ mv debian/samtools/usr/share/man/man1/samtools-faidx.1.dh-new debian/samtools/usr/share/man/man1/samtools-faidx.1 mv debian/samtools/usr/share/man/man1/samtools-fasta.1.dh-new debian/samtools/usr/share/man/man1/samtools-fasta.1 chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-dict.1 debian/samtools/usr/share/man/man1/samtools-faidx.1 debian/samtools/usr/share/man/man1/samtools-fasta.1 - mv debian/samtools/usr/share/man/man1/ace2sam.1.dh-new debian/samtools/usr/share/man/man1/ace2sam.1 - mv debian/samtools/usr/share/man/man1/samtools-addreplacerg.1.dh-new debian/samtools/usr/share/man/man1/samtools-addreplacerg.1 - mv debian/samtools/usr/share/man/man1/samtools-ampliconclip.1.dh-new debian/samtools/usr/share/man/man1/samtools-ampliconclip.1 - 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-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 - 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-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-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 - 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 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 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 + 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 + 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-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-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-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-coverage.1.dh-new debian/samtools/usr/share/man/man1/samtools-coverage.1 + 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-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 + 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 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-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-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-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-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 @@ -3752,9 +3772,9 @@ chmod a-x usr/share/doc/samtools-test/NEWS.Debian usr/share/doc/samtools-test/changelog usr/share/doc/samtools-test/changelog.Debian 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 - cd '/build/samtools-1.16.1' 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' rm -f debian/samtools/usr/share/man/man1/samtools-fastq.1 debian/samtools/usr/share/man/man1/samtools-fastq.1.gz ln -s samtools-fasta.1.gz debian/samtools/usr/share/man/man1/samtools-fastq.1.gz dh_fixperms @@ -3781,31 +3801,31 @@ chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/4d/4b1664ca21952c504243c49258ff3829a394db.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/4d/4b1664ca21952c504243c49258ff3829a394db.debug debian/samtools/usr/bin/wgsim - install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/7e - objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5sum-lite debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/7e/55340b7c34067c484fe9470ec9dd0936360546.debug - chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/7e/55340b7c34067c484fe9470ec9dd0936360546.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/7e/55340b7c34067c484fe9470ec9dd0936360546.debug debian/samtools/usr/bin/md5sum-lite install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/95 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5fa debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/95/4cff469f359b4af3c3cfdf971d9d22c8389348.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/95/4cff469f359b4af3c3cfdf971d9d22c8389348.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/95/4cff469f359b4af3c3cfdf971d9d22c8389348.debug debian/samtools/usr/bin/md5fa + install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/7e + objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5sum-lite debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/7e/55340b7c34067c484fe9470ec9dd0936360546.debug + chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/7e/55340b7c34067c484fe9470ec9dd0936360546.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/7e/55340b7c34067c484fe9470ec9dd0936360546.debug debian/samtools/usr/bin/md5sum-lite install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/1f objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/ace2sam debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/1f/eb5b9250a29c3f42354170a1343309af6207ea.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/1f/eb5b9250a29c3f42354170a1343309af6207ea.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/1f/eb5b9250a29c3f42354170a1343309af6207ea.debug debian/samtools/usr/bin/ace2sam install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/6b - objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-short debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/6b/f97d34fe9185dcf371b4a4af48e30a0fd562f1.debug - chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/6b/f97d34fe9185dcf371b4a4af48e30a0fd562f1.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/6b/f97d34fe9185dcf371b4a4af48e30a0fd562f1.debug debian/samtools/usr/bin/maq2sam-short - install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/6b objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-long debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/6b/bb381383bb492f402af7ecc92f537d230e4582.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/6b/bb381383bb492f402af7ecc92f537d230e4582.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/6b/bb381383bb492f402af7ecc92f537d230e4582.debug debian/samtools/usr/bin/maq2sam-long + install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/6b + objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-short debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/6b/f97d34fe9185dcf371b4a4af48e30a0fd562f1.debug + chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/6b/f97d34fe9185dcf371b4a4af48e30a0fd562f1.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/6b/f97d34fe9185dcf371b4a4af48e30a0fd562f1.debug debian/samtools/usr/bin/maq2sam-short install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/bd objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/samtools debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/bd/065e2cba5f0c1768ea2fcd29fe818a69f3643f.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/bd/065e2cba5f0c1768ea2fcd29fe818a69f3643f.debug @@ -3822,20 +3842,20 @@ rm -f debian/samtools/DEBIAN/shlibs dh_shlibdeps -a install -m0755 -d debian/samtools/DEBIAN - dpkg-shlibdeps -Tdebian/samtools.substvars debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/samtools + dpkg-shlibdeps -Tdebian/samtools.substvars debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/samtools 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 -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=1feb5b9250a29c3f42354170a1343309af6207ea 4d4b1664ca21952c504243c49258ff3829a394db 6bbb381383bb492f402af7ecc92f537d230e4582 6bf97d34fe9185dcf371b4a4af48e30a0fd562f1 7e55340b7c34067c484fe9470ec9dd0936360546 954cff469f359b4af3c3cfdf971d9d22c8389348 bd065e2cba5f0c1768ea2fcd29fe818a69f3643f" -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-test: substitution variable ${perl:Depends} unused, but is defined chmod 0644 -- debian/samtools-test/DEBIAN/control dpkg-gencontrol: warning: package samtools: substitution variable ${perl:Depends} unused, but is defined @@ -3844,8 +3864,8 @@ 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-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 @@ -3857,9 +3877,9 @@ dpkg-deb --root-owner-group --build debian/samtools .. dpkg-deb --root-owner-group --build debian/.debhelper/samtools/dbgsym-root .. dpkg-deb --root-owner-group --build debian/samtools-test .. +dpkg-deb: building package 'samtools-test' in '../samtools-test_1.16.1-1_all.deb'. dpkg-deb: building package 'samtools' in '../samtools_1.16.1-1_amd64.deb'. dpkg-deb: building package 'samtools-dbgsym' in '../samtools-dbgsym_1.16.1-1_amd64.deb'. -dpkg-deb: building package 'samtools-test' in '../samtools-test_1.16.1-1_all.deb'. dpkg-genbuildinfo --build=binary -O../samtools_1.16.1-1_amd64.buildinfo dpkg-genchanges --build=binary -O../samtools_1.16.1-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -3868,12 +3888,14 @@ 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/1487910/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1487910/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/1554661 and its subdirectories -I: Current time: Thu May 16 14:08:03 -12 2024 -I: pbuilder-time-stamp: 1715911683 +I: removing directory /srv/workspace/pbuilder/1487910 and its subdirectories +I: Current time: Sat Apr 15 09:52:11 +14 2023 +I: pbuilder-time-stamp: 1681501931