Diff of the two buildlogs: -- --- b1/build.log 2023-06-06 11:10:38.669397265 +0000 +++ b2/build.log 2023-06-06 11:12:08.149481304 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Jun 5 23:07:52 -12 2023 -I: pbuilder-time-stamp: 1686049672 +I: Current time: Tue Jul 9 07:33:37 +14 2024 +I: pbuilder-time-stamp: 1720460017 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -17,7 +17,7 @@ I: copying [./htslib_1.16+ds.orig.tar.bz2] I: copying [./htslib_1.16+ds-3.debian.tar.xz] I: Extracting source -gpgv: Signature made Wed Oct 19 08:47:31 2022 -12 +gpgv: Signature made Thu Oct 20 10:47:31 2022 +14 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key @@ -36,137 +36,169 @@ dpkg-source: info: applying trim-file-prefix.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/20964/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/74099/tmp/hooks/D01_modify_environment starting +debug: Running on ionos6-i386. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Jul 9 07:33 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/74099/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/74099/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='i386' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8 ' - DISTRIBUTION='bookworm' - HOME='/root' - HOST_ARCH='i386' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") + BASH_VERSION='5.2.15(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=i386 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15 ' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - INVOCATION_ID='e63da77fd8b34143a9e245b322f181e8' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - LD_LIBRARY_PATH='/usr/lib/libeatmydata' - LD_PRELOAD='libeatmydata.so' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='20964' - PS1='# ' - PS2='> ' + INVOCATION_ID=1df72be587c6475d83426b453866c1d0 + LANG=C + LANGUAGE=de_CH:de + LC_ALL=C + LD_LIBRARY_PATH=/usr/lib/libeatmydata + LD_PRELOAD=libeatmydata.so + MACHTYPE=i686-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=74099 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.JaoQDG35/pbuilderrc_54Dc --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.JaoQDG35/b1 --logfile b1/build.log htslib_1.16+ds-3.dsc' - SUDO_GID='112' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://78.137.99.97:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.JaoQDG35/pbuilderrc_CcFC --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.JaoQDG35/b2 --logfile b2/build.log --extrapackages usrmerge htslib_1.16+ds-3.dsc' + SUDO_GID=112 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://85.184.249.68:3128 I: uname -a - Linux ionos12-i386 5.10.0-23-686-pae #1 SMP Debian 5.10.179-1 (2023-05-12) i686 GNU/Linux + Linux i-capture-the-hostname 5.10.0-23-amd64 #1 SMP Debian 5.10.179-1 (2023-05-12) x86_64 GNU/Linux I: ls -l /bin total 6036 - -rwxr-xr-x 1 root root 1408088 Apr 23 09:24 bash - -rwxr-xr-x 3 root root 38404 Sep 18 2022 bunzip2 - -rwxr-xr-x 3 root root 38404 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 38404 Sep 18 2022 bzip2 - -rwxr-xr-x 1 root root 17892 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 42920 Sep 20 2022 cat - -rwxr-xr-x 1 root root 79816 Sep 20 2022 chgrp - -rwxr-xr-x 1 root root 67496 Sep 20 2022 chmod - -rwxr-xr-x 1 root root 79816 Sep 20 2022 chown - -rwxr-xr-x 1 root root 162024 Sep 20 2022 cp - -rwxr-xr-x 1 root root 136916 Jan 5 01:20 dash - -rwxr-xr-x 1 root root 137160 Sep 20 2022 date - -rwxr-xr-x 1 root root 100364 Sep 20 2022 dd - -rwxr-xr-x 1 root root 108940 Sep 20 2022 df - -rwxr-xr-x 1 root root 162152 Sep 20 2022 dir - -rwxr-xr-x 1 root root 87760 Mar 22 22:20 dmesg - lrwxrwxrwx 1 root root 8 Dec 19 01:33 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Dec 19 01:33 domainname -> hostname - -rwxr-xr-x 1 root root 38760 Sep 20 2022 echo - -rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep - -rwxr-xr-x 1 root root 34664 Sep 20 2022 false - -rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep - -rwxr-xr-x 1 root root 84272 Mar 22 22:20 findmnt - -rwsr-xr-x 1 root root 30240 Mar 22 20:38 fusermount - -rwxr-xr-x 1 root root 218680 Jan 24 02:43 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 100952 Apr 9 2022 gzip - -rwxr-xr-x 1 root root 21916 Dec 19 01:33 hostname - -rwxr-xr-x 1 root root 75756 Sep 20 2022 ln - -rwxr-xr-x 1 root root 55600 Mar 22 23:43 login - -rwxr-xr-x 1 root root 162152 Sep 20 2022 ls - -rwxr-xr-x 1 root root 214568 Mar 22 22:20 lsblk - -rwxr-xr-x 1 root root 96328 Sep 20 2022 mkdir - -rwxr-xr-x 1 root root 84008 Sep 20 2022 mknod - -rwxr-xr-x 1 root root 38792 Sep 20 2022 mktemp - -rwxr-xr-x 1 root root 63016 Mar 22 22:20 more - -rwsr-xr-x 1 root root 58912 Mar 22 22:20 mount - -rwxr-xr-x 1 root root 13856 Mar 22 22:20 mountpoint - -rwxr-xr-x 1 root root 157932 Sep 20 2022 mv - lrwxrwxrwx 1 root root 8 Dec 19 01:33 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 2 18:25 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 38792 Sep 20 2022 pwd - lrwxrwxrwx 1 root root 4 Apr 23 09:24 rbash -> bash - -rwxr-xr-x 1 root root 51080 Sep 20 2022 readlink - -rwxr-xr-x 1 root root 75720 Sep 20 2022 rm - -rwxr-xr-x 1 root root 51080 Sep 20 2022 rmdir - -rwxr-xr-x 1 root root 22308 Nov 2 2022 run-parts - -rwxr-xr-x 1 root root 133224 Jan 5 07:55 sed - lrwxrwxrwx 1 root root 4 Jan 5 01:20 sh -> dash - -rwxr-xr-x 1 root root 38760 Sep 20 2022 sleep - -rwxr-xr-x 1 root root 87976 Sep 20 2022 stty - -rwsr-xr-x 1 root root 83492 Mar 22 22:20 su - -rwxr-xr-x 1 root root 38792 Sep 20 2022 sync - -rwxr-xr-x 1 root root 598456 Apr 6 02:25 tar - -rwxr-xr-x 1 root root 13860 Nov 2 2022 tempfile - -rwxr-xr-x 1 root root 120776 Sep 20 2022 touch - -rwxr-xr-x 1 root root 34664 Sep 20 2022 true - -rwxr-xr-x 1 root root 17892 Mar 22 20:38 ulockmgr_server - -rwsr-xr-x 1 root root 30236 Mar 22 22:20 umount - -rwxr-xr-x 1 root root 38760 Sep 20 2022 uname - -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress - -rwxr-xr-x 1 root root 162152 Sep 20 2022 vdir - -rwxr-xr-x 1 root root 71216 Mar 22 22:20 wdctl - lrwxrwxrwx 1 root root 8 Dec 19 01:33 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/20964/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1408088 Apr 24 2023 bash + -rwxr-xr-x 3 root root 38404 Sep 19 2022 bunzip2 + -rwxr-xr-x 3 root root 38404 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 38404 Sep 19 2022 bzip2 + -rwxr-xr-x 1 root root 17892 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 42920 Sep 21 2022 cat + -rwxr-xr-x 1 root root 79816 Sep 21 2022 chgrp + -rwxr-xr-x 1 root root 67496 Sep 21 2022 chmod + -rwxr-xr-x 1 root root 79816 Sep 21 2022 chown + -rwxr-xr-x 1 root root 162024 Sep 21 2022 cp + -rwxr-xr-x 1 root root 136916 Jan 6 2023 dash + -rwxr-xr-x 1 root root 137160 Sep 21 2022 date + -rwxr-xr-x 1 root root 100364 Sep 21 2022 dd + -rwxr-xr-x 1 root root 108940 Sep 21 2022 df + -rwxr-xr-x 1 root root 162152 Sep 21 2022 dir + -rwxr-xr-x 1 root root 87760 Mar 24 2023 dmesg + lrwxrwxrwx 1 root root 8 Dec 20 2022 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Dec 20 2022 domainname -> hostname + -rwxr-xr-x 1 root root 38760 Sep 21 2022 echo + -rwxr-xr-x 1 root root 41 Jan 25 2023 egrep + -rwxr-xr-x 1 root root 34664 Sep 21 2022 false + -rwxr-xr-x 1 root root 41 Jan 25 2023 fgrep + -rwxr-xr-x 1 root root 84272 Mar 24 2023 findmnt + -rwsr-xr-x 1 root root 30240 Mar 23 2023 fusermount + -rwxr-xr-x 1 root root 218680 Jan 25 2023 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 100952 Apr 10 2022 gzip + -rwxr-xr-x 1 root root 21916 Dec 20 2022 hostname + -rwxr-xr-x 1 root root 75756 Sep 21 2022 ln + -rwxr-xr-x 1 root root 55600 Mar 24 2023 login + -rwxr-xr-x 1 root root 162152 Sep 21 2022 ls + -rwxr-xr-x 1 root root 214568 Mar 24 2023 lsblk + -rwxr-xr-x 1 root root 96328 Sep 21 2022 mkdir + -rwxr-xr-x 1 root root 84008 Sep 21 2022 mknod + -rwxr-xr-x 1 root root 38792 Sep 21 2022 mktemp + -rwxr-xr-x 1 root root 63016 Mar 24 2023 more + -rwsr-xr-x 1 root root 58912 Mar 24 2023 mount + -rwxr-xr-x 1 root root 13856 Mar 24 2023 mountpoint + -rwxr-xr-x 1 root root 157932 Sep 21 2022 mv + lrwxrwxrwx 1 root root 8 Dec 20 2022 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 3 2023 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 38792 Sep 21 2022 pwd + lrwxrwxrwx 1 root root 4 Apr 24 2023 rbash -> bash + -rwxr-xr-x 1 root root 51080 Sep 21 2022 readlink + -rwxr-xr-x 1 root root 75720 Sep 21 2022 rm + -rwxr-xr-x 1 root root 51080 Sep 21 2022 rmdir + -rwxr-xr-x 1 root root 22308 Nov 3 2022 run-parts + -rwxr-xr-x 1 root root 133224 Jan 6 2023 sed + lrwxrwxrwx 1 root root 9 Jul 9 07:33 sh -> /bin/bash + -rwxr-xr-x 1 root root 38760 Sep 21 2022 sleep + -rwxr-xr-x 1 root root 87976 Sep 21 2022 stty + -rwsr-xr-x 1 root root 83492 Mar 24 2023 su + -rwxr-xr-x 1 root root 38792 Sep 21 2022 sync + -rwxr-xr-x 1 root root 598456 Apr 7 2023 tar + -rwxr-xr-x 1 root root 13860 Nov 3 2022 tempfile + -rwxr-xr-x 1 root root 120776 Sep 21 2022 touch + -rwxr-xr-x 1 root root 34664 Sep 21 2022 true + -rwxr-xr-x 1 root root 17892 Mar 23 2023 ulockmgr_server + -rwsr-xr-x 1 root root 30236 Mar 24 2023 umount + -rwxr-xr-x 1 root root 38760 Sep 21 2022 uname + -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress + -rwxr-xr-x 1 root root 162152 Sep 21 2022 vdir + -rwxr-xr-x 1 root root 71216 Mar 24 2023 wdctl + lrwxrwxrwx 1 root root 8 Dec 20 2022 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/74099/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -264,7 +296,7 @@ Get: 46 http://deb.debian.org/debian bookworm/main i386 liblzma-dev i386 5.4.1-0.2 [272 kB] Get: 47 http://deb.debian.org/debian bookworm/main i386 libssl-dev i386 3.0.9-1 [2487 kB] Get: 48 http://deb.debian.org/debian bookworm/main i386 zlib1g-dev i386 1:1.2.13.dfsg-1 [913 kB] -Fetched 27.6 MB in 1s (46.6 MB/s) +Fetched 27.6 MB in 0s (92.7 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (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 ... 19599 files and directories currently installed.) @@ -470,8 +502,19 @@ 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/htslib-1.16+ds/ && 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 > ../htslib_1.16+ds-3_source.changes +I: user script /srv/workspace/pbuilder/74099/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/74099/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/htslib-1.16+ds/ && 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 > ../htslib_1.16+ds-3_source.changes dpkg-buildpackage: info: source package htslib dpkg-buildpackage: info: source version 1.16+ds-3 dpkg-buildpackage: info: source distribution unstable @@ -484,7 +527,7 @@ debian/rules override_dh_auto_clean make[1]: Entering directory '/build/htslib-1.16+ds' dh_auto_clean - make -j8 distclean + make -j15 distclean make[2]: Entering directory '/build/htslib-1.16+ds' rm -f test/*.tmp test/*.tmp.* test/longrefs/*.tmp.* test/tabix/*.tmp.* test/tabix/FAIL* header-exports.txt shlib-exports-so.txt rm -f libhts.so libhts.so.* @@ -552,7 +595,7 @@ checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking for ranlib... ranlib -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 whether C compiler accepts -mssse3 -mpopcnt -msse4.1... yes checking whether C compiler accepts -mavx2... no @@ -618,7 +661,7 @@ CPPFLAGS="-I. -DSAMTOOLS=1 $(dpkg-buildflags --get CPPFLAGS)" \ PACKAGE_VERSION="1.16" \ libdir=/usr/lib/i386-linux-gnu - make -j8 "CFLAGS=-g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -msse -mfpmath=sse -ffat-lto-objects" "CPPFLAGS=-I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2" PACKAGE_VERSION=1.16 libdir=/usr/lib/i386-linux-gnu + make -j15 "CFLAGS=-g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -msse -mfpmath=sse -ffat-lto-objects" "CPPFLAGS=-I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2" PACKAGE_VERSION=1.16 libdir=/usr/lib/i386-linux-gnu make[2]: Entering directory '/build/htslib-1.16+ds' gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -msse -mfpmath=sse -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kfunc.o kfunc.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -msse -mfpmath=sse -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kstring.o kstring.c @@ -630,18 +673,18 @@ gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -msse -mfpmath=sse -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hfile.o hfile.c echo '#define HTS_VERSION_TEXT "1.16"' > version.h echo '#define HTS_CC "gcc"' > config_vars.h -echo '#define HTS_CPPFLAGS "-I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2"' >> config_vars.h -echo '#define HTS_CFLAGS "-g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -msse -mfpmath=sse -ffat-lto-objects"' \ -| sed 's/-ffile-prefix-map=[^ ]*=.//' \ ->> config_vars.h -echo '#define HTS_LDFLAGS "-Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic"' >> config_vars.h -echo '#define HTS_LIBS "-ldeflate -lhtscodecs -llzma -lbz2 -lz -lm "' >> config_vars.h gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -msse -mfpmath=sse -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hts_expr.o hts_expr.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -msse -mfpmath=sse -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hts_os.o hts_os.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -msse -mfpmath=sse -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o md5.o md5.c +echo '#define HTS_CPPFLAGS "-I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2"' >> config_vars.h gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -msse -mfpmath=sse -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o multipart.o multipart.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -msse -mfpmath=sse -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o probaln.o probaln.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -msse -mfpmath=sse -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o realn.o realn.c +echo '#define HTS_CFLAGS "-g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -msse -mfpmath=sse -ffat-lto-objects"' \ +| sed 's/-ffile-prefix-map=[^ ]*=.//' \ +>> config_vars.h +echo '#define HTS_LDFLAGS "-Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic"' >> config_vars.h +echo '#define HTS_LIBS "-ldeflate -lhtscodecs -llzma -lbz2 -lz -lm "' >> config_vars.h gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -msse -mfpmath=sse -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o regidx.o regidx.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -msse -mfpmath=sse -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o region.o region.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -msse -mfpmath=sse -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam.o sam.c @@ -706,6 +749,8 @@ gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -msse -mfpmath=sse -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tabix.o tabix.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -msse -mfpmath=sse -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile_libcurl.pico hfile_libcurl.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -msse -mfpmath=sse -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile_gcs.pico hfile_gcs.c +gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -msse -mfpmath=sse -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile_s3.pico hfile_s3.c +gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -msse -mfpmath=sse -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile_s3_write.pico hfile_s3_write.c hfile_libcurl.c: In function 'libcurl_open': hfile_libcurl.c:1335:9: warning: 'CURLINFO_CONTENT_LENGTH_DOWNLOAD' is deprecated: since 7.55.0. Use CURLINFO_CONTENT_LENGTH_DOWNLOAD_T [-Wdeprecated-declarations] 1335 | if (curl_easy_getinfo(fp->easy, CURLINFO_CONTENT_LENGTH_DOWNLOAD, @@ -714,8 +759,6 @@ /usr/include/i386-linux-gnu/curl/curl.h:2858:3: note: declared here 2858 | CURLINFO_CONTENT_LENGTH_DOWNLOAD | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -msse -mfpmath=sse -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile_s3.pico hfile_s3.c -gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -msse -mfpmath=sse -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile_s3_write.pico hfile_s3_write.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -msse -mfpmath=sse -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/hts_endian.o test/hts_endian.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -msse -mfpmath=sse -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/fieldarith.o test/fieldarith.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -msse -mfpmath=sse -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/hfile.o test/hfile.c @@ -795,7 +838,7 @@ if find . -name "FAIL*" > /dev/null ; then \ for file in $(find . -name "FAIL*"); do echo ${file}; cat ${file}; done && false ; \ fi - make -j8 test "TESTSUITEFLAGS=-j8 --verbose" VERBOSE=1 "CFLAGS=-g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -msse -mfpmath=sse -ffat-lto-objects" "CPPFLAGS=-I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2" PACKAGE_VERSION=1.16 libdir=/usr/lib/i386-linux-gnu + make -j15 test "TESTSUITEFLAGS=-j15 --verbose" VERBOSE=1 "CFLAGS=-g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -msse -mfpmath=sse -ffat-lto-objects" "CPPFLAGS=-I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2" PACKAGE_VERSION=1.16 libdir=/usr/lib/i386-linux-gnu make[2]: Entering directory '/build/htslib-1.16+ds' test/hts_endian test/test_expr @@ -985,203 +1028,203 @@ bgzip -b -I 4 threads: .. ok test_index: - /build/htslib-1.16+ds/test/test_view -l 0 -b -m 14 -x /tmp/NyHdtPrvgN/index.bam.csi /build/htslib-1.16+ds/test/index.sam > /tmp/NyHdtPrvgN/index.bam + /build/htslib-1.16+ds/test/test_view -l 0 -b -m 14 -x /tmp/LWNXXrg34W/index.bam.csi /build/htslib-1.16+ds/test/index.sam > /tmp/LWNXXrg34W/index.bam .. ok test_index: - /build/htslib-1.16+ds/test/test_index -c /tmp/NyHdtPrvgN/index.bam + /build/htslib-1.16+ds/test/test_index -c /tmp/LWNXXrg34W/index.bam .. ok test_index: - /build/htslib-1.16+ds/test/test_view -l 0 -b -m 0 -x /tmp/NyHdtPrvgN/index.bam.bai /build/htslib-1.16+ds/test/index.sam > /tmp/NyHdtPrvgN/index.bam + /build/htslib-1.16+ds/test/test_view -l 0 -b -m 0 -x /tmp/LWNXXrg34W/index.bam.bai /build/htslib-1.16+ds/test/index.sam > /tmp/LWNXXrg34W/index.bam .. ok test_index: - /build/htslib-1.16+ds/test/test_index -b /tmp/NyHdtPrvgN/index.bam + /build/htslib-1.16+ds/test/test_index -b /tmp/LWNXXrg34W/index.bam .. ok test_index: - /build/htslib-1.16+ds/test/test_view -l 0 -z -m 14 -x /tmp/NyHdtPrvgN/index.sam.gz.csi /build/htslib-1.16+ds/test/index.sam > /tmp/NyHdtPrvgN/index.sam.gz + /build/htslib-1.16+ds/test/test_view -l 0 -z -m 14 -x /tmp/LWNXXrg34W/index.sam.gz.csi /build/htslib-1.16+ds/test/index.sam > /tmp/LWNXXrg34W/index.sam.gz .. ok test_index: - /build/htslib-1.16+ds/test/test_index -c /tmp/NyHdtPrvgN/index.sam.gz + /build/htslib-1.16+ds/test/test_index -c /tmp/LWNXXrg34W/index.sam.gz .. ok test_index: - /build/htslib-1.16+ds/test/test_view -l 0 -z -m 0 -x /tmp/NyHdtPrvgN/index.sam.gz.bai /build/htslib-1.16+ds/test/index.sam > /tmp/NyHdtPrvgN/index.sam.gz + /build/htslib-1.16+ds/test/test_view -l 0 -z -m 0 -x /tmp/LWNXXrg34W/index.sam.gz.bai /build/htslib-1.16+ds/test/index.sam > /tmp/LWNXXrg34W/index.sam.gz .. ok test_index: - /build/htslib-1.16+ds/test/test_index -b /tmp/NyHdtPrvgN/index.sam.gz + /build/htslib-1.16+ds/test/test_index -b /tmp/LWNXXrg34W/index.sam.gz .. ok test_index: - /build/htslib-1.16+ds/test/test_view -l 0 -z -m 14 -x /tmp/NyHdtPrvgN/index.sam.gz.csi /build/htslib-1.16+ds/test/index_dos.sam > /tmp/NyHdtPrvgN/index.sam.gz + /build/htslib-1.16+ds/test/test_view -l 0 -z -m 14 -x /tmp/LWNXXrg34W/index.sam.gz.csi /build/htslib-1.16+ds/test/index_dos.sam > /tmp/LWNXXrg34W/index.sam.gz .. ok test_index: - /build/htslib-1.16+ds/test/test_index -c /tmp/NyHdtPrvgN/index.sam.gz + /build/htslib-1.16+ds/test/test_index -c /tmp/LWNXXrg34W/index.sam.gz .. ok test_index: - /build/htslib-1.16+ds/test/test_view -l 0 -z -m 0 -x /tmp/NyHdtPrvgN/index.sam.gz.bai /build/htslib-1.16+ds/test/index_dos.sam > /tmp/NyHdtPrvgN/index.sam.gz + /build/htslib-1.16+ds/test/test_view -l 0 -z -m 0 -x /tmp/LWNXXrg34W/index.sam.gz.bai /build/htslib-1.16+ds/test/index_dos.sam > /tmp/LWNXXrg34W/index.sam.gz .. ok test_index: - /build/htslib-1.16+ds/test/test_index -b /tmp/NyHdtPrvgN/index.sam.gz + /build/htslib-1.16+ds/test/test_index -b /tmp/LWNXXrg34W/index.sam.gz .. ok test_index: - /build/htslib-1.16+ds/test/test_view -l 0 -C -x /tmp/NyHdtPrvgN/index.cram.crai /build/htslib-1.16+ds/test/index.sam > /tmp/NyHdtPrvgN/index.cram + /build/htslib-1.16+ds/test/test_view -l 0 -C -x /tmp/LWNXXrg34W/index.cram.crai /build/htslib-1.16+ds/test/index.sam > /tmp/LWNXXrg34W/index.cram .. ok test_index: - /build/htslib-1.16+ds/test/test_index /tmp/NyHdtPrvgN/index.cram + /build/htslib-1.16+ds/test/test_index /tmp/LWNXXrg34W/index.cram .. ok test_index: - /build/htslib-1.16+ds/test/test_view -l 0 -b -m 14 -x /tmp/NyHdtPrvgN/index.bcf.csi /build/htslib-1.16+ds/test/index.vcf > /tmp/NyHdtPrvgN/index.bcf + /build/htslib-1.16+ds/test/test_view -l 0 -b -m 14 -x /tmp/LWNXXrg34W/index.bcf.csi /build/htslib-1.16+ds/test/index.vcf > /tmp/LWNXXrg34W/index.bcf .. ok test_index: - /build/htslib-1.16+ds/test/test_index -c /tmp/NyHdtPrvgN/index.bcf + /build/htslib-1.16+ds/test/test_index -c /tmp/LWNXXrg34W/index.bcf .. ok test_index: - /build/htslib-1.16+ds/test/test_view -l 0 -z -m 14 -x /tmp/NyHdtPrvgN/index.vcf.gz.csi /build/htslib-1.16+ds/test/index.vcf > /tmp/NyHdtPrvgN/index.vcf.gz + /build/htslib-1.16+ds/test/test_view -l 0 -z -m 14 -x /tmp/LWNXXrg34W/index.vcf.gz.csi /build/htslib-1.16+ds/test/index.vcf > /tmp/LWNXXrg34W/index.vcf.gz .. ok test_index: - /build/htslib-1.16+ds/test/test_index -c /tmp/NyHdtPrvgN/index.vcf.gz + /build/htslib-1.16+ds/test/test_index -c /tmp/LWNXXrg34W/index.vcf.gz .. ok test_index: - /build/htslib-1.16+ds/test/test_view -l 0 -z -m 0 -x /tmp/NyHdtPrvgN/index.vcf.gz.tbi /build/htslib-1.16+ds/test/index.vcf > /tmp/NyHdtPrvgN/index.vcf.gz + /build/htslib-1.16+ds/test/test_view -l 0 -z -m 0 -x /tmp/LWNXXrg34W/index.vcf.gz.tbi /build/htslib-1.16+ds/test/index.vcf > /tmp/LWNXXrg34W/index.vcf.gz .. ok test_index: - /build/htslib-1.16+ds/test/test_index -t /tmp/NyHdtPrvgN/index.vcf.gz + /build/htslib-1.16+ds/test/test_index -t /tmp/LWNXXrg34W/index.vcf.gz .. ok test_index: - /build/htslib-1.16+ds/tabix /tmp/NyHdtPrvgN/index.vcf.gz##idx##/tmp/NyHdtPrvgN/index.vcf.gz.tbi 1:10000060-10000060 + /build/htslib-1.16+ds/tabix /tmp/LWNXXrg34W/index.vcf.gz##idx##/tmp/LWNXXrg34W/index.vcf.gz.tbi 1:10000060-10000060 .. ok test_index: - /build/htslib-1.16+ds/test/test_view /tmp/NyHdtPrvgN/index2.bam 1:1000000-1000000 + /build/htslib-1.16+ds/test/test_view /tmp/LWNXXrg34W/index2.bam 1:1000000-1000000 .. ok test_index: - /build/htslib-1.16+ds/test/test_view /tmp/NyHdtPrvgN/index2.bam 1:2000000-2000000 + /build/htslib-1.16+ds/test/test_view /tmp/LWNXXrg34W/index2.bam 1:2000000-2000000 .. ok test_index: - /build/htslib-1.16+ds/test/test_view /tmp/NyHdtPrvgN/index2.bam 2:1000000-1000000 + /build/htslib-1.16+ds/test/test_view /tmp/LWNXXrg34W/index2.bam 2:1000000-1000000 .. ok test_index: - /build/htslib-1.16+ds/test/test_view /tmp/NyHdtPrvgN/index2.bam 2:2000000-2000000 + /build/htslib-1.16+ds/test/test_view /tmp/LWNXXrg34W/index2.bam 2:2000000-2000000 .. ok test_index: - /build/htslib-1.16+ds/test/test_view -@4 -l 0 -b -m 14 -x /tmp/NyHdtPrvgN/index.bam.csi /build/htslib-1.16+ds/test/index.sam > /tmp/NyHdtPrvgN/index.bam + /build/htslib-1.16+ds/test/test_view -@4 -l 0 -b -m 14 -x /tmp/LWNXXrg34W/index.bam.csi /build/htslib-1.16+ds/test/index.sam > /tmp/LWNXXrg34W/index.bam .. ok test_index: - /build/htslib-1.16+ds/test/test_index -c /tmp/NyHdtPrvgN/index.bam + /build/htslib-1.16+ds/test/test_index -c /tmp/LWNXXrg34W/index.bam .. ok test_index: - /build/htslib-1.16+ds/test/test_view -@4 -l 0 -b -m 0 -x /tmp/NyHdtPrvgN/index.bam.bai /build/htslib-1.16+ds/test/index.sam > /tmp/NyHdtPrvgN/index.bam + /build/htslib-1.16+ds/test/test_view -@4 -l 0 -b -m 0 -x /tmp/LWNXXrg34W/index.bam.bai /build/htslib-1.16+ds/test/index.sam > /tmp/LWNXXrg34W/index.bam .. ok test_index: - /build/htslib-1.16+ds/test/test_index -b /tmp/NyHdtPrvgN/index.bam + /build/htslib-1.16+ds/test/test_index -b /tmp/LWNXXrg34W/index.bam .. ok test_index: - /build/htslib-1.16+ds/test/test_view -@4 -l 0 -z -m 14 -x /tmp/NyHdtPrvgN/index.sam.gz.csi /build/htslib-1.16+ds/test/index.sam > /tmp/NyHdtPrvgN/index.sam.gz + /build/htslib-1.16+ds/test/test_view -@4 -l 0 -z -m 14 -x /tmp/LWNXXrg34W/index.sam.gz.csi /build/htslib-1.16+ds/test/index.sam > /tmp/LWNXXrg34W/index.sam.gz .. ok test_index: - /build/htslib-1.16+ds/test/test_index -c /tmp/NyHdtPrvgN/index.sam.gz + /build/htslib-1.16+ds/test/test_index -c /tmp/LWNXXrg34W/index.sam.gz .. ok test_index: - /build/htslib-1.16+ds/test/test_view -@4 -l 0 -z -m 0 -x /tmp/NyHdtPrvgN/index.sam.gz.bai /build/htslib-1.16+ds/test/index.sam > /tmp/NyHdtPrvgN/index.sam.gz + /build/htslib-1.16+ds/test/test_view -@4 -l 0 -z -m 0 -x /tmp/LWNXXrg34W/index.sam.gz.bai /build/htslib-1.16+ds/test/index.sam > /tmp/LWNXXrg34W/index.sam.gz .. ok test_index: - /build/htslib-1.16+ds/test/test_index -b /tmp/NyHdtPrvgN/index.sam.gz + /build/htslib-1.16+ds/test/test_index -b /tmp/LWNXXrg34W/index.sam.gz .. ok test_index: - /build/htslib-1.16+ds/test/test_view -@4 -l 0 -z -m 14 -x /tmp/NyHdtPrvgN/index.sam.gz.csi /build/htslib-1.16+ds/test/index_dos.sam > /tmp/NyHdtPrvgN/index.sam.gz + /build/htslib-1.16+ds/test/test_view -@4 -l 0 -z -m 14 -x /tmp/LWNXXrg34W/index.sam.gz.csi /build/htslib-1.16+ds/test/index_dos.sam > /tmp/LWNXXrg34W/index.sam.gz .. ok test_index: - /build/htslib-1.16+ds/test/test_index -c /tmp/NyHdtPrvgN/index.sam.gz + /build/htslib-1.16+ds/test/test_index -c /tmp/LWNXXrg34W/index.sam.gz .. ok test_index: - /build/htslib-1.16+ds/test/test_view -@4 -l 0 -z -m 0 -x /tmp/NyHdtPrvgN/index.sam.gz.bai /build/htslib-1.16+ds/test/index_dos.sam > /tmp/NyHdtPrvgN/index.sam.gz + /build/htslib-1.16+ds/test/test_view -@4 -l 0 -z -m 0 -x /tmp/LWNXXrg34W/index.sam.gz.bai /build/htslib-1.16+ds/test/index_dos.sam > /tmp/LWNXXrg34W/index.sam.gz .. ok test_index: - /build/htslib-1.16+ds/test/test_index -b /tmp/NyHdtPrvgN/index.sam.gz + /build/htslib-1.16+ds/test/test_index -b /tmp/LWNXXrg34W/index.sam.gz .. ok test_index: - /build/htslib-1.16+ds/test/test_view -@4 -l 0 -C -x /tmp/NyHdtPrvgN/index.cram.crai /build/htslib-1.16+ds/test/index.sam > /tmp/NyHdtPrvgN/index.cram + /build/htslib-1.16+ds/test/test_view -@4 -l 0 -C -x /tmp/LWNXXrg34W/index.cram.crai /build/htslib-1.16+ds/test/index.sam > /tmp/LWNXXrg34W/index.cram .. ok test_index: - /build/htslib-1.16+ds/test/test_index /tmp/NyHdtPrvgN/index.cram + /build/htslib-1.16+ds/test/test_index /tmp/LWNXXrg34W/index.cram .. ok test_index: - /build/htslib-1.16+ds/test/test_view -@4 -l 0 -b -m 14 -x /tmp/NyHdtPrvgN/index.bcf.csi /build/htslib-1.16+ds/test/index.vcf > /tmp/NyHdtPrvgN/index.bcf + /build/htslib-1.16+ds/test/test_view -@4 -l 0 -b -m 14 -x /tmp/LWNXXrg34W/index.bcf.csi /build/htslib-1.16+ds/test/index.vcf > /tmp/LWNXXrg34W/index.bcf .. ok test_index: - /build/htslib-1.16+ds/test/test_index -c /tmp/NyHdtPrvgN/index.bcf + /build/htslib-1.16+ds/test/test_index -c /tmp/LWNXXrg34W/index.bcf .. ok test_index: - /build/htslib-1.16+ds/test/test_view -@4 -l 0 -z -m 14 -x /tmp/NyHdtPrvgN/index.vcf.gz.csi /build/htslib-1.16+ds/test/index.vcf > /tmp/NyHdtPrvgN/index.vcf.gz + /build/htslib-1.16+ds/test/test_view -@4 -l 0 -z -m 14 -x /tmp/LWNXXrg34W/index.vcf.gz.csi /build/htslib-1.16+ds/test/index.vcf > /tmp/LWNXXrg34W/index.vcf.gz .. ok test_index: - /build/htslib-1.16+ds/test/test_index -c /tmp/NyHdtPrvgN/index.vcf.gz + /build/htslib-1.16+ds/test/test_index -c /tmp/LWNXXrg34W/index.vcf.gz .. ok test_index: - /build/htslib-1.16+ds/test/test_view -@4 -l 0 -z -m 0 -x /tmp/NyHdtPrvgN/index.vcf.gz.tbi /build/htslib-1.16+ds/test/index.vcf > /tmp/NyHdtPrvgN/index.vcf.gz + /build/htslib-1.16+ds/test/test_view -@4 -l 0 -z -m 0 -x /tmp/LWNXXrg34W/index.vcf.gz.tbi /build/htslib-1.16+ds/test/index.vcf > /tmp/LWNXXrg34W/index.vcf.gz .. ok test_index: - /build/htslib-1.16+ds/test/test_index -t /tmp/NyHdtPrvgN/index.vcf.gz + /build/htslib-1.16+ds/test/test_index -t /tmp/LWNXXrg34W/index.vcf.gz .. ok test_index: - /build/htslib-1.16+ds/tabix /tmp/NyHdtPrvgN/index.vcf.gz##idx##/tmp/NyHdtPrvgN/index.vcf.gz.tbi 1:10000060-10000060 + /build/htslib-1.16+ds/tabix /tmp/LWNXXrg34W/index.vcf.gz##idx##/tmp/LWNXXrg34W/index.vcf.gz.tbi 1:10000060-10000060 .. ok test_index: - /build/htslib-1.16+ds/test/test_view /tmp/NyHdtPrvgN/index2.bam 1:1000000-1000000 + /build/htslib-1.16+ds/test/test_view /tmp/LWNXXrg34W/index2.bam 1:1000000-1000000 .. ok test_index: - /build/htslib-1.16+ds/test/test_view /tmp/NyHdtPrvgN/index2.bam 1:2000000-2000000 + /build/htslib-1.16+ds/test/test_view /tmp/LWNXXrg34W/index2.bam 1:2000000-2000000 .. ok test_index: - /build/htslib-1.16+ds/test/test_view /tmp/NyHdtPrvgN/index2.bam 2:1000000-1000000 + /build/htslib-1.16+ds/test/test_view /tmp/LWNXXrg34W/index2.bam 2:1000000-1000000 .. ok test_index: - /build/htslib-1.16+ds/test/test_view /tmp/NyHdtPrvgN/index2.bam 2:2000000-2000000 + /build/htslib-1.16+ds/test/test_view /tmp/LWNXXrg34W/index2.bam 2:2000000-2000000 .. ok test_view testing multi-ref CRAM modes: @@ -2855,10 +2898,10 @@ .. ok test_vcf_api: - /build/htslib-1.16+ds/test/test-vcf-api /tmp/NyHdtPrvgN/test-vcf-api.bcf + /build/htslib-1.16+ds/test/test-vcf-api /tmp/LWNXXrg34W/test-vcf-api.bcf [W::bcf_record_check] Bad BCF record at 1:1: No REF allele [E::bcf_index_build3] TBI indices for BCF files are not supported -[E::idx_find_and_load] Could not retrieve index file for '/tmp/NyHdtPrvgN/test-vcf-api.bcf' +[E::idx_find_and_load] Could not retrieve index file for '/tmp/LWNXXrg34W/test-vcf-api.bcf' .. ok test_bcf2vcf: @@ -2866,7 +2909,7 @@ .. ok test_vcf_sweep: - /build/htslib-1.16+ds/test/test-vcf-sweep /tmp/NyHdtPrvgN/test-vcf-api.bcf + /build/htslib-1.16+ds/test/test-vcf-sweep /tmp/LWNXXrg34W/test-vcf-api.bcf .. ok test_vcf_various: @@ -2890,43 +2933,43 @@ .. ok test-bcf-sr: - /build/htslib-1.16+ds/test/test-bcf-sr.pl -t /tmp/NyHdtPrvgN -s 74452500 + /build/htslib-1.16+ds/test/test-bcf-sr.pl -t /tmp/LWNXXrg34W -s 74452500 .. ok test-bcf-sr: - /build/htslib-1.16+ds/test/test-bcf-sr.pl -t /tmp/NyHdtPrvgN -s 34270147 + /build/htslib-1.16+ds/test/test-bcf-sr.pl -t /tmp/LWNXXrg34W -s 34270147 .. ok test-bcf-sr: - /build/htslib-1.16+ds/test/test-bcf-sr.pl -t /tmp/NyHdtPrvgN -s 11108528 + /build/htslib-1.16+ds/test/test-bcf-sr.pl -t /tmp/LWNXXrg34W -s 11108528 .. ok test-bcf-sr: - /build/htslib-1.16+ds/test/test-bcf-sr.pl -t /tmp/NyHdtPrvgN -s 42233895 + /build/htslib-1.16+ds/test/test-bcf-sr.pl -t /tmp/LWNXXrg34W -s 42233895 .. ok test-bcf-sr: - /build/htslib-1.16+ds/test/test-bcf-sr.pl -t /tmp/NyHdtPrvgN -s 8111117 + /build/htslib-1.16+ds/test/test-bcf-sr.pl -t /tmp/LWNXXrg34W -s 8111117 .. ok test-bcf-sr: - /build/htslib-1.16+ds/test/test-bcf-sr.pl -t /tmp/NyHdtPrvgN -s 85644070 + /build/htslib-1.16+ds/test/test-bcf-sr.pl -t /tmp/LWNXXrg34W -s 85644070 .. ok test-bcf-sr: - /build/htslib-1.16+ds/test/test-bcf-sr.pl -t /tmp/NyHdtPrvgN -s 49879942 + /build/htslib-1.16+ds/test/test-bcf-sr.pl -t /tmp/LWNXXrg34W -s 49879942 .. ok test-bcf-sr: - /build/htslib-1.16+ds/test/test-bcf-sr.pl -t /tmp/NyHdtPrvgN -s 47881429 + /build/htslib-1.16+ds/test/test-bcf-sr.pl -t /tmp/LWNXXrg34W -s 47881429 .. ok test-bcf-sr: - /build/htslib-1.16+ds/test/test-bcf-sr.pl -t /tmp/NyHdtPrvgN -s 69081244 + /build/htslib-1.16+ds/test/test-bcf-sr.pl -t /tmp/LWNXXrg34W -s 69081244 .. ok test-bcf-sr: - /build/htslib-1.16+ds/test/test-bcf-sr.pl -t /tmp/NyHdtPrvgN -s 83459376 + /build/htslib-1.16+ds/test/test-bcf-sr.pl -t /tmp/LWNXXrg34W -s 83459376 .. ok test_command: @@ -2934,15 +2977,15 @@ .. ok test_convert_padded_header: - /build/htslib-1.16+ds/test/test_view -t ce.fa -C /tmp/NyHdtPrvgN/headernul0.bam + /build/htslib-1.16+ds/test/test_view -t ce.fa -C /tmp/LWNXXrg34W/headernul0.bam .. ok test_convert_padded_header: - /build/htslib-1.16+ds/test/test_view -t ce.fa -C /tmp/NyHdtPrvgN/headernul1.bam + /build/htslib-1.16+ds/test/test_view -t ce.fa -C /tmp/LWNXXrg34W/headernul1.bam .. ok test_convert_padded_header: - /build/htslib-1.16+ds/test/test_view -t ce.fa -C /tmp/NyHdtPrvgN/headernul678.bam + /build/htslib-1.16+ds/test/test_view -t ce.fa -C /tmp/LWNXXrg34W/headernul678.bam .. ok test_rebgzip: Alternate zlib/deflate library detected @@ -3005,7 +3048,7 @@ failed .. 0 make[2]: Leaving directory '/build/htslib-1.16+ds' - rm -fr -- /tmp/dh-xdg-rundir-LM_MVgNZ + rm -fr -- /tmp/dh-xdg-rundir-UNNLkUXd make[1]: Leaving directory '/build/htslib-1.16+ds' rm -f debian/libhts-dev.debhelper.log debian/libhts3.debhelper.log debian/tabix.debhelper.log debian/rules override_dh_auto_test-indep @@ -3028,7 +3071,7 @@ PACKAGE_VERSION="1.16" \ libdir=/usr/lib/i386-linux-gnu install -m0755 -d /build/htslib-1.16\+ds/debian/tmp - make -j8 install DESTDIR=/build/htslib-1.16\+ds/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr "CFLAGS=-g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -msse -mfpmath=sse -ffat-lto-objects" "CPPFLAGS=-I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2" PACKAGE_VERSION=1.16 libdir=/usr/lib/i386-linux-gnu + make -j15 install DESTDIR=/build/htslib-1.16\+ds/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr "CFLAGS=-g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -msse -mfpmath=sse -ffat-lto-objects" "CPPFLAGS=-I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2" PACKAGE_VERSION=1.16 libdir=/usr/lib/i386-linux-gnu make[2]: Entering directory '/build/htslib-1.16+ds' mkdir -p -m 755 /build/htslib-1.16+ds/debian/tmp/usr/bin /build/htslib-1.16+ds/debian/tmp/usr/include /build/htslib-1.16+ds/debian/tmp/usr/include/htslib /build/htslib-1.16+ds/debian/tmp/usr/lib/i386-linux-gnu /build/htslib-1.16+ds/debian/tmp/usr/share/man/man1 /build/htslib-1.16+ds/debian/tmp/usr/share/man/man5 /build/htslib-1.16+ds/debian/tmp/usr/share/man/man7 /build/htslib-1.16+ds/debian/tmp/usr/lib/i386-linux-gnu/pkgconfig if test -n "/usr/lib/i386-linux-gnu/htslib"; then mkdir -p -m 755 /build/htslib-1.16+ds/debian/tmp/usr/lib/i386-linux-gnu/htslib; fi @@ -3106,15 +3149,15 @@ debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/htslib-1.16+ds' dh_installchangelogs NEWS - install -m0755 -d debian/htslib-test/usr/share/doc/htslib-test - install -p -m0644 debian/.debhelper/generated/htslib-test/dh_installchangelogs.dch.trimmed debian/htslib-test/usr/share/doc/htslib-test/changelog.Debian - install -p -m0644 NEWS debian/htslib-test/usr/share/doc/htslib-test/changelog install -m0755 -d debian/libhts3/usr/share/doc/libhts3 install -p -m0644 debian/.debhelper/generated/libhts3/dh_installchangelogs.dch.trimmed debian/libhts3/usr/share/doc/libhts3/changelog.Debian install -p -m0644 NEWS debian/libhts3/usr/share/doc/libhts3/changelog install -m0755 -d debian/libhts-dev/usr/share/doc/libhts-dev install -p -m0644 debian/.debhelper/generated/libhts-dev/dh_installchangelogs.dch.trimmed debian/libhts-dev/usr/share/doc/libhts-dev/changelog.Debian install -p -m0644 NEWS debian/libhts-dev/usr/share/doc/libhts-dev/changelog + install -m0755 -d debian/htslib-test/usr/share/doc/htslib-test + install -p -m0644 debian/.debhelper/generated/htslib-test/dh_installchangelogs.dch.trimmed debian/htslib-test/usr/share/doc/htslib-test/changelog.Debian + install -p -m0644 NEWS debian/htslib-test/usr/share/doc/htslib-test/changelog install -m0755 -d debian/tabix/usr/share/doc/tabix install -p -m0644 debian/.debhelper/generated/tabix/dh_installchangelogs.dch.trimmed debian/tabix/usr/share/doc/tabix/changelog.Debian install -p -m0644 NEWS debian/tabix/usr/share/doc/tabix/changelog @@ -3129,26 +3172,26 @@ install -m0755 -d debian/tabix/usr/share/man/man1/ install -p -m0644 ./bgzip.1 debian/tabix/usr/share/man/man1/bgzip.1 man-recode --to-code UTF-8 --suffix .dh-new debian/libhts3/usr/share/man/man5/faidx.5 - man-recode --to-code UTF-8 --suffix .dh-new debian/libhts3/usr/share/man/man7/htslib-s3-plugin.7 - man-recode --to-code UTF-8 --suffix .dh-new debian/libhts3/usr/share/man/man5/vcf.5 man-recode --to-code UTF-8 --suffix .dh-new debian/libhts3/usr/share/man/man5/sam.5 + man-recode --to-code UTF-8 --suffix .dh-new debian/libhts3/usr/share/man/man5/vcf.5 + man-recode --to-code UTF-8 --suffix .dh-new debian/libhts3/usr/share/man/man7/htslib-s3-plugin.7 man-recode --to-code UTF-8 --suffix .dh-new debian/tabix/usr/share/man/man1/bgzip.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/tabix/usr/share/man/man1/tabix.1 man-recode --to-code UTF-8 --suffix .dh-new debian/tabix/usr/share/man/man1/htsfile.1 - mv debian/libhts3/usr/share/man/man7/htslib-s3-plugin.7.dh-new debian/libhts3/usr/share/man/man7/htslib-s3-plugin.7 - chmod 0644 -- debian/libhts3/usr/share/man/man7/htslib-s3-plugin.7 + man-recode --to-code UTF-8 --suffix .dh-new debian/tabix/usr/share/man/man1/tabix.1 mv debian/libhts3/usr/share/man/man5/faidx.5.dh-new debian/libhts3/usr/share/man/man5/faidx.5 chmod 0644 -- debian/libhts3/usr/share/man/man5/faidx.5 + mv debian/libhts3/usr/share/man/man5/vcf.5.dh-new debian/libhts3/usr/share/man/man5/vcf.5 + chmod 0644 -- debian/libhts3/usr/share/man/man5/vcf.5 + mv debian/libhts3/usr/share/man/man5/sam.5.dh-new debian/libhts3/usr/share/man/man5/sam.5 + chmod 0644 -- debian/libhts3/usr/share/man/man5/sam.5 mv debian/tabix/usr/share/man/man1/bgzip.1.dh-new debian/tabix/usr/share/man/man1/bgzip.1 chmod 0644 -- debian/tabix/usr/share/man/man1/bgzip.1 + mv debian/libhts3/usr/share/man/man7/htslib-s3-plugin.7.dh-new debian/libhts3/usr/share/man/man7/htslib-s3-plugin.7 + chmod 0644 -- debian/libhts3/usr/share/man/man7/htslib-s3-plugin.7 mv debian/tabix/usr/share/man/man1/htsfile.1.dh-new debian/tabix/usr/share/man/man1/htsfile.1 chmod 0644 -- debian/tabix/usr/share/man/man1/htsfile.1 - mv debian/libhts3/usr/share/man/man5/sam.5.dh-new debian/libhts3/usr/share/man/man5/sam.5 - chmod 0644 -- debian/libhts3/usr/share/man/man5/sam.5 mv debian/tabix/usr/share/man/man1/tabix.1.dh-new debian/tabix/usr/share/man/man1/tabix.1 chmod 0644 -- debian/tabix/usr/share/man/man1/tabix.1 - mv debian/libhts3/usr/share/man/man5/vcf.5.dh-new debian/libhts3/usr/share/man/man5/vcf.5 - chmod 0644 -- debian/libhts3/usr/share/man/man5/vcf.5 dh_lintian install -m0755 -d debian/htslib-test/usr/share/lintian/overrides install -p -m0644 debian/htslib-test.lintian-overrides debian/htslib-test/usr/share/lintian/overrides/htslib-test @@ -3167,19 +3210,19 @@ dh_strip_nondeterminism dh_compress cd debian/libhts3 + cd debian/libhts-dev cd debian/htslib-test cd debian/tabix - cd debian/libhts-dev + chmod a-x usr/share/doc/libhts-dev/README.large_positions.md usr/share/doc/libhts-dev/changelog usr/share/doc/libhts-dev/changelog.Debian chmod a-x usr/share/doc/htslib-test/changelog usr/share/doc/htslib-test/changelog.Debian - gzip -9nf usr/share/doc/htslib-test/changelog usr/share/doc/htslib-test/changelog.Debian - chmod a-x usr/share/doc/tabix/changelog usr/share/doc/tabix/changelog.Debian usr/share/man/man1/bgzip.1 usr/share/man/man1/htsfile.1 usr/share/man/man1/tabix.1 chmod a-x usr/share/doc/libhts3/changelog usr/share/doc/libhts3/changelog.Debian usr/share/man/man5/faidx.5 usr/share/man/man5/sam.5 usr/share/man/man5/vcf.5 usr/share/man/man7/htslib-s3-plugin.7 + chmod a-x usr/share/doc/tabix/changelog usr/share/doc/tabix/changelog.Debian usr/share/man/man1/bgzip.1 usr/share/man/man1/htsfile.1 usr/share/man/man1/tabix.1 + gzip -9nf usr/share/doc/libhts-dev/README.large_positions.md usr/share/doc/libhts-dev/changelog usr/share/doc/libhts-dev/changelog.Debian + gzip -9nf usr/share/doc/htslib-test/changelog usr/share/doc/htslib-test/changelog.Debian + gzip -9nf usr/share/doc/libhts3/changelog usr/share/doc/libhts3/changelog.Debian usr/share/man/man5/faidx.5 usr/share/man/man5/sam.5 usr/share/man/man5/vcf.5 usr/share/man/man7/htslib-s3-plugin.7 gzip -9nf usr/share/doc/tabix/changelog usr/share/doc/tabix/changelog.Debian usr/share/man/man1/bgzip.1 usr/share/man/man1/htsfile.1 usr/share/man/man1/tabix.1 cd '/build/htslib-1.16+ds' - gzip -9nf usr/share/doc/libhts3/changelog usr/share/doc/libhts3/changelog.Debian usr/share/man/man5/faidx.5 usr/share/man/man5/sam.5 usr/share/man/man5/vcf.5 usr/share/man/man7/htslib-s3-plugin.7 cd '/build/htslib-1.16+ds' - chmod a-x usr/share/doc/libhts-dev/README.large_positions.md usr/share/doc/libhts-dev/changelog usr/share/doc/libhts-dev/changelog.Debian - gzip -9nf usr/share/doc/libhts-dev/README.large_positions.md usr/share/doc/libhts-dev/changelog usr/share/doc/libhts-dev/changelog.Debian cd '/build/htslib-1.16+ds' cd '/build/htslib-1.16+ds' rm -f debian/htslib-test.debhelper.log debian/libhts-dev.debhelper.log debian/libhts3.debhelper.log debian/tabix.debhelper.log @@ -3191,23 +3234,23 @@ find debian/htslib-test ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/tabix ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/libhts3/usr/share/doc -type f -a -true -a ! -regex 'debian/libhts3/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 - find debian/tabix/usr/share/doc -type f -a -true -a ! -regex 'debian/tabix/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libhts-dev/usr/share/doc -type f -a -true -a ! -regex 'debian/libhts-dev/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 - find debian/libhts3/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 + find debian/tabix/usr/share/doc -type f -a -true -a ! -regex 'debian/tabix/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/htslib-test/usr/share/doc -type f -a -true -a ! -regex 'debian/htslib-test/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 - find debian/tabix/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 - find debian/libhts3/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 + find debian/libhts3/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/libhts-dev/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 + find debian/tabix/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/htslib-test/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 - find debian/libhts3 -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 - find debian/tabix/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 + find debian/libhts3/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libhts-dev/usr/include -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 + find debian/tabix/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/htslib-test/usr/share/lintian/overrides -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 + find debian/libhts3 -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/tabix -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 - find debian/libhts3/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w find debian/libhts-dev -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/htslib-test -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/tabix/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x + find debian/libhts3/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w find debian/libhts-dev/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w find debian -name simple_test_driver.sh -exec chmod +x \{\} \; make[1]: Leaving directory '/build/htslib-1.16+ds' @@ -3235,21 +3278,16 @@ dh_strip -Xlibhts.a install -m0755 -d debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/5e objcopy --only-keep-debug --compress-debug-sections debian/libhts3/usr/lib/i386-linux-gnu/libhts.so.1.16 debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/5e/9132f77100d9eec3d1527ec3f03684c9b1af94.debug - install -m0755 -d debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/d4 - objcopy --only-keep-debug --compress-debug-sections debian/tabix/usr/bin/bgzip debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/d4/cced750e69c3f0f8be307f845c31a760b038a3.debug - chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/d4/cced750e69c3f0f8be307f845c31a760b038a3.debug - strip --remove-section=.comment --remove-section=.note debian/tabix/usr/bin/bgzip - objcopy --add-gnu-debuglink debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/d4/cced750e69c3f0f8be307f845c31a760b038a3.debug debian/tabix/usr/bin/bgzip install -m0755 -d debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/be objcopy --only-keep-debug --compress-debug-sections debian/tabix/usr/bin/htsfile debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/be/6d060f414203283801621e4739b22c12584772.debug + chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/be/6d060f414203283801621e4739b22c12584772.debug + strip --remove-section=.comment --remove-section=.note debian/tabix/usr/bin/htsfile + objcopy --add-gnu-debuglink debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/be/6d060f414203283801621e4739b22c12584772.debug debian/tabix/usr/bin/htsfile + install -m0755 -d debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/fe + objcopy --only-keep-debug --compress-debug-sections debian/tabix/usr/bin/tabix debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/fe/2c96bc050913283b9e883e8b8d117acc8bd497.debug chmod 0644 -- debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/5e/9132f77100d9eec3d1527ec3f03684c9b1af94.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libhts3/usr/lib/i386-linux-gnu/libhts.so.1.16 objcopy --add-gnu-debuglink debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/5e/9132f77100d9eec3d1527ec3f03684c9b1af94.debug debian/libhts3/usr/lib/i386-linux-gnu/libhts.so.1.16 - install -m0755 -d debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/95 - objcopy --only-keep-debug --compress-debug-sections debian/libhts3/usr/lib/i386-linux-gnu/htslib/hfile_s3_write.so debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/95/d42a2a3b8e2b75bb5fa83d888eb4235b825f76.debug - chmod 0644 -- debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/95/d42a2a3b8e2b75bb5fa83d888eb4235b825f76.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libhts3/usr/lib/i386-linux-gnu/htslib/hfile_s3_write.so - objcopy --add-gnu-debuglink debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/95/d42a2a3b8e2b75bb5fa83d888eb4235b825f76.debug debian/libhts3/usr/lib/i386-linux-gnu/htslib/hfile_s3_write.so install -m0755 -d debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/a1 objcopy --only-keep-debug --compress-debug-sections debian/libhts3/usr/lib/i386-linux-gnu/htslib/hfile_s3.so debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/a1/f91b9971e14a14a2d2f1e4844043484b23e39f.debug chmod 0644 -- debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/a1/f91b9971e14a14a2d2f1e4844043484b23e39f.debug @@ -3260,6 +3298,11 @@ chmod 0644 -- debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/80/eaa0749198dfddb4c9b66e9958c9837072ca17.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libhts3/usr/lib/i386-linux-gnu/htslib/hfile_gcs.so objcopy --add-gnu-debuglink debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/80/eaa0749198dfddb4c9b66e9958c9837072ca17.debug debian/libhts3/usr/lib/i386-linux-gnu/htslib/hfile_gcs.so + install -m0755 -d debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/95 + objcopy --only-keep-debug --compress-debug-sections debian/libhts3/usr/lib/i386-linux-gnu/htslib/hfile_s3_write.so debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/95/d42a2a3b8e2b75bb5fa83d888eb4235b825f76.debug + chmod 0644 -- debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/95/d42a2a3b8e2b75bb5fa83d888eb4235b825f76.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libhts3/usr/lib/i386-linux-gnu/htslib/hfile_s3_write.so + objcopy --add-gnu-debuglink debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/95/d42a2a3b8e2b75bb5fa83d888eb4235b825f76.debug debian/libhts3/usr/lib/i386-linux-gnu/htslib/hfile_s3_write.so install -m0755 -d debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/2c objcopy --only-keep-debug --compress-debug-sections debian/libhts3/usr/lib/i386-linux-gnu/htslib/hfile_libcurl.so debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/2c/e39c78ecd9fe399c0ab0060628b865aaf97461.debug chmod 0644 -- debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/2c/e39c78ecd9fe399c0ab0060628b865aaf97461.debug @@ -3272,14 +3315,14 @@ install -m0755 -d debian/.debhelper/libhts3/dbgsym-root/usr/share/doc ln -s libhts3 debian/.debhelper/libhts3/dbgsym-root/usr/share/doc/libhts3-dbgsym install -m0755 -d debian/.debhelper/libhts3 - chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/be/6d060f414203283801621e4739b22c12584772.debug - strip --remove-section=.comment --remove-section=.note debian/tabix/usr/bin/htsfile - objcopy --add-gnu-debuglink debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/be/6d060f414203283801621e4739b22c12584772.debug debian/tabix/usr/bin/htsfile - install -m0755 -d debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/fe - objcopy --only-keep-debug --compress-debug-sections debian/tabix/usr/bin/tabix debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/fe/2c96bc050913283b9e883e8b8d117acc8bd497.debug chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/fe/2c96bc050913283b9e883e8b8d117acc8bd497.debug strip --remove-section=.comment --remove-section=.note debian/tabix/usr/bin/tabix objcopy --add-gnu-debuglink debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/fe/2c96bc050913283b9e883e8b8d117acc8bd497.debug debian/tabix/usr/bin/tabix + install -m0755 -d debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/d4 + objcopy --only-keep-debug --compress-debug-sections debian/tabix/usr/bin/bgzip debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/d4/cced750e69c3f0f8be307f845c31a760b038a3.debug + chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/d4/cced750e69c3f0f8be307f845c31a760b038a3.debug + strip --remove-section=.comment --remove-section=.note debian/tabix/usr/bin/bgzip + objcopy --add-gnu-debuglink debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/d4/cced750e69c3f0f8be307f845c31a760b038a3.debug debian/tabix/usr/bin/bgzip install -m0755 -d debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.dwz cp --reflink=auto -a debian/tabix/usr/lib/debug/.dwz/i386-linux-gnu debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.dwz rm -fr debian/tabix/usr/lib/debug/.dwz @@ -3299,9 +3342,9 @@ rm -f debian/tabix/DEBIAN/shlibs dh_shlibdeps -a install -m0755 -d debian/tabix/DEBIAN - dpkg-shlibdeps -Tdebian/tabix.substvars debian/tabix/usr/bin/bgzip debian/tabix/usr/bin/htsfile debian/tabix/usr/bin/tabix + dpkg-shlibdeps -Tdebian/tabix.substvars debian/tabix/usr/bin/htsfile debian/tabix/usr/bin/tabix debian/tabix/usr/bin/bgzip install -m0755 -d debian/libhts3/DEBIAN - dpkg-shlibdeps -Tdebian/libhts3.substvars debian/libhts3/usr/lib/i386-linux-gnu/libhts.so.1.16 debian/libhts3/usr/lib/i386-linux-gnu/htslib/hfile_s3_write.so debian/libhts3/usr/lib/i386-linux-gnu/htslib/hfile_s3.so debian/libhts3/usr/lib/i386-linux-gnu/htslib/hfile_gcs.so debian/libhts3/usr/lib/i386-linux-gnu/htslib/hfile_libcurl.so + dpkg-shlibdeps -Tdebian/libhts3.substvars debian/libhts3/usr/lib/i386-linux-gnu/libhts.so.1.16 debian/libhts3/usr/lib/i386-linux-gnu/htslib/hfile_s3.so debian/libhts3/usr/lib/i386-linux-gnu/htslib/hfile_gcs.so debian/libhts3/usr/lib/i386-linux-gnu/htslib/hfile_s3_write.so debian/libhts3/usr/lib/i386-linux-gnu/htslib/hfile_libcurl.so dh_installdeb install -m0755 -d debian/libhts3/DEBIAN install -p -m0644 debian/.debhelper/generated/libhts3/triggers debian/libhts3/DEBIAN/triggers @@ -3327,32 +3370,32 @@ echo misc:Pre-Depends= >> debian/tabix.substvars install -m0755 -d debian/.debhelper/tabix/dbgsym-root/DEBIAN dpkg-gencontrol -ptabix -ldebian/changelog -Tdebian/tabix.substvars -Pdebian/.debhelper/tabix/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -UBuilt-Using -DAuto-Built-Package=debug-symbols -UProtected -DPackage=tabix-dbgsym "-DDepends=tabix (= \${binary:Version})" "-DDescription=debug symbols for tabix" "-DBuild-Ids=be6d060f414203283801621e4739b22c12584772 d4cced750e69c3f0f8be307f845c31a760b038a3 fe2c96bc050913283b9e883e8b8d117acc8bd497" -DSection=debug -UMulti-Arch -UReplaces -UBreaks - chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/DEBIAN/control - dpkg-gencontrol -ptabix -ldebian/changelog -Tdebian/tabix.substvars -Pdebian/tabix - chmod 0644 -- debian/htslib-test/DEBIAN/control chmod 0644 -- debian/libhts-dev/DEBIAN/control + chmod 0644 -- debian/htslib-test/DEBIAN/control chmod 0644 -- debian/.debhelper/libhts3/dbgsym-root/DEBIAN/control dpkg-gencontrol -plibhts3 -ldebian/changelog -Tdebian/libhts3.substvars -Pdebian/libhts3 - chmod 0644 -- debian/tabix/DEBIAN/control + chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/DEBIAN/control + dpkg-gencontrol -ptabix -ldebian/changelog -Tdebian/tabix.substvars -Pdebian/tabix chmod 0644 -- debian/libhts3/DEBIAN/control + chmod 0644 -- debian/tabix/DEBIAN/control dh_md5sums install -m0755 -d debian/libhts3/DEBIAN - install -m0755 -d debian/htslib-test/DEBIAN - cd debian/libhts3 >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums install -m0755 -d debian/libhts-dev/DEBIAN + install -m0755 -d debian/htslib-test/DEBIAN install -m0755 -d debian/tabix/DEBIAN - cd debian/htslib-test >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums + cd debian/libhts3 >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/libhts-dev >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/tabix >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums - chmod 0644 -- debian/tabix/DEBIAN/md5sums - install -m0755 -d debian/.debhelper/tabix/dbgsym-root/DEBIAN + cd debian/htslib-test >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/libhts3/DEBIAN/md5sums install -m0755 -d debian/.debhelper/libhts3/dbgsym-root/DEBIAN - cd debian/.debhelper/tabix/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/.debhelper/libhts3/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums + chmod 0644 -- debian/tabix/DEBIAN/md5sums + install -m0755 -d debian/.debhelper/tabix/dbgsym-root/DEBIAN + cd debian/.debhelper/tabix/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums + chmod 0644 -- debian/.debhelper/libhts3/dbgsym-root/DEBIAN/md5sums chmod 0644 -- debian/libhts-dev/DEBIAN/md5sums chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/DEBIAN/md5sums - chmod 0644 -- debian/.debhelper/libhts3/dbgsym-root/DEBIAN/md5sums chmod 0644 -- debian/htslib-test/DEBIAN/md5sums dh_builddeb dpkg-deb --root-owner-group --build debian/libhts3 .. @@ -3363,8 +3406,8 @@ dpkg-deb --root-owner-group --build debian/.debhelper/tabix/dbgsym-root .. dpkg-deb: building package 'libhts3' in '../libhts3_1.16+ds-3_i386.deb'. dpkg-deb: building package 'libhts3-dbgsym' in '../libhts3-dbgsym_1.16+ds-3_i386.deb'. -dpkg-deb: building package 'htslib-test' in '../htslib-test_1.16+ds-3_all.deb'. dpkg-deb: building package 'libhts-dev' in '../libhts-dev_1.16+ds-3_i386.deb'. +dpkg-deb: building package 'htslib-test' in '../htslib-test_1.16+ds-3_all.deb'. dpkg-deb: building package 'tabix' in '../tabix_1.16+ds-3_i386.deb'. dpkg-deb: building package 'tabix-dbgsym' in '../tabix-dbgsym_1.16+ds-3_i386.deb'. dpkg-genbuildinfo --build=binary -O../htslib_1.16+ds-3_i386.buildinfo @@ -3375,12 +3418,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/74099/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/74099/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/20964 and its subdirectories -I: Current time: Mon Jun 5 23:10:38 -12 2023 -I: pbuilder-time-stamp: 1686049838 +I: removing directory /srv/workspace/pbuilder/74099 and its subdirectories +I: Current time: Tue Jul 9 07:35:04 +14 2024 +I: pbuilder-time-stamp: 1720460104