Diff of the two buildlogs: -- --- b1/build.log 2021-05-20 10:12:13.704963693 +0000 +++ b2/build.log 2021-05-20 10:21:59.462128675 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Jun 22 04:32:43 -12 2022 -I: pbuilder-time-stamp: 1655915563 +I: Current time: Fri May 21 00:12:22 +14 2021 +I: pbuilder-time-stamp: 1621505542 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration @@ -17,8 +17,8 @@ I: copying [./subread_2.0.1+dfsg-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig.9fKJ7PFu/trustedkeys.kbx': General error -gpgv: Signature made Fri May 22 05:56:50 2020 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.lCpeFjCZ/trustedkeys.kbx': General error +gpgv: Signature made Sat May 23 07:56:50 2020 +14 gpgv: using RSA key 84C1977A89E7EFED3E5CA62E2FD8BEDAC020EED1 gpgv: issuer "moeller@debian.org" gpgv: Can't check signature: No public key @@ -34,137 +34,171 @@ dpkg-source: info: applying gcc10.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/15088/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/16409/tmp/hooks/D01_modify_environment starting +debug: Running on ionos12-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 +Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' +Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' +Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' +Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by 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/16409/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/16409/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,-fixfilepath parallel=18' - DISTRIBUTION='' - HOME='/root' - HOST_ARCH='i386' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") + BASH_VERSION='5.1.4(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,-fixfilepath parallel=10' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - INVOCATION_ID='7833738b5d834e97b5de5df2cefe78ac' - 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='15088' - PS1='# ' - PS2='> ' + INVOCATION_ID=61542d9678324d0282e28b8a0c01d821 + 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=16409 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/tmp.yFzUywYJBf/pbuilderrc_lh0j --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.yFzUywYJBf/b1 --logfile b1/build.log subread_2.0.1+dfsg-1.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://85.184.249.68:3128' + 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/tmp.yFzUywYJBf/pbuilderrc_AGdE --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.yFzUywYJBf/b2 --logfile b2/build.log --extrapackages usrmerge subread_2.0.1+dfsg-1.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://78.137.99.97:3128 I: uname -a - Linux ionos6-i386 4.19.0-16-amd64 #1 SMP Debian 4.19.181-1 (2021-03-19) x86_64 GNU/Linux + Linux i-capture-the-hostname 4.19.0-16-686-pae #1 SMP Debian 4.19.181-1 (2021-03-19) i686 GNU/Linux I: ls -l /bin - total 5776 - -rwxr-xr-x 1 root root 1367848 Feb 24 2021 bash - -rwxr-xr-x 3 root root 38280 Jul 20 2020 bunzip2 - -rwxr-xr-x 3 root root 38280 Jul 20 2020 bzcat - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep - -rwxr-xr-x 3 root root 38280 Jul 20 2020 bzip2 - -rwxr-xr-x 1 root root 17768 Jul 20 2020 bzip2recover - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore - -rwxr-xr-x 1 root root 38824 Sep 22 2020 cat - -rwxr-xr-x 1 root root 71624 Sep 22 2020 chgrp - -rwxr-xr-x 1 root root 67528 Sep 22 2020 chmod - -rwxr-xr-x 1 root root 75752 Sep 22 2020 chown - -rwxr-xr-x 1 root root 157960 Sep 22 2020 cp - -rwxr-xr-x 1 root root 128724 Dec 10 2020 dash - -rwxr-xr-x 1 root root 124904 Sep 22 2020 date - -rwxr-xr-x 1 root root 92172 Sep 22 2020 dd - -rwxr-xr-x 1 root root 100752 Sep 22 2020 df - -rwxr-xr-x 1 root root 153964 Sep 22 2020 dir - -rwxr-xr-x 1 root root 83644 Feb 7 2021 dmesg - lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname - -rwxr-xr-x 1 root root 34664 Sep 22 2020 echo - -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep - -rwxr-xr-x 1 root root 34664 Sep 22 2020 false - -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep - -rwxr-xr-x 1 root root 71928 Feb 7 2021 findmnt - -rwsr-xr-x 1 root root 30112 Feb 26 2021 fusermount - -rwxr-xr-x 1 root root 210488 Nov 9 2020 grep - -rwxr-xr-x 2 root root 2346 Mar 2 2021 gunzip - -rwxr-xr-x 1 root root 6376 Mar 2 2021 gzexe - -rwxr-xr-x 1 root root 100952 Mar 2 2021 gzip - -rwxr-xr-x 1 root root 21916 Nov 6 2019 hostname - -rwxr-xr-x 1 root root 83980 Sep 22 2020 ln - -rwxr-xr-x 1 root root 55572 Feb 7 2020 login - -rwxr-xr-x 1 root root 153964 Sep 22 2020 ls - -rwxr-xr-x 1 root root 153124 Feb 7 2021 lsblk - -rwxr-xr-x 1 root root 96328 Sep 22 2020 mkdir - -rwxr-xr-x 1 root root 79912 Sep 22 2020 mknod - -rwxr-xr-x 1 root root 47048 Sep 22 2020 mktemp - -rwxr-xr-x 1 root root 58920 Feb 7 2021 more - -rwsr-xr-x 1 root root 50720 Feb 7 2021 mount - -rwxr-xr-x 1 root root 13856 Feb 7 2021 mountpoint - -rwxr-xr-x 1 root root 157996 Sep 22 2020 mv - lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 18 2021 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 38824 Sep 22 2020 pwd - lrwxrwxrwx 1 root root 4 Feb 24 2021 rbash -> bash - -rwxr-xr-x 1 root root 46984 Sep 22 2020 readlink - -rwxr-xr-x 1 root root 75720 Sep 22 2020 rm - -rwxr-xr-x 1 root root 46984 Sep 22 2020 rmdir - -rwxr-xr-x 1 root root 22292 Sep 27 2020 run-parts - -rwxr-xr-x 1 root root 125036 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Jun 21 03:47 sh -> dash - -rwxr-xr-x 1 root root 34696 Sep 22 2020 sleep - -rwxr-xr-x 1 root root 83880 Sep 22 2020 stty - -rwsr-xr-x 1 root root 79396 Feb 7 2021 su - -rwxr-xr-x 1 root root 34696 Sep 22 2020 sync - -rwxr-xr-x 1 root root 602584 Feb 16 2021 tar - -rwxr-xr-x 1 root root 13860 Sep 27 2020 tempfile - -rwxr-xr-x 1 root root 108520 Sep 22 2020 touch - -rwxr-xr-x 1 root root 34664 Sep 22 2020 true - -rwxr-xr-x 1 root root 17768 Feb 26 2021 ulockmgr_server - -rwsr-xr-x 1 root root 30236 Feb 7 2021 umount - -rwxr-xr-x 1 root root 34664 Sep 22 2020 uname - -rwxr-xr-x 2 root root 2346 Mar 2 2021 uncompress - -rwxr-xr-x 1 root root 153964 Sep 22 2020 vdir - -rwxr-xr-x 1 root root 63024 Feb 7 2021 wdctl - lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Mar 2 2021 zcat - -rwxr-xr-x 1 root root 1678 Mar 2 2021 zcmp - -rwxr-xr-x 1 root root 5880 Mar 2 2021 zdiff - -rwxr-xr-x 1 root root 29 Mar 2 2021 zegrep - -rwxr-xr-x 1 root root 29 Mar 2 2021 zfgrep - -rwxr-xr-x 1 root root 2081 Mar 2 2021 zforce - -rwxr-xr-x 1 root root 7585 Mar 2 2021 zgrep - -rwxr-xr-x 1 root root 2206 Mar 2 2021 zless - -rwxr-xr-x 1 root root 1842 Mar 2 2021 zmore - -rwxr-xr-x 1 root root 4553 Mar 2 2021 znew -I: user script /srv/workspace/pbuilder/15088/tmp/hooks/D02_print_environment finished + total 5792 + -rwxr-xr-x 1 root root 1367848 Feb 25 10:57 bash + -rwxr-xr-x 3 root root 38280 Jul 21 2020 bunzip2 + -rwxr-xr-x 3 root root 38280 Jul 21 2020 bzcat + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep + -rwxr-xr-x 3 root root 38280 Jul 21 2020 bzip2 + -rwxr-xr-x 1 root root 17768 Jul 21 2020 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore + -rwxr-xr-x 1 root root 38824 Sep 23 2020 cat + -rwxr-xr-x 1 root root 71624 Sep 23 2020 chgrp + -rwxr-xr-x 1 root root 67528 Sep 23 2020 chmod + -rwxr-xr-x 1 root root 75752 Sep 23 2020 chown + -rwxr-xr-x 1 root root 157960 Sep 23 2020 cp + -rwxr-xr-x 1 root root 128724 Dec 11 03:23 dash + -rwxr-xr-x 1 root root 124904 Sep 23 2020 date + -rwxr-xr-x 1 root root 92172 Sep 23 2020 dd + -rwxr-xr-x 1 root root 100752 Sep 23 2020 df + -rwxr-xr-x 1 root root 153964 Sep 23 2020 dir + -rwxr-xr-x 1 root root 83644 Feb 8 04:38 dmesg + lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname + -rwxr-xr-x 1 root root 34664 Sep 23 2020 echo + -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep + -rwxr-xr-x 1 root root 34664 Sep 23 2020 false + -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep + -rwxr-xr-x 1 root root 71928 Feb 8 04:38 findmnt + -rwsr-xr-x 1 root root 30112 Feb 27 06:12 fusermount + -rwxr-xr-x 1 root root 210488 Nov 10 2020 grep + -rwxr-xr-x 2 root root 2346 Mar 3 13:30 gunzip + -rwxr-xr-x 1 root root 6376 Mar 3 13:30 gzexe + -rwxr-xr-x 1 root root 100952 Mar 3 13:30 gzip + -rwxr-xr-x 1 root root 21916 Nov 8 2019 hostname + -rwxr-xr-x 1 root root 83980 Sep 23 2020 ln + -rwxr-xr-x 1 root root 55572 Feb 8 2020 login + -rwxr-xr-x 1 root root 153964 Sep 23 2020 ls + -rwxr-xr-x 1 root root 153124 Feb 8 04:38 lsblk + -rwxr-xr-x 1 root root 96328 Sep 23 2020 mkdir + -rwxr-xr-x 1 root root 79912 Sep 23 2020 mknod + -rwxr-xr-x 1 root root 47048 Sep 23 2020 mktemp + -rwxr-xr-x 1 root root 58920 Feb 8 04:38 more + -rwsr-xr-x 1 root root 50720 Feb 8 04:38 mount + -rwxr-xr-x 1 root root 13856 Feb 8 04:38 mountpoint + -rwxr-xr-x 1 root root 157996 Sep 23 2020 mv + lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 19 05:38 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 38824 Sep 23 2020 pwd + lrwxrwxrwx 1 root root 4 Feb 25 10:57 rbash -> bash + -rwxr-xr-x 1 root root 46984 Sep 23 2020 readlink + -rwxr-xr-x 1 root root 75720 Sep 23 2020 rm + -rwxr-xr-x 1 root root 46984 Sep 23 2020 rmdir + -rwxr-xr-x 1 root root 22292 Sep 28 2020 run-parts + -rwxr-xr-x 1 root root 125036 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 May 21 00:16 sh -> bash + lrwxrwxrwx 1 root root 4 May 20 23:26 sh.distrib -> dash + -rwxr-xr-x 1 root root 34696 Sep 23 2020 sleep + -rwxr-xr-x 1 root root 83880 Sep 23 2020 stty + -rwsr-xr-x 1 root root 79396 Feb 8 04:38 su + -rwxr-xr-x 1 root root 34696 Sep 23 2020 sync + -rwxr-xr-x 1 root root 602584 Feb 17 23:55 tar + -rwxr-xr-x 1 root root 13860 Sep 28 2020 tempfile + -rwxr-xr-x 1 root root 108520 Sep 23 2020 touch + -rwxr-xr-x 1 root root 34664 Sep 23 2020 true + -rwxr-xr-x 1 root root 17768 Feb 27 06:12 ulockmgr_server + -rwsr-xr-x 1 root root 30236 Feb 8 04:38 umount + -rwxr-xr-x 1 root root 34664 Sep 23 2020 uname + -rwxr-xr-x 2 root root 2346 Mar 3 13:30 uncompress + -rwxr-xr-x 1 root root 153964 Sep 23 2020 vdir + -rwxr-xr-x 1 root root 63024 Feb 8 04:38 wdctl + lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Mar 3 13:30 zcat + -rwxr-xr-x 1 root root 1678 Mar 3 13:30 zcmp + -rwxr-xr-x 1 root root 5880 Mar 3 13:30 zdiff + -rwxr-xr-x 1 root root 29 Mar 3 13:30 zegrep + -rwxr-xr-x 1 root root 29 Mar 3 13:30 zfgrep + -rwxr-xr-x 1 root root 2081 Mar 3 13:30 zforce + -rwxr-xr-x 1 root root 7585 Mar 3 13:30 zgrep + -rwxr-xr-x 1 root root 2206 Mar 3 13:30 zless + -rwxr-xr-x 1 root root 1842 Mar 3 13:30 zmore + -rwxr-xr-x 1 root root 4553 Mar 3 13:30 znew +I: user script /srv/workspace/pbuilder/16409/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -256,7 +290,7 @@ Get: 46 http://deb.debian.org/debian bullseye/main i386 debhelper all 13.3.4 [1049 kB] Get: 47 http://deb.debian.org/debian bullseye/main i386 help2man i386 1.48.1 [190 kB] Get: 48 http://deb.debian.org/debian bullseye/main i386 zlib1g-dev i386 1:1.2.11.dfsg-2 [194 kB] -Fetched 24.7 MB in 1s (46.4 MB/s) +Fetched 24.7 MB in 5s (5274 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 19674 files and directories currently installed.) @@ -465,8 +499,44 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +The following additional packages will be installed: + libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl +The following NEW packages will be installed: + libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl usrmerge +0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. +Need to get 59.4 kB of archives. +After this operation, 156 kB of additional disk space will be used. +Get:1 http://deb.debian.org/debian bullseye/main i386 libnumber-compare-perl all 0.03-1.1 [6956 B] +Get:2 http://deb.debian.org/debian bullseye/main i386 libtext-glob-perl all 0.11-1 [8888 B] +Get:3 http://deb.debian.org/debian bullseye/main i386 libfile-find-rule-perl all 0.34-1 [30.6 kB] +Get:4 http://deb.debian.org/debian bullseye/main i386 usrmerge all 24 [13.0 kB] +debconf: delaying package configuration, since apt-utils is not installed +Fetched 59.4 kB in 0s (1589 kB/s) +Selecting previously unselected package libnumber-compare-perl. +(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 ... 22433 files and directories currently installed.) +Preparing to unpack .../libnumber-compare-perl_0.03-1.1_all.deb ... +Unpacking libnumber-compare-perl (0.03-1.1) ... +Selecting previously unselected package libtext-glob-perl. +Preparing to unpack .../libtext-glob-perl_0.11-1_all.deb ... +Unpacking libtext-glob-perl (0.11-1) ... +Selecting previously unselected package libfile-find-rule-perl. +Preparing to unpack .../libfile-find-rule-perl_0.34-1_all.deb ... +Unpacking libfile-find-rule-perl (0.34-1) ... +Selecting previously unselected package usrmerge. +Preparing to unpack .../archives/usrmerge_24_all.deb ... +Unpacking usrmerge (24) ... +Setting up libtext-glob-perl (0.11-1) ... +Setting up libnumber-compare-perl (0.03-1.1) ... +Setting up libfile-find-rule-perl (0.34-1) ... +Setting up usrmerge (24) ... +The system has been successfully converted. +Processing triggers for man-db (2.9.4-2) ... +Not building database; man-db/auto-update is not 'true'. I: Building the package -I: Running cd /build/subread-2.0.1+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b +I: Running cd /build/subread-2.0.1+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package subread dpkg-buildpackage: info: source version 2.0.1+dfsg-1 dpkg-buildpackage: info: source distribution unstable @@ -741,7 +811,7 @@ || Repeat threshold : 100 repeats || || Gapped index : no || || || -|| Free / total memory : 2.0GB / 0.0GB || +|| Free / total memory : 1.8GB / 0.0GB || || || || Input files : 1 file in total || || o chr901.fa || @@ -759,7 +829,7 @@ || The notes can be found in the log file, '../small1.log'. || || Scan uninformative subreads in reference sequences ... || subread-buildindex: hashtable.c:444: HashTablePutReplaceEx: Assertion `key != NULL' failed. -Aborted +subread-align-test.sh: line 7: 11029 Aborted $SUBREAD_HOME/subread-buildindex -B -F -o ../small1 -M100 ../chr901.fa md5sum: ../small1.00.b.array: No such file or directory md5sum: ../small1.00.b.tab: No such file or directory @@ -790,7 +860,7 @@ || || \\============================================================================// -//================ Running (22-Jun-2022 04:34:29, pid=16862) =================\\ +//================ Running (21-May-2021 00:19:49, pid=11072) =================\\ || || || Check the input reads. || || The input file contains base space reads. || @@ -835,7 +905,7 @@ || || \\============================================================================// -//================ Running (22-Jun-2022 04:34:29, pid=16865) =================\\ +//================ Running (21-May-2021 00:19:49, pid=11084) =================\\ || || || Check the input reads. || || The input file contains base space reads. || @@ -885,7 +955,7 @@ || || \\============================================================================// -//================ Running (22-Jun-2022 04:34:29, pid=16868) =================\\ +//================ Running (21-May-2021 00:19:49, pid=11093) =================\\ || || || Check the input reads. || || The input file contains base space reads. || @@ -935,7 +1005,7 @@ || || \\============================================================================// -//================ Running (22-Jun-2022 04:34:29, pid=16871) =================\\ +//================ Running (21-May-2021 00:19:49, pid=11099) =================\\ || || || Check the input reads. || || The input file contains base space reads. || @@ -985,7 +1055,7 @@ || || \\============================================================================// -//================ Running (22-Jun-2022 04:34:29, pid=16874) =================\\ +//================ Running (21-May-2021 00:19:49, pid=11102) =================\\ || || || Check the input reads. || || The input file contains base space reads. || @@ -1036,7 +1106,7 @@ || || \\============================================================================// -//================ Running (22-Jun-2022 04:34:29, pid=16879) =================\\ +//================ Running (21-May-2021 00:19:50, pid=11105) =================\\ || || ERROR: unable to open file 'data/test-err-mut-r1.fq.gz'. File name might be incorrect, or you do not have the permission to read the file. ERROR: unable to open file 'data/test-err-mut-r2.fq.gz'. File name might be incorrect, or you do not have the permission to read the file. @@ -1098,7 +1168,7 @@ || Repeat threshold : 100 repeats || || Gapped index : yes || || || -|| Free / total memory : 2.0GB / 0.0GB || +|| Free / total memory : 1.7GB / 0.0GB || || || || Input files : 1 file in total || || o chr901.fa || @@ -1116,7 +1186,7 @@ || The notes can be found in the log file, '../small1.log'. || || Scan uninformative subreads in reference sequences ... || subread-buildindex: hashtable.c:444: HashTablePutReplaceEx: Assertion `key != NULL' failed. -Aborted +subjunc-test.sh: line 3: 11111 Aborted ../../bin/subread-buildindex -o ../small1 ../chr901.fa ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ @@ -1150,7 +1220,7 @@ || || \\============================================================================// -//================ Running (22-Jun-2022 04:34:30, pid=16886) =================\\ +//================ Running (21-May-2021 00:19:51, pid=11151) =================\\ || || || Check the input reads. || || The input file contains base space reads. || @@ -1194,7 +1264,7 @@ || || \\============================================================================// -//================ Running (22-Jun-2022 04:34:30, pid=16887) =================\\ +//================ Running (21-May-2021 00:19:51, pid=11152) =================\\ || || || Check the input reads. || || The input file contains base space reads. || @@ -1303,9 +1373,7 @@ Testing Allowing multi-mapped reads ... [PASS] Testing not sorting input file ... [PASS] Testing minimum overlapping length ... [PASS] -Testing minimum overlapping fraction ... [data/compare.sh: line 12: 17064 Aborted nohup ../../bin/featureCounts $PARAMETERS -o $TMPF.FC -a $ANNO_FILE $SAM_FILE > /dev/null 2>&1 -cat: data/DEL4-1655915670.FC: No such file or directory -FAILED] +Testing minimum overlapping fraction ... [PASS] Testing Largest Overlapping ... [PASS] Testing paired-end distance ... [PASS] Testing Read to position (5' end) ... [PASS] @@ -1316,9 +1384,7 @@ Testing minimum mapping quality ... [PASS] Testing Ignoring duplicated reads ... [PASS] Testing Fraction counting ... [PASS] -Testing Advanced fractions ... [data/compare.sh: line 12: 17173 Aborted nohup ../../bin/featureCounts $PARAMETERS -o $TMPF.FC -a $ANNO_FILE $SAM_FILE > /dev/null 2>&1 -cat: data/DEL4-1655915670.FC: No such file or directory -FAILED] +Testing Advanced fractions ... [PASS] Testing Junction counting ... [PASS,PASS] Skipping Junction counting (with genome). Testing GTF format annotations ... [PASS] @@ -1373,9 +1439,9 @@ || || \\============================================================================// -//====================== Running (22-Jun-2022 04:34:31) ======================\\ +//====================== Running (21-May-2021 00:19:53) ======================\\ || || -|| Split BAM file into result/temp-snps-017423-4A411E2E03C2-* ... || +|| Split BAM file into result/temp-snps-011701-4D7082F344B7-* ... || || processed block chr901@999950 by thread 1/1 [block number=1/1] || || || || Completed successfully. || @@ -1388,7 +1454,7 @@ || Reported SNPs : 416 || || Reported indels : 22 || || || -|| Running time : 0.0 minutes || +|| Running time : 0.1 minutes || || || \\============================================================================// @@ -1482,58 +1548,44 @@ -cJf /build/subread-2.0.1+dfsg/debian/subread-data/usr/share/doc/subread/examples/test.tar.xz test/ make[1]: Leaving directory '/build/subread-2.0.1+dfsg' dh_installman - man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/exactSNP.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/featureCounts.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/flattenGTF.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/genRandomReads.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/propmapped.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/qualityScores.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/removeDup.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/repair.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/subindel.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/subjunc.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/sublong.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/subread-align.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/subread-buildindex.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/subread-fullscan.1 - mv debian/subread/usr/share/man/man1/propmapped.1.dh-new debian/subread/usr/share/man/man1/propmapped.1 - chmod 0644 -- debian/subread/usr/share/man/man1/propmapped.1 - mv debian/subread/usr/share/man/man1/subjunc.1.dh-new debian/subread/usr/share/man/man1/subjunc.1 - chmod 0644 -- debian/subread/usr/share/man/man1/subjunc.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/exactSNP.1 debian/subread/usr/share/man/man1/featureCounts.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/flattenGTF.1 debian/subread/usr/share/man/man1/genRandomReads.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/propmapped.1 debian/subread/usr/share/man/man1/qualityScores.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/removeDup.1 debian/subread/usr/share/man/man1/repair.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/subindel.1 debian/subread/usr/share/man/man1/subjunc.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/sublong.1 debian/subread/usr/share/man/man1/subread-align.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/subread-buildindex.1 debian/subread/usr/share/man/man1/subread-fullscan.1 + mv debian/subread/usr/share/man/man1/flattenGTF.1.dh-new debian/subread/usr/share/man/man1/flattenGTF.1 mv debian/subread/usr/share/man/man1/genRandomReads.1.dh-new debian/subread/usr/share/man/man1/genRandomReads.1 - chmod 0644 -- debian/subread/usr/share/man/man1/genRandomReads.1 + chmod 0644 -- debian/subread/usr/share/man/man1/flattenGTF.1 debian/subread/usr/share/man/man1/genRandomReads.1 mv debian/subread/usr/share/man/man1/exactSNP.1.dh-new debian/subread/usr/share/man/man1/exactSNP.1 - chmod 0644 -- debian/subread/usr/share/man/man1/exactSNP.1 mv debian/subread/usr/share/man/man1/featureCounts.1.dh-new debian/subread/usr/share/man/man1/featureCounts.1 - chmod 0644 -- debian/subread/usr/share/man/man1/featureCounts.1 - mv debian/subread/usr/share/man/man1/subindel.1.dh-new debian/subread/usr/share/man/man1/subindel.1 - chmod 0644 -- debian/subread/usr/share/man/man1/subindel.1 - mv debian/subread/usr/share/man/man1/flattenGTF.1.dh-new debian/subread/usr/share/man/man1/flattenGTF.1 - chmod 0644 -- debian/subread/usr/share/man/man1/flattenGTF.1 - mv debian/subread/usr/share/man/man1/repair.1.dh-new debian/subread/usr/share/man/man1/repair.1 - chmod 0644 -- debian/subread/usr/share/man/man1/repair.1 - mv debian/subread/usr/share/man/man1/removeDup.1.dh-new debian/subread/usr/share/man/man1/removeDup.1 - chmod 0644 -- debian/subread/usr/share/man/man1/removeDup.1 + chmod 0644 -- debian/subread/usr/share/man/man1/exactSNP.1 debian/subread/usr/share/man/man1/featureCounts.1 + mv debian/subread/usr/share/man/man1/propmapped.1.dh-new debian/subread/usr/share/man/man1/propmapped.1 mv debian/subread/usr/share/man/man1/qualityScores.1.dh-new debian/subread/usr/share/man/man1/qualityScores.1 - chmod 0644 -- debian/subread/usr/share/man/man1/qualityScores.1 + chmod 0644 -- debian/subread/usr/share/man/man1/propmapped.1 debian/subread/usr/share/man/man1/qualityScores.1 + mv debian/subread/usr/share/man/man1/subread-buildindex.1.dh-new debian/subread/usr/share/man/man1/subread-buildindex.1 + mv debian/subread/usr/share/man/man1/subread-fullscan.1.dh-new debian/subread/usr/share/man/man1/subread-fullscan.1 + chmod 0644 -- debian/subread/usr/share/man/man1/subread-buildindex.1 debian/subread/usr/share/man/man1/subread-fullscan.1 + mv debian/subread/usr/share/man/man1/removeDup.1.dh-new debian/subread/usr/share/man/man1/removeDup.1 + mv debian/subread/usr/share/man/man1/repair.1.dh-new debian/subread/usr/share/man/man1/repair.1 + chmod 0644 -- debian/subread/usr/share/man/man1/removeDup.1 debian/subread/usr/share/man/man1/repair.1 + mv debian/subread/usr/share/man/man1/subindel.1.dh-new debian/subread/usr/share/man/man1/subindel.1 + mv debian/subread/usr/share/man/man1/subjunc.1.dh-new debian/subread/usr/share/man/man1/subjunc.1 + chmod 0644 -- debian/subread/usr/share/man/man1/subindel.1 debian/subread/usr/share/man/man1/subjunc.1 mv debian/subread/usr/share/man/man1/sublong.1.dh-new debian/subread/usr/share/man/man1/sublong.1 - chmod 0644 -- debian/subread/usr/share/man/man1/sublong.1 mv debian/subread/usr/share/man/man1/subread-align.1.dh-new debian/subread/usr/share/man/man1/subread-align.1 - chmod 0644 -- debian/subread/usr/share/man/man1/subread-align.1 - mv debian/subread/usr/share/man/man1/subread-fullscan.1.dh-new debian/subread/usr/share/man/man1/subread-fullscan.1 - chmod 0644 -- debian/subread/usr/share/man/man1/subread-fullscan.1 - mv debian/subread/usr/share/man/man1/subread-buildindex.1.dh-new debian/subread/usr/share/man/man1/subread-buildindex.1 - chmod 0644 -- debian/subread/usr/share/man/man1/subread-buildindex.1 + chmod 0644 -- debian/subread/usr/share/man/man1/sublong.1 debian/subread/usr/share/man/man1/subread-align.1 dh_perl dh_link dh_strip_nondeterminism dh_compress cd debian/subread cd debian/subread-data - chmod a-x usr/share/doc/subread-data/changelog.Debian usr/share/doc/subread/examples/annotation/hg19_RefSeq_exon.txt usr/share/doc/subread/examples/annotation/hg38_RefSeq_exon.txt usr/share/doc/subread/examples/annotation/mm10_RefSeq_exon.txt usr/share/doc/subread/examples/annotation/mm9_RefSeq_exon.txt chmod a-x usr/share/doc/subread/README.txt usr/share/doc/subread/changelog.Debian usr/share/man/man1/exactSNP.1 usr/share/man/man1/featureCounts.1 usr/share/man/man1/flattenGTF.1 usr/share/man/man1/genRandomReads.1 usr/share/man/man1/propmapped.1 usr/share/man/man1/qualityScores.1 usr/share/man/man1/removeDup.1 usr/share/man/man1/repair.1 usr/share/man/man1/subindel.1 usr/share/man/man1/subjunc.1 usr/share/man/man1/sublong.1 usr/share/man/man1/subread-align.1 usr/share/man/man1/subread-buildindex.1 usr/share/man/man1/subread-fullscan.1 - gzip -9nf usr/share/doc/subread-data/changelog.Debian usr/share/doc/subread/examples/annotation/hg19_RefSeq_exon.txt usr/share/doc/subread/examples/annotation/hg38_RefSeq_exon.txt usr/share/doc/subread/examples/annotation/mm10_RefSeq_exon.txt usr/share/doc/subread/examples/annotation/mm9_RefSeq_exon.txt + chmod a-x usr/share/doc/subread-data/changelog.Debian usr/share/doc/subread/examples/annotation/hg19_RefSeq_exon.txt usr/share/doc/subread/examples/annotation/hg38_RefSeq_exon.txt usr/share/doc/subread/examples/annotation/mm10_RefSeq_exon.txt usr/share/doc/subread/examples/annotation/mm9_RefSeq_exon.txt gzip -9nf usr/share/doc/subread/README.txt usr/share/doc/subread/changelog.Debian usr/share/man/man1/exactSNP.1 usr/share/man/man1/featureCounts.1 usr/share/man/man1/flattenGTF.1 usr/share/man/man1/genRandomReads.1 usr/share/man/man1/propmapped.1 usr/share/man/man1/qualityScores.1 usr/share/man/man1/removeDup.1 usr/share/man/man1/repair.1 usr/share/man/man1/subindel.1 usr/share/man/man1/subjunc.1 usr/share/man/man1/sublong.1 usr/share/man/man1/subread-align.1 usr/share/man/man1/subread-buildindex.1 usr/share/man/man1/subread-fullscan.1 + gzip -9nf usr/share/doc/subread-data/changelog.Debian usr/share/doc/subread/examples/annotation/hg19_RefSeq_exon.txt usr/share/doc/subread/examples/annotation/hg38_RefSeq_exon.txt usr/share/doc/subread/examples/annotation/mm10_RefSeq_exon.txt usr/share/doc/subread/examples/annotation/mm9_RefSeq_exon.txt cd '/build/subread-2.0.1+dfsg' cd '/build/subread-2.0.1+dfsg' dh_fixperms @@ -1554,26 +1606,16 @@ dwz -mdebian/subread/usr/lib/debug/.dwz/i386-linux-gnu/subread.debug -M/usr/lib/debug/.dwz/i386-linux-gnu/subread.debug -- debian/subread/usr/bin/exactSNP debian/subread/usr/bin/featureCounts debian/subread/usr/bin/subindel debian/subread/usr/bin/subjunc debian/subread/usr/bin/sublong debian/subread/usr/bin/subread-align debian/subread/usr/bin/subread-buildindex debian/subread/usr/lib/subread/flattenGTF debian/subread/usr/lib/subread/genRandomReads debian/subread/usr/lib/subread/propmapped debian/subread/usr/lib/subread/qualityScores debian/subread/usr/lib/subread/removeDup debian/subread/usr/lib/subread/repair debian/subread/usr/lib/subread/subread-fullscan debian/subread/usr/lib/subread/txUnique objcopy --compress-debug-sections debian/subread/usr/lib/debug/.dwz/i386-linux-gnu/subread.debug dh_strip - install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/64 - objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/subread-fullscan debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/64/67b88c4daf8e8fdb728d1d50a8e69f78fa1d8e.debug - chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/64/67b88c4daf8e8fdb728d1d50a8e69f78fa1d8e.debug - strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/subread-fullscan - objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/64/67b88c4daf8e8fdb728d1d50a8e69f78fa1d8e.debug debian/subread/usr/lib/subread/subread-fullscan install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/1c objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/propmapped debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/1c/6aeda56ba65c8a4d53a51bcbdf1c79c8b0be1e.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/1c/6aeda56ba65c8a4d53a51bcbdf1c79c8b0be1e.debug strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/propmapped objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/1c/6aeda56ba65c8a4d53a51bcbdf1c79c8b0be1e.debug debian/subread/usr/lib/subread/propmapped - install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/eb - objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/qualityScores debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/eb/c2edecd1c1b479aa69d52ea885c8069392e439.debug - chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/eb/c2edecd1c1b479aa69d52ea885c8069392e439.debug - strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/qualityScores - objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/eb/c2edecd1c1b479aa69d52ea885c8069392e439.debug debian/subread/usr/lib/subread/qualityScores - install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/88 - objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/flattenGTF debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/88/f79f9ebe24c40085017ab3ab88d559774c7e16.debug - chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/88/f79f9ebe24c40085017ab3ab88d559774c7e16.debug - strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/flattenGTF - objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/88/f79f9ebe24c40085017ab3ab88d559774c7e16.debug debian/subread/usr/lib/subread/flattenGTF + install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/64 + objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/subread-fullscan debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/64/67b88c4daf8e8fdb728d1d50a8e69f78fa1d8e.debug + chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/64/67b88c4daf8e8fdb728d1d50a8e69f78fa1d8e.debug + strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/subread-fullscan + objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/64/67b88c4daf8e8fdb728d1d50a8e69f78fa1d8e.debug debian/subread/usr/lib/subread/subread-fullscan install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/df objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/repair debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/df/18689b36761c21d67f4bd010d049797ede36b1.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/df/18689b36761c21d67f4bd010d049797ede36b1.debug @@ -1589,46 +1631,56 @@ chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/a1/b0541f6514a80054496495994b5268885c2828.debug strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/removeDup objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/a1/b0541f6514a80054496495994b5268885c2828.debug debian/subread/usr/lib/subread/removeDup + install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/88 + objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/flattenGTF debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/88/f79f9ebe24c40085017ab3ab88d559774c7e16.debug + chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/88/f79f9ebe24c40085017ab3ab88d559774c7e16.debug + strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/flattenGTF + objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/88/f79f9ebe24c40085017ab3ab88d559774c7e16.debug debian/subread/usr/lib/subread/flattenGTF + install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/eb + objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/qualityScores debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/eb/c2edecd1c1b479aa69d52ea885c8069392e439.debug + chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/eb/c2edecd1c1b479aa69d52ea885c8069392e439.debug + strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/qualityScores + objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/eb/c2edecd1c1b479aa69d52ea885c8069392e439.debug debian/subread/usr/lib/subread/qualityScores install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/c8 objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/txUnique debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/c8/5d16184d381c7378a9f965f07df5aa5bfe046b.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/c8/5d16184d381c7378a9f965f07df5aa5bfe046b.debug strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/txUnique objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/c8/5d16184d381c7378a9f965f07df5aa5bfe046b.debug debian/subread/usr/lib/subread/txUnique - install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/33 - objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subjunc debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/33/0d7a0f47672631fecd86a703df03e727f87f7a.debug - chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/33/0d7a0f47672631fecd86a703df03e727f87f7a.debug - strip --remove-section=.comment --remove-section=.note debian/subread/usr/bin/subjunc - objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/33/0d7a0f47672631fecd86a703df03e727f87f7a.debug debian/subread/usr/bin/subjunc - install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/26 - objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/exactSNP debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/26/af4d06dfe08da5b9e6a310c9d4d7c6f2bdcbad.debug - chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/26/af4d06dfe08da5b9e6a310c9d4d7c6f2bdcbad.debug - strip --remove-section=.comment --remove-section=.note debian/subread/usr/bin/exactSNP - objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/26/af4d06dfe08da5b9e6a310c9d4d7c6f2bdcbad.debug debian/subread/usr/bin/exactSNP install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/65 objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/featureCounts debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/65/289187a21a31e58a708788f0e39dd2af0c1214.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/65/289187a21a31e58a708788f0e39dd2af0c1214.debug strip --remove-section=.comment --remove-section=.note debian/subread/usr/bin/featureCounts objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/65/289187a21a31e58a708788f0e39dd2af0c1214.debug debian/subread/usr/bin/featureCounts - install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ae - objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/sublong debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ae/254bd2dca13a58680457cf0c347f52c8a4fa30.debug - chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ae/254bd2dca13a58680457cf0c347f52c8a4fa30.debug - strip --remove-section=.comment --remove-section=.note debian/subread/usr/bin/sublong - objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ae/254bd2dca13a58680457cf0c347f52c8a4fa30.debug debian/subread/usr/bin/sublong install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/4e objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subread-align debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/4e/37c4761a09443e4701994e3eb73d692ee0e533.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/4e/37c4761a09443e4701994e3eb73d692ee0e533.debug strip --remove-section=.comment --remove-section=.note debian/subread/usr/bin/subread-align objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/4e/37c4761a09443e4701994e3eb73d692ee0e533.debug debian/subread/usr/bin/subread-align - install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/7a - objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subindel debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/7a/a3544c951547a442c0fa0fed97bdbab8fa372a.debug - chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/7a/a3544c951547a442c0fa0fed97bdbab8fa372a.debug - strip --remove-section=.comment --remove-section=.note debian/subread/usr/bin/subindel - objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/7a/a3544c951547a442c0fa0fed97bdbab8fa372a.debug debian/subread/usr/bin/subindel install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/f4 objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subread-buildindex debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/f4/7d66c9748fccb1008eab3c1419cbb71991516f.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/f4/7d66c9748fccb1008eab3c1419cbb71991516f.debug strip --remove-section=.comment --remove-section=.note debian/subread/usr/bin/subread-buildindex objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/f4/7d66c9748fccb1008eab3c1419cbb71991516f.debug debian/subread/usr/bin/subread-buildindex + install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/26 + objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/exactSNP debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/26/af4d06dfe08da5b9e6a310c9d4d7c6f2bdcbad.debug + chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/26/af4d06dfe08da5b9e6a310c9d4d7c6f2bdcbad.debug + strip --remove-section=.comment --remove-section=.note debian/subread/usr/bin/exactSNP + objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/26/af4d06dfe08da5b9e6a310c9d4d7c6f2bdcbad.debug debian/subread/usr/bin/exactSNP + install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/33 + objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subjunc debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/33/0d7a0f47672631fecd86a703df03e727f87f7a.debug + chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/33/0d7a0f47672631fecd86a703df03e727f87f7a.debug + strip --remove-section=.comment --remove-section=.note debian/subread/usr/bin/subjunc + objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/33/0d7a0f47672631fecd86a703df03e727f87f7a.debug debian/subread/usr/bin/subjunc + install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ae + objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/sublong debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ae/254bd2dca13a58680457cf0c347f52c8a4fa30.debug + chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ae/254bd2dca13a58680457cf0c347f52c8a4fa30.debug + strip --remove-section=.comment --remove-section=.note debian/subread/usr/bin/sublong + objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ae/254bd2dca13a58680457cf0c347f52c8a4fa30.debug debian/subread/usr/bin/sublong + install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/7a + objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subindel debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/7a/a3544c951547a442c0fa0fed97bdbab8fa372a.debug + chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/7a/a3544c951547a442c0fa0fed97bdbab8fa372a.debug + strip --remove-section=.comment --remove-section=.note debian/subread/usr/bin/subindel + objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/7a/a3544c951547a442c0fa0fed97bdbab8fa372a.debug debian/subread/usr/bin/subindel install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.dwz cp --reflink=auto -a debian/subread/usr/lib/debug/.dwz/i386-linux-gnu debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.dwz rm -fr debian/subread/usr/lib/debug/.dwz @@ -1640,7 +1692,7 @@ rm -f debian/subread-data/DEBIAN/shlibs dh_shlibdeps install -d debian/subread/DEBIAN - dpkg-shlibdeps -Tdebian/subread.substvars debian/subread/usr/lib/subread/subread-fullscan debian/subread/usr/lib/subread/propmapped debian/subread/usr/lib/subread/qualityScores debian/subread/usr/lib/subread/flattenGTF debian/subread/usr/lib/subread/repair debian/subread/usr/lib/subread/genRandomReads debian/subread/usr/lib/subread/removeDup debian/subread/usr/lib/subread/txUnique debian/subread/usr/bin/subjunc debian/subread/usr/bin/exactSNP debian/subread/usr/bin/featureCounts debian/subread/usr/bin/sublong debian/subread/usr/bin/subread-align debian/subread/usr/bin/subindel debian/subread/usr/bin/subread-buildindex + dpkg-shlibdeps -Tdebian/subread.substvars debian/subread/usr/lib/subread/propmapped debian/subread/usr/lib/subread/subread-fullscan debian/subread/usr/lib/subread/repair debian/subread/usr/lib/subread/genRandomReads debian/subread/usr/lib/subread/removeDup debian/subread/usr/lib/subread/flattenGTF debian/subread/usr/lib/subread/qualityScores debian/subread/usr/lib/subread/txUnique debian/subread/usr/bin/featureCounts debian/subread/usr/bin/subread-align debian/subread/usr/bin/subread-buildindex debian/subread/usr/bin/exactSNP debian/subread/usr/bin/subjunc debian/subread/usr/bin/sublong debian/subread/usr/bin/subindel dh_installdeb install -d debian/subread-data/DEBIAN dh_gencontrol @@ -1652,9 +1704,9 @@ install -d debian/.debhelper/subread/dbgsym-root/DEBIAN dpkg-gencontrol -psubread -ldebian/changelog -Tdebian/subread.substvars -Pdebian/.debhelper/subread/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -UBuilt-Using -DAuto-Built-Package=debug-symbols -UProtected -DPackage=subread-dbgsym "-DDepends=subread (= \${binary:Version})" "-DDescription=debug symbols for subread" "-DBuild-Ids=1c6aeda56ba65c8a4d53a51bcbdf1c79c8b0be1e 26af4d06dfe08da5b9e6a310c9d4d7c6f2bdcbad 330d7a0f47672631fecd86a703df03e727f87f7a 4e37c4761a09443e4701994e3eb73d692ee0e533 6467b88c4daf8e8fdb728d1d50a8e69f78fa1d8e 65289187a21a31e58a708788f0e39dd2af0c1214 7aa3544c951547a442c0fa0fed97bdbab8fa372a 88f79f9ebe24c40085017ab3ab88d559774c7e16 a1b0541f6514a80054496495994b5268885c2828 a69fd35619e9d3a9557ef4712d7481065dda368a ae254bd2dca13a58680457cf0c347f52c8a4fa30 c85d16184d381c7378a9f965f07df5aa5bfe046b df18689b36761c21d67f4bd010d049797ede36b1 ebc2edecd1c1b479aa69d52ea885c8069392e439 f47d66c9748fccb1008eab3c1419cbb71991516f" -DSection=debug -UMulti-Arch -UReplaces -UBreaks dpkg-gencontrol: warning: Depends field of package subread-data: substitution variable ${shlibs:Depends} used, but is not defined - chmod 0644 -- debian/subread-data/DEBIAN/control chmod 0644 -- debian/.debhelper/subread/dbgsym-root/DEBIAN/control dpkg-gencontrol -psubread -ldebian/changelog -Tdebian/subread.substvars -Pdebian/subread + chmod 0644 -- debian/subread-data/DEBIAN/control chmod 0644 -- debian/subread/DEBIAN/control dh_md5sums cd debian/subread >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums @@ -1667,21 +1719,23 @@ dpkg-deb --root-owner-group --build debian/subread .. dpkg-deb --root-owner-group --build debian/.debhelper/subread/dbgsym-root .. dpkg-deb --root-owner-group --build debian/subread-data .. -dpkg-deb: building package 'subread' in '../subread_2.0.1+dfsg-1_i386.deb'. -dpkg-deb: building package 'subread-dbgsym' in '../subread-dbgsym_2.0.1+dfsg-1_i386.deb'. dpkg-deb: building package 'subread-data' in '../subread-data_2.0.1+dfsg-1_all.deb'. +dpkg-deb: building package 'subread-dbgsym' in '../subread-dbgsym_2.0.1+dfsg-1_i386.deb'. +dpkg-deb: building package 'subread' in '../subread_2.0.1+dfsg-1_i386.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../subread_2.0.1+dfsg-1_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration +I: user script /srv/workspace/pbuilder/16409/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/16409/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/15088 and its subdirectories -I: Current time: Wed Jun 22 04:35:12 -12 2022 -I: pbuilder-time-stamp: 1655915712 +I: removing directory /srv/workspace/pbuilder/16409 and its subdirectories +I: Current time: Fri May 21 00:21:58 +14 2021 +I: pbuilder-time-stamp: 1621506118